From francis at oicr.on.ca Sat Sep 10 10:32:45 2016 From: francis at oicr.on.ca (Francis Ouellette) Date: Sat, 10 Sep 2016 14:32:45 +0000 Subject: [DOCKTESTERS] getting some testing done! In-Reply-To: References: Message-ID: <0FCE34A4-E34E-48E9-98DF-72C01ADCEDF1@oicr.on.ca> looks like I actually forgot to set up doodle! sorry about that ? my bad! Here it is! The other option is to simply meet in Boston. Brian suggested we do a ?Birds of a feather? (simple gathering or who ever is interested in the topic). I think that is also a great idea. (and I think doing a conference call next week would help maximize what we do when we are face-2-face in Boston, so I hope we can schedule both). Here is the doodle poll: http://doodle.com/poll/z3wpvkka84qw7hed Thank you for responding as soon as possible. francis On Aug 29, 2016, at 7:17 AM, Francis Ouellette > wrote: Dear Docktesters, Sorry I?ve quiet for last couple of months. I?ve been at the hospital supporting my partner, and she passed away 2.5 weeks ago, and i am now getting back into the swing of things. She died of complications related to her breast/bone and liver cancer, and so I am now even more (although I was already very much there) dedicated to doing something about this friggen disease! So, what do we need to do? Well, first and foremost we need to agree on an SOP on what we need to do to test these containers. For that I would like for us to meet this week. Meeting with people from west coast to Europe time zones is difficult, but we should manage at least once, and then, we can follow-up via e-mail, or documentation on the wiki. As a reminder, the docktester?s wiki page is here: https://wiki.oicr.on.ca/x/9pfnAw And on this page I added two recent links that Brian put together in my absence: * Workflow testing SOP * Workflow testing Data We need to agree on the SOP, and that is what our next discussion will be about. I?ve added Zhibin Lu to this mailing list. Zhibin is somebody from my group that will work with you and provide you, should you need it, some AWS dollars/CPU etc should you need somewhere to test. I will set up a doodle later today, and I would really like for us to meet this week. Thank you for your effort in making this happen, and getting this testing started. Talk to some of you later today on the PCAWG-tech call, @bffo _______________________________________________ docktesters mailing list docktesters at lists.icgc.org https://lists.icgc.org/mailman/listinfo/docktesters -------------- next part -------------- An HTML attachment was scrubbed... URL: From francis at oicr.on.ca Tue Sep 13 16:27:05 2016 From: francis at oicr.on.ca (Francis Ouellette) Date: Tue, 13 Sep 2016 20:27:05 +0000 Subject: [DOCKTESTERS] call on Wednesday Message-ID: OK, we will do call this Wednesday. 11:00 in Toronto, see attached image for a time zone near you ? Conference call info Dial in: 800 747 5150 Access code: 3592059 Talk to you in 19 hrs or so. Agenda will be found here later: https://wiki.oicr.on.ca/pages/viewpage.action?pageId=65510046 Talk to you tomorrow, francis Dial in from USA/Canada: 1-800-747-5150 Dial in from UK: 08004960577 Dial in from UK mobile: 02079040082 Dial in from Argentina: 08008007388 Dial in from Australia: 1-800-422-903 Dial in from Belgium: 080039117 Dial in from China: 4006208033 or 4008108940 or 8008190299 Dial in from Germany: 08001014525 Dial in from Hong Kong: 800968124 Dial in from India: 000180 or 0008001006002 Dial in from Japan: 00531001555 Dial in from Netherlands: 08002658213 Dial in from Norway: 80056401 Dial in from Qatar: 00800100036 Dial in from Singapore: 8001011435 Dial in from South Africa: 0800990930 Dial in from Spain: 900800371 Dial in from Sweden: 0201400589 Dial in from Switzerland: 0800700283 [cid:B23EB94E-5EE3-402A-8163-A57D1DC1509E at oicr.on.ca] [cid:66582CC1-0EA3-4B68-9B32-07E4B9B2EF00 at oicr.on.ca] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot 2016-09-13 07.19.13.png Type: image/png Size: 102433 bytes Desc: Screenshot 2016-09-13 07.19.13.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot 2016-09-13 16.23.38.png Type: image/png Size: 183461 bytes Desc: Screenshot 2016-09-13 16.23.38.png URL: From ohofmann72 at gmail.com Wed Sep 14 09:44:17 2016 From: ohofmann72 at gmail.com (Oliver Hofmann) Date: Wed, 14 Sep 2016 14:44:17 +0100 Subject: [DOCKTESTERS] call on Wednesday In-Reply-To: References: Message-ID: Dear all, I'll have to pass on this call. Flying out in a bit and still juggling all kinds of deadlines for the upcoming move. Hope to be able to catch up with everyone in Boston. Best, Oliver On Tue, Sep 13, 2016 at 9:27 PM, Francis Ouellette wrote: > > OK, we will do call this Wednesday. > > 11:00 in Toronto, see attached image for a time zone near you ? > > Conference call info > > Dial in: 800 747 5150 > Access code: 3592059 > > Talk to you in 19 hrs or so. > > Agenda will be found here later: > > https://wiki.oicr.on.ca/pages/viewpage.action?pageId=65510046 > > Talk to you tomorrow, > > francis > > > > > Dial in from USA/Canada: 1-800-747-5150 > Dial in from UK: 08004960577 > Dial in from UK mobile: 02079040082 > Dial in from Argentina: 08008007388 > Dial in from Australia: 1-800-422-903 > Dial in from Belgium: 080039117 > Dial in from China: 4006208033 or 4008108940 or 8008190299 > Dial in from Germany: 08001014525 > Dial in from Hong Kong: 800968124 > Dial in from India: 000180 or 0008001006002 > Dial in from Japan: 00531001555 > Dial in from Netherlands: 08002658213 > Dial in from Norway: 80056401 > Dial in from Qatar: 00800100036 > Dial in from Singapore: 8001011435 > Dial in from South Africa: 0800990930 > Dial in from Spain: 900800371 > Dial in from Sweden: 0201400589 > Dial in from Switzerland: 0800700283 > > > > > > > > _______________________________________________ > docktesters mailing list > docktesters at lists.icgc.org > https://lists.icgc.org/mailman/listinfo/docktesters > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From francis at oicr.on.ca Wed Sep 14 10:07:21 2016 From: francis at oicr.on.ca (Francis Ouellette) Date: Wed, 14 Sep 2016 14:07:21 +0000 Subject: [DOCKTESTERS] call in 53 minutes In-Reply-To: References: Message-ID: I picked that time because you said you could make it :-( We will see each other (those of you in Boston), but I know not all will be there ? Finding a time is proving to be challenging as well. talk to others in 53 minutes. @bffo On Sep 14, 2016, at 9:44 AM, Oliver Hofmann > wrote: Dear all, I'll have to pass on this call. Flying out in a bit and still juggling all kinds of deadlines for the upcoming move. Hope to be able to catch up with everyone in Boston. Best, Oliver On Tue, Sep 13, 2016 at 9:27 PM, Francis Ouellette > wrote: OK, we will do call this Wednesday. 11:00 in Toronto, see attached image for a time zone near you ? Conference call info Dial in: 800 747 5150 Access code: 3592059 Talk to you in 19 hrs or so. Agenda will be found here later: https://wiki.oicr.on.ca/pages/viewpage.action?pageId=65510046 Talk to you tomorrow, francis Dial in from USA/Canada: 1-800-747-5150 Dial in from UK: 08004960577 Dial in from UK mobile: 02079040082 Dial in from Argentina: 08008007388 Dial in from Australia: 1-800-422-903 Dial in from Belgium: 080039117 Dial in from China: 4006208033 or 4008108940 or 8008190299 Dial in from Germany: 08001014525 Dial in from Hong Kong: 800968124 Dial in from India: 000180 or 0008001006002 Dial in from Japan: 00531001555 Dial in from Netherlands: 08002658213 Dial in from Norway: 80056401 Dial in from Qatar: 00800100036 Dial in from Singapore: 8001011435 Dial in from South Africa: 0800990930 Dial in from Spain: 900800371 Dial in from Sweden: 0201400589 Dial in from Switzerland: 0800700283 [X] [X] _______________________________________________ docktesters mailing list docktesters at lists.icgc.org https://lists.icgc.org/mailman/listinfo/docktesters -------------- next part -------------- An HTML attachment was scrubbed... URL: From ohofmann72 at gmail.com Wed Sep 14 10:10:31 2016 From: ohofmann72 at gmail.com (Oliver Hofmann) Date: Wed, 14 Sep 2016 15:10:31 +0100 Subject: [DOCKTESTERS] call in 53 minutes In-Reply-To: References: Message-ID: <83caecda-583a-68c4-f2b2-52081d182cb6@google.com> Argh. Okay. Lemme reshuffle, I'll be there at least for half an hour. > > I picked that time because you said you could make it :-( > > We will see each other (those of you in Boston), but I know not all will > be there ? > Finding a time is proving to be challenging as well. > > talk to others in 53 minutes. > > @bffo > > > > >> On Sep 14, 2016, at 9:44 AM, Oliver Hofmann > > wrote: >> >> Dear all, >> >> I'll have to pass on this call. Flying out in a bit and still juggling >> all kinds of deadlines for the upcoming move. Hope to be able to catch >> up with everyone in Boston. >> >> Best, Oliver >> >> On Tue, Sep 13, 2016 at 9:27 PM, Francis Ouellette > > wrote: >> >> >> OK, we will do call this Wednesday. >> >> 11:00 in Toronto, see attached image for a time zone near you ? >> >> Conference call info >> >> Dial in: 800 747 5150 >> Access code: 3592059 >> >> Talk to you in 19 hrs or so. >> >> Agenda will be found here later: >> >> https://wiki.oicr.on.ca/pages/viewpage.action?pageId=65510046 >> >> >> Talk to you tomorrow, >> >> francis >> >> >> >> >> Dial in from USA/Canada: 1-800-747-5150 >> Dial in from UK: 08004960577 >> Dial in from UK mobile: 02079040082 >> Dial in from Argentina: 08008007388 >> Dial in from Australia: 1-800-422-903 >> Dial in from Belgium: 080039117 >> Dial in from China: 4006208033 or 4008108940 or 8008190299 >> Dial in from Germany: 08001014525 >> Dial in from Hong Kong: 800968124 >> Dial in from India: 000180 or 0008001006002 >> Dial in from Japan: 00531001555 >> Dial in from Netherlands: 08002658213 >> Dial in from Norway: 80056401 >> Dial in from Qatar: 00800100036 >> Dial in from Singapore: 8001011435 >> Dial in from South Africa: 0800990930 >> Dial in from Spain: 900800371 >> Dial in from Sweden: 0201400589 >> Dial in from Switzerland: 0800700283 >> >> >> >> >> >> >> >> _______________________________________________ >> docktesters mailing list >> docktesters at lists.icgc.org >> https://lists.icgc.org/mailman/listinfo/docktesters >> >> >> > -- @fiamh Skype: ohofmann +44 795 621 5540 From francis at oicr.on.ca Wed Sep 14 11:02:49 2016 From: francis at oicr.on.ca (Francis Ouellette) Date: Wed, 14 Sep 2016 15:02:49 +0000 Subject: [DOCKTESTERS] wiki & call Message-ID: <33AE6CA6-0D07-4C9C-98CA-F14DA931F0E4@oicr.on.ca> https://wiki.oicr.on.ca/display/PANCANCER/2016-09-14+PCAWG+Docker+%28Dockstore%29+tester+WG+Meeting+notes Conference call info Dial in: 800 747 5150 Access code: 3592059 Chairperson code: 5569 Dial in from USA/Canada: 1-800-747-5150 Dial in from UK: 08004960577 Dial in from UK mobile: 02079040082 Dial in from Argentina: 08008007388 Dial in from Australia: 1-800-422-903 Dial in from Belgium: 080039117 Dial in from China: 4006208033 or 4008108940 or 8008190299 Dial in from Germany: 08001014525 Dial in from Hong Kong: 800968124 Dial in from India: 000180 or 0008001006002 Dial in from Japan: 00531001555 Dial in from Netherlands: 08002658213 Dial in from Norway: 80056401 Dial in from Qatar: 00800100036 Dial in from Singapore: 8001011435 Dial in from South Africa: 0800990930 Dial in from Spain: 900800371 Dial in from Sweden: 0201400589 Dial in from Switzerland: 0800700283 -------------- next part -------------- An HTML attachment was scrubbed... URL: From francis at oicr.on.ca Mon Sep 19 08:20:01 2016 From: francis at oicr.on.ca (Francis Ouellette) Date: Mon, 19 Sep 2016 12:20:01 +0000 Subject: [DOCKTESTERS] meet in Boston Message-ID: <375505DD-A67D-420A-A772-84F903AE62B3@oicr.on.ca> We would like to meet this afternoon at 13:00, Look for Brian or I in loby area. @bffo -- B.F. Francis Ouellette http://oicr.on.ca/person/francis-ouellette From ohofmann72 at gmail.com Mon Sep 19 08:24:44 2016 From: ohofmann72 at gmail.com (Oliver Hofmann) Date: Mon, 19 Sep 2016 05:24:44 -0700 Subject: [DOCKTESTERS] meet in Boston In-Reply-To: <375505DD-A67D-420A-A772-84F903AE62B3@oicr.on.ca> References: <375505DD-A67D-420A-A772-84F903AE62B3@oicr.on.ca> Message-ID: Francis, I'm in the Longwood area for meetings, will have to catch up tomorrow / Wednesday. best, Oliver On 19 September 2016 at 08:20:17, Francis Ouellette (francis at oicr.on.ca) wrote: > > We would like to meet this afternoon at 13:00, Look for Brian or I in loby area. > > @bffo > > -- > B.F. Francis Ouellette http://oicr.on.ca/person/francis-ouellette > > > > _______________________________________________ > docktesters mailing list > docktesters at lists.icgc.org > https://lists.icgc.org/mailman/listinfo/docktesters > -- @fiamh Skype: ohofmann +44 795 621 5540 From Junjun.Zhang at oicr.on.ca Mon Sep 19 13:15:28 2016 From: Junjun.Zhang at oicr.on.ca (Junjun Zhang) Date: Mon, 19 Sep 2016 17:15:28 +0000 Subject: [DOCKTESTERS] meet in Boston In-Reply-To: References: <375505DD-A67D-420A-A772-84F903AE62B3@oicr.on.ca>, Message-ID: Brian and Francis, are you meeting somewhere? Miguel and I are interested to join. Junjun > On Sep 19, 2016, at 8:24 AM, Oliver Hofmann wrote: > > Francis, > > > I'm in the Longwood area for meetings, will have to catch up tomorrow > / Wednesday. > > best, Oliver > > >> On 19 September 2016 at 08:20:17, Francis Ouellette (francis at oicr.on.ca) wrote: >> >> We would like to meet this afternoon at 13:00, Look for Brian or I in loby area. >> >> @bffo >> >> -- >> B.F. Francis Ouellette http://oicr.on.ca/person/francis-ouellette >> >> >> >> _______________________________________________ >> docktesters mailing list >> docktesters at lists.icgc.org >> https://lists.icgc.org/mailman/listinfo/docktesters > > -- > @fiamh > Skype: ohofmann > +44 795 621 5540 > _______________________________________________ > docktesters mailing list > docktesters at lists.icgc.org > https://lists.icgc.org/mailman/listinfo/docktesters From francis at oicr.on.ca Mon Sep 19 13:16:08 2016 From: francis at oicr.on.ca (Francis Ouellette) Date: Mon, 19 Sep 2016 17:16:08 +0000 Subject: [DOCKTESTERS] meet in Boston In-Reply-To: References: <375505DD-A67D-420A-A772-84F903AE62B3@oicr.on.ca> Message-ID: <32A1E681-DFF7-4D8B-8379-6AFA298834F7@oicr.on.ca> maybe we try lunch tomorrow? @bffo -- B.F. Francis Ouellette http://oicr.on.ca/person/francis-ouellette > On Sep 19, 2016, at 8:24 AM, Oliver Hofmann wrote: > > Francis, > > > I'm in the Longwood area for meetings, will have to catch up tomorrow > / Wednesday. > > best, Oliver > > > On 19 September 2016 at 08:20:17, Francis Ouellette (francis at oicr.on.ca) wrote: >> >> We would like to meet this afternoon at 13:00, Look for Brian or I in loby area. >> >> @bffo >> >> -- >> B.F. Francis Ouellette http://oicr.on.ca/person/francis-ouellette >> >> >> >> _______________________________________________ >> docktesters mailing list >> docktesters at lists.icgc.org >> https://lists.icgc.org/mailman/listinfo/docktesters >> > > -- > @fiamh > Skype: ohofmann > +44 795 621 5540 From Brian.OConnor at oicr.on.ca Mon Sep 19 13:16:58 2016 From: Brian.OConnor at oicr.on.ca (Brian O'Connor) Date: Mon, 19 Sep 2016 17:16:58 +0000 Subject: [DOCKTESTERS] meet in Boston In-Reply-To: References: <375505DD-A67D-420A-A772-84F903AE62B3@oicr.on.ca>, , Message-ID: <115B1C4D-7F6B-4B19-B25E-16D2A64247F8@oicr.on.ca> I'm in the lobby. Sent from my iPhone On Sep 19, 2016, at 1:15 PM, Junjun Zhang > wrote: Brian and Francis, are you meeting somewhere? Miguel and I are interested to join. Junjun On Sep 19, 2016, at 8:24 AM, Oliver Hofmann > wrote: Francis, I'm in the Longwood area for meetings, will have to catch up tomorrow / Wednesday. best, Oliver On 19 September 2016 at 08:20:17, Francis Ouellette (francis at oicr.on.ca) wrote: We would like to meet this afternoon at 13:00, Look for Brian or I in loby area. @bffo -- B.F. Francis Ouellette http://oicr.on.ca/person/francis-ouellette _______________________________________________ docktesters mailing list docktesters at lists.icgc.org https://lists.icgc.org/mailman/listinfo/docktesters -- @fiamh Skype: ohofmann +44 795 621 5540 _______________________________________________ docktesters mailing list docktesters at lists.icgc.org https://lists.icgc.org/mailman/listinfo/docktesters _______________________________________________ docktesters mailing list docktesters at lists.icgc.org https://lists.icgc.org/mailman/listinfo/docktesters -------------- next part -------------- An HTML attachment was scrubbed... URL: From francis at oicr.on.ca Mon Sep 19 13:53:10 2016 From: francis at oicr.on.ca (Francis Ouellette) Date: Mon, 19 Sep 2016 17:53:10 +0000 Subject: [DOCKTESTERS] testing docker Message-ID: <6ECAE345-D1CB-4896-8FF8-0C470BB1B6A0@oicr.on.ca> Please log your testing file here https://wiki.oicr.on.ca/display/PANCANCER/Workflow+Testing+Data @bffo -- B.F. Francis Ouellette http://oicr.on.ca/person/francis-ouellette -------------- next part -------------- An HTML attachment was scrubbed... URL: From francis at oicr.on.ca Mon Sep 19 15:22:55 2016 From: francis at oicr.on.ca (Francis Ouellette) Date: Mon, 19 Sep 2016 19:22:55 +0000 Subject: [DOCKTESTERS] Amazon account In-Reply-To: References: Message-ID: Hi Miguel, I?m CCing docktester .. I think Junjun or Brian will be best to answer this ? I think a bit more RAM would be OK, so could do: m4.10xlarge (10 CPU and 160 GB RAM). Would that be good Brian? @bffo -- B.F. Francis Ouellette http://oicr.on.ca/person/francis-ouellette On Sep 19, 2016, at 3:09 PM, Zhibin > wrote: Jo Miguel, I am not familiar with Sanger pipeline. You should launch instances based on the number of CPUs and memory you need. Best, Zhibin On Mon, Sep 19, 2016 at 3:05 PM, Miguel Vazquez > wrote: Hello again, What image will you suggest to run the Sanger pipeline? I'm not very used to AWS and I wouldn't want to burn through your credit accidentally. I was thinking of r3.4xlarge that has 16 cores, 122GB memmory and 1x320 (SSD), would that be a good choice? Best Miguel On Mon, Sep 19, 2016 at 8:42 PM, Miguel Vazquez > wrote: Thanks Zhibin Best regards Miguel -------------- next part -------------- An HTML attachment was scrubbed... URL: From mikisvaz at gmail.com Mon Sep 19 15:26:29 2016 From: mikisvaz at gmail.com (Miguel Vazquez) Date: Mon, 19 Sep 2016 21:26:29 +0200 Subject: [DOCKTESTERS] Amazon account In-Reply-To: References: Message-ID: Thanks Francis. BTW Brian and Junjun, I think I might not have enough disk space in the instance you got for me, gtdownload croaks: Error: The system *might* run out of disk space before all downloads are complete, Downloading will continue until less than 1.00 GB is available. and does not seem to download anything. I took the liberty to make a directory in /mn/, which has 95GB avai. but it does not seem to change things. Excuse my ignorance, but how big are these files? Miguel On Mon, Sep 19, 2016 at 9:22 PM, Francis Ouellette wrote: > Hi Miguel, > > I?m CCing docktester .. I think Junjun or Brian will be best to answer > this ? > I think a bit more RAM would be OK, so could do: m4.10xlarge (10 CPU and > 160 GB RAM). > > Would that be good Brian? > > @bffo > > > -- > B.F. Francis Ouellette http://oicr.on.ca/person/francis-ouellette > > > > > On Sep 19, 2016, at 3:09 PM, Zhibin wrote: > > Jo Miguel, > > I am not familiar with Sanger pipeline. You should launch instances based > on the number of CPUs and memory you need. > > Best, > > Zhibin > > On Mon, Sep 19, 2016 at 3:05 PM, Miguel Vazquez > wrote: > >> Hello again, >> >> What image will you suggest to run the Sanger pipeline? I'm not very used >> to AWS and I wouldn't want to burn through your credit accidentally. I was >> thinking of r3.4xlarge that has 16 cores, 122GB memmory and 1x320 (SSD), >> would that be a good choice? >> >> Best >> >> Miguel >> >> On Mon, Sep 19, 2016 at 8:42 PM, Miguel Vazquez >> wrote: >> >>> Thanks Zhibin >>> >>> Best regards >>> >>> Miguel >>> >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From miguel.vazquez at cnio.es Mon Sep 19 15:29:09 2016 From: miguel.vazquez at cnio.es (Miguel Vazquez) Date: Mon, 19 Sep 2016 21:29:09 +0200 Subject: [DOCKTESTERS] Amazon account In-Reply-To: References: Message-ID: Sorry, my previous attempt to send this email bounced. I'm trying again with my CNIO account On Mon, Sep 19, 2016 at 9:26 PM, Miguel Vazquez wrote: > Thanks Francis. > > BTW Brian and Junjun, I think I might not have enough disk space in the > instance you got for me, gtdownload croaks: > > Error: The system *might* run out of disk space before all downloads are > complete, Downloading will continue until less than 1.00 GB is available. > > > and does not seem to download anything. > > I took the liberty to make a directory in /mn/, which has 95GB avai. but > it does not seem to change things. Excuse my ignorance, but how big are > these files? > > Miguel > > On Mon, Sep 19, 2016 at 9:22 PM, Francis Ouellette > wrote: > >> Hi Miguel, >> >> I?m CCing docktester .. I think Junjun or Brian will be best to answer >> this ? >> I think a bit more RAM would be OK, so could do: m4.10xlarge (10 CPU >> and 160 GB RAM). >> >> Would that be good Brian? >> >> @bffo >> >> >> -- >> B.F. Francis Ouellette http://oicr.on.ca/person/fran >> cis-ouellette >> >> >> >> On Sep 19, 2016, at 3:09 PM, Zhibin wrote: >> >> Jo Miguel, >> >> I am not familiar with Sanger pipeline. You should launch instances based >> on the number of CPUs and memory you need. >> >> Best, >> >> Zhibin >> >> On Mon, Sep 19, 2016 at 3:05 PM, Miguel Vazquez >> wrote: >> >>> Hello again, >>> >>> What image will you suggest to run the Sanger pipeline? I'm not very >>> used to AWS and I wouldn't want to burn through your credit accidentally. I >>> was thinking of r3.4xlarge that has 16 cores, 122GB memmory and 1x320 >>> (SSD), would that be a good choice? >>> >>> Best >>> >>> Miguel >>> >>> On Mon, Sep 19, 2016 at 8:42 PM, Miguel Vazquez >>> wrote: >>> >>>> Thanks Zhibin >>>> >>>> Best regards >>>> >>>> Miguel >>>> >>> >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Denis.Yuen at oicr.on.ca Mon Sep 19 15:39:57 2016 From: Denis.Yuen at oicr.on.ca (Denis Yuen) Date: Mon, 19 Sep 2016 19:39:57 +0000 Subject: [DOCKTESTERS] Amazon account In-Reply-To: References: , Message-ID: <27512884B2D81B41AAB7BB266248F240C099E23C@exmb2.ad.oicr.on.ca> Hi, Quoting myself from an email since it is applicable here too Hi, Sounds reasonable, the hardware requirements listed at https://github.com/ICGC-TCGA-PanCancer/CGP-Somatic-Docker#hardware-requirements match my recollection and a r3.4xlarge matches that handily in terms of RAM and CPU The only thing I would check would be to make sure that the working directory (where you run Dockstore) is in a large 1TB volume. The workflow should be able to overwhelm 320 GB if that's all you have, causing it to crash. When we were running for Pan-cancer, we sometimes used lvm to merge all ephemeral drives on an AWS instance into one larger drive. But for testing, it would probably be simpler just to use one large EBS volume. Denis Yuen Bioinformatics Software Developer Ontario Institute for Cancer Research MaRS Centre 661 University Avenue Suite 510 Toronto, Ontario, Canada M5G 0A3 Toll-free: 1-866-678-6427 Twitter: @OICR_news www.oicr.on.ca This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization. ________________________________ From: docktesters-bounces+denis.yuen=oicr.on.ca at lists.icgc.org [docktesters-bounces+denis.yuen=oicr.on.ca at lists.icgc.org] on behalf of Miguel Vazquez [mikisvaz at gmail.com] Sent: September 19, 2016 3:26 PM To: Francis Ouellette Cc: docktesters at lists.icgc.org; Zhibin Subject: Re: [DOCKTESTERS] Amazon account Thanks Francis. BTW Brian and Junjun, I think I might not have enough disk space in the instance you got for me, gtdownload croaks: Error: The system *might* run out of disk space before all downloads are complete, Downloading will continue until less than 1.00 GB is available. and does not seem to download anything. I took the liberty to make a directory in /mn/, which has 95GB avai. but it does not seem to change things. Excuse my ignorance, but how big are these files? Miguel On Mon, Sep 19, 2016 at 9:22 PM, Francis Ouellette > wrote: Hi Miguel, I?m CCing docktester .. I think Junjun or Brian will be best to answer this ? I think a bit more RAM would be OK, so could do: m4.10xlarge (10 CPU and 160 GB RAM). Would that be good Brian? @bffo -- B.F. Francis Ouellette http://oicr.on.ca/person/francis-ouellette On Sep 19, 2016, at 3:09 PM, Zhibin > wrote: Jo Miguel, I am not familiar with Sanger pipeline. You should launch instances based on the number of CPUs and memory you need. Best, Zhibin On Mon, Sep 19, 2016 at 3:05 PM, Miguel Vazquez > wrote: Hello again, What image will you suggest to run the Sanger pipeline? I'm not very used to AWS and I wouldn't want to burn through your credit accidentally. I was thinking of r3.4xlarge that has 16 cores, 122GB memmory and 1x320 (SSD), would that be a good choice? Best Miguel On Mon, Sep 19, 2016 at 8:42 PM, Miguel Vazquez > wrote: Thanks Zhibin Best regards Miguel -------------- next part -------------- An HTML attachment was scrubbed... URL: From Junjun.Zhang at oicr.on.ca Mon Sep 19 23:02:06 2016 From: Junjun.Zhang at oicr.on.ca (Junjun Zhang) Date: Tue, 20 Sep 2016 03:02:06 +0000 Subject: [DOCKTESTERS] Amazon account In-Reply-To: <27512884B2D81B41AAB7BB266248F240C099E23C@exmb2.ad.oicr.on.ca> References: , , <27512884B2D81B41AAB7BB266248F240C099E23C@exmb2.ad.oicr.on.ca> Message-ID: <2C84FF4CF2F0A04EB7691F988A717B47CB65E809@exmb2.ad.oicr.on.ca> Good news, both Miguel and myself have Sanger pipeline running on AWS and Collab respectively. Here is the documentation on all steps we went through to get things set up: https://docs.google.com/document/d/1EPo2Wgh-WJz75GdykgTI1fpm89yIdoGGHAyVlJ9PbcA/edit As you can see there are quite some steps to go through, does it make sense to build a docker image for setting up testing environment? It's kind of like docker in docker, is that OK? Junjun ________________________________ From: docktesters-bounces+junjun.zhang=oicr.on.ca at lists.icgc.org [docktesters-bounces+junjun.zhang=oicr.on.ca at lists.icgc.org] on behalf of Denis Yuen [Denis.Yuen at oicr.on.ca] Sent: Monday, September 19, 2016 3:39 PM To: Miguel Vazquez Cc: docktesters at lists.icgc.org Subject: Re: [DOCKTESTERS] Amazon account Hi, Quoting myself from an email since it is applicable here too Hi, Sounds reasonable, the hardware requirements listed at https://github.com/ICGC-TCGA-PanCancer/CGP-Somatic-Docker#hardware-requirements match my recollection and a r3.4xlarge matches that handily in terms of RAM and CPU The only thing I would check would be to make sure that the working directory (where you run Dockstore) is in a large 1TB volume. The workflow should be able to overwhelm 320 GB if that's all you have, causing it to crash. When we were running for Pan-cancer, we sometimes used lvm to merge all ephemeral drives on an AWS instance into one larger drive. But for testing, it would probably be simpler just to use one large EBS volume. Denis Yuen Bioinformatics Software Developer Ontario Institute for Cancer Research MaRS Centre 661 University Avenue Suite 510 Toronto, Ontario, Canada M5G 0A3 Toll-free: 1-866-678-6427 Twitter: @OICR_news www.oicr.on.ca This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization. ________________________________ From: docktesters-bounces+denis.yuen=oicr.on.ca at lists.icgc.org [docktesters-bounces+denis.yuen=oicr.on.ca at lists.icgc.org] on behalf of Miguel Vazquez [mikisvaz at gmail.com] Sent: September 19, 2016 3:26 PM To: Francis Ouellette Cc: docktesters at lists.icgc.org; Zhibin Subject: Re: [DOCKTESTERS] Amazon account Thanks Francis. BTW Brian and Junjun, I think I might not have enough disk space in the instance you got for me, gtdownload croaks: Error: The system *might* run out of disk space before all downloads are complete, Downloading will continue until less than 1.00 GB is available. and does not seem to download anything. I took the liberty to make a directory in /mn/, which has 95GB avai. but it does not seem to change things. Excuse my ignorance, but how big are these files? Miguel On Mon, Sep 19, 2016 at 9:22 PM, Francis Ouellette > wrote: Hi Miguel, I?m CCing docktester .. I think Junjun or Brian will be best to answer this ? I think a bit more RAM would be OK, so could do: m4.10xlarge (10 CPU and 160 GB RAM). Would that be good Brian? @bffo -- B.F. Francis Ouellette http://oicr.on.ca/person/francis-ouellette On Sep 19, 2016, at 3:09 PM, Zhibin > wrote: Jo Miguel, I am not familiar with Sanger pipeline. You should launch instances based on the number of CPUs and memory you need. Best, Zhibin On Mon, Sep 19, 2016 at 3:05 PM, Miguel Vazquez > wrote: Hello again, What image will you suggest to run the Sanger pipeline? I'm not very used to AWS and I wouldn't want to burn through your credit accidentally. I was thinking of r3.4xlarge that has 16 cores, 122GB memmory and 1x320 (SSD), would that be a good choice? Best Miguel On Mon, Sep 19, 2016 at 8:42 PM, Miguel Vazquez > wrote: Thanks Zhibin Best regards Miguel -------------- next part -------------- An HTML attachment was scrubbed... URL: From Brian.OConnor at oicr.on.ca Tue Sep 20 09:42:57 2016 From: Brian.OConnor at oicr.on.ca (Brian O'Connor) Date: Tue, 20 Sep 2016 13:42:57 +0000 Subject: [DOCKTESTERS] Amazon account In-Reply-To: <2C84FF4CF2F0A04EB7691F988A717B47CB65E809@exmb2.ad.oicr.on.ca> References: <27512884B2D81B41AAB7BB266248F240C099E23C@exmb2.ad.oicr.on.ca> <2C84FF4CF2F0A04EB7691F988A717B47CB65E809@exmb2.ad.oicr.on.ca> Message-ID: Hi Junjun, Great to hear this! I would recommend against trying to make this a docker in docker. It?s something to be avoided because it really causes problems running in various environments. Maybe a well commented bash script? I think the instructions are long but really we expect these workflows to run in a lot of different environments and it?s better to explain how it works so users can customize for their environment. What do you all think? Brian > On Sep 19, 2016, at 11:02 PM, Junjun Zhang wrote: > > Good news, both Miguel and myself have Sanger pipeline running on AWS and Collab respectively. > > Here is the documentation on all steps we went through to get things set up: https://docs.google.com/document/d/1EPo2Wgh-WJz75GdykgTI1fpm89yIdoGGHAyVlJ9PbcA/edit > > As you can see there are quite some steps to go through, does it make sense to build a docker image for setting up testing environment? > > It's kind of like docker in docker, is that OK? > > Junjun > > > From: docktesters-bounces+junjun.zhang=oicr.on.ca at lists.icgc.org [docktesters-bounces+junjun.zhang=oicr.on.ca at lists.icgc.org] on behalf of Denis Yuen [Denis.Yuen at oicr.on.ca] > Sent: Monday, September 19, 2016 3:39 PM > To: Miguel Vazquez > Cc: docktesters at lists.icgc.org > Subject: Re: [DOCKTESTERS] Amazon account > > Hi, > > Quoting myself from an email since it is applicable here too > > Hi, > Sounds reasonable, the hardware requirements listed at https://github.com/ICGC-TCGA-PanCancer/CGP-Somatic-Docker#hardware-requirements match my recollection and a r3.4xlarge matches that handily in terms of RAM and CPU > > The only thing I would check would be to make sure that the working directory (where you run Dockstore) is in a large 1TB volume. The workflow should be able to overwhelm 320 GB if that's all you have, causing it to crash. > > When we were running for Pan-cancer, we sometimes used lvm to merge all ephemeral drives on an AWS instance into one larger drive. > But for testing, it would probably be simpler just to use one large EBS volume. > > Denis Yuen > Bioinformatics Software Developer > > Ontario Institute for Cancer Research > MaRS Centre > 661 University Avenue > Suite 510 > Toronto, Ontario, Canada M5G 0A3 > Toll-free: 1-866-678-6427 > Twitter: @OICR_news > www.oicr.on.ca > This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization. > From: docktesters-bounces+denis.yuen=oicr.on.ca at lists.icgc.org [docktesters-bounces+denis.yuen=oicr.on.ca at lists.icgc.org] on behalf of Miguel Vazquez [mikisvaz at gmail.com] > Sent: September 19, 2016 3:26 PM > To: Francis Ouellette > Cc: docktesters at lists.icgc.org; Zhibin > Subject: Re: [DOCKTESTERS] Amazon account > > Thanks Francis. > > BTW Brian and Junjun, I think I might not have enough disk space in the instance you got for me, gtdownload croaks: > > Error: The system *might* run out of disk space before all downloads are complete, Downloading will continue until less than 1.00 GB is available. > > and does not seem to download anything. > > I took the liberty to make a directory in /mn/, which has 95GB avai. but it does not seem to change things. Excuse my ignorance, but how big are these files? > > Miguel > > On Mon, Sep 19, 2016 at 9:22 PM, Francis Ouellette wrote: > Hi Miguel, > > I?m CCing docktester .. I think Junjun or Brian will be best to answer this ? > I think a bit more RAM would be OK, so could do: m4.10xlarge (10 CPU and 160 GB RAM). > > Would that be good Brian? > > @bffo > > > -- > B.F. Francis Ouellette http://oicr.on.ca/person/francis-ouellette > > > >> On Sep 19, 2016, at 3:09 PM, Zhibin wrote: >> >> Jo Miguel, >> >> I am not familiar with Sanger pipeline. You should launch instances based on the number of CPUs and memory you need. >> >> Best, >> >> Zhibin >> >> On Mon, Sep 19, 2016 at 3:05 PM, Miguel Vazquez wrote: >> Hello again, >> >> What image will you suggest to run the Sanger pipeline? I'm not very used to AWS and I wouldn't want to burn through your credit accidentally. I was thinking of r3.4xlarge that has 16 cores, 122GB memmory and 1x320 (SSD), would that be a good choice? >> >> Best >> >> Miguel >> >> On Mon, Sep 19, 2016 at 8:42 PM, Miguel Vazquez wrote: >> Thanks Zhibin >> Best regards >> Miguel > > > > _______________________________________________ > docktesters mailing list > docktesters at lists.icgc.org > https://lists.icgc.org/mailman/listinfo/docktesters From ohofmann72 at gmail.com Tue Sep 20 09:44:28 2016 From: ohofmann72 at gmail.com (Oliver Hofmann) Date: Tue, 20 Sep 2016 06:44:28 -0700 Subject: [DOCKTESTERS] Amazon account In-Reply-To: References: <27512884B2D81B41AAB7BB266248F240C099E23C@exmb2.ad.oicr.on.ca> <2C84FF4CF2F0A04EB7691F988A717B47CB65E809@exmb2.ad.oicr.on.ca> Message-ID: I'll second that. A lot of this is specific to the ICGC samples as well (data access, etc.) whereas I expect many end users will want to just run this on their own WGS data. Oliver On 20 September 2016 at 09:43:02, Brian O'Connor (brian.oconnor at oicr.on.ca) wrote: > Hi Junjun, > > Great to hear this! > > I would recommend against trying to make this a docker in docker. It?s something to be > avoided because it really causes problems running in various environments. > > Maybe a well commented bash script? I think the instructions are long but really we expect > these workflows to run in a lot of different environments and it?s better to explain how > it works so users can customize for their environment. > > What do you all think? > > Brian > > > On Sep 19, 2016, at 11:02 PM, Junjun Zhang wrote: > > > > Good news, both Miguel and myself have Sanger pipeline running on AWS and Collab respectively. > > > > Here is the documentation on all steps we went through to get things set up: https://docs.google.com/document/d/1EPo2Wgh-WJz75GdykgTI1fpm89yIdoGGHAyVlJ9PbcA/edit > > > > As you can see there are quite some steps to go through, does it make sense to build a docker > image for setting up testing environment? > > > > It's kind of like docker in docker, is that OK? > > > > Junjun > > > > > > From: docktesters-bounces+junjun.zhang=oicr.on.ca at lists.icgc.org [docktesters-bounces+junjun.zhang=oicr.on.ca at lists.icgc.org] > on behalf of Denis Yuen [Denis.Yuen at oicr.on.ca] > > Sent: Monday, September 19, 2016 3:39 PM > > To: Miguel Vazquez > > Cc: docktesters at lists.icgc.org > > Subject: Re: [DOCKTESTERS] Amazon account > > > > Hi, > > > > Quoting myself from an email since it is applicable here too > > > > Hi, > > Sounds reasonable, the hardware requirements listed at https://github.com/ICGC-TCGA-PanCancer/CGP-Somatic-Docker#hardware-requirements > match my recollection and a r3.4xlarge matches that handily in terms of RAM and CPU > > > > The only thing I would check would be to make sure that the working directory (where you > run Dockstore) is in a large 1TB volume. The workflow should be able to overwhelm 320 GB > if that's all you have, causing it to crash. > > > > When we were running for Pan-cancer, we sometimes used lvm to merge all ephemeral drives > on an AWS instance into one larger drive. > > But for testing, it would probably be simpler just to use one large EBS volume. > > > > Denis Yuen > > Bioinformatics Software Developer > > > > Ontario Institute for Cancer Research > > MaRS Centre > > 661 University Avenue > > Suite 510 > > Toronto, Ontario, Canada M5G 0A3 > > Toll-free: 1-866-678-6427 > > Twitter: @OICR_news > > www.oicr.on.ca > > This message and any attachments may contain confidential and/or privileged information > for the sole use of the intended recipient. Any review or distribution by anyone other > than the person for whom it was originally intended is strictly prohibited. If you have > received this message in error, please contact the sender and delete all copies. Opinions, > conclusions or other information contained in this message may not be that of the organization. > > From: docktesters-bounces+denis.yuen=oicr.on.ca at lists.icgc.org [docktesters-bounces+denis.yuen=oicr.on.ca at lists.icgc.org] > on behalf of Miguel Vazquez [mikisvaz at gmail.com] > > Sent: September 19, 2016 3:26 PM > > To: Francis Ouellette > > Cc: docktesters at lists.icgc.org; Zhibin > > Subject: Re: [DOCKTESTERS] Amazon account > > > > Thanks Francis. > > > > BTW Brian and Junjun, I think I might not have enough disk space in the instance you got > for me, gtdownload croaks: > > > > Error: The system *might* run out of disk space before all downloads are complete, Downloading > will continue until less than 1.00 GB is available. > > > > and does not seem to download anything. > > > > I took the liberty to make a directory in /mn/, which has 95GB avai. but it does not seem > to change things. Excuse my ignorance, but how big are these files? > > > > Miguel > > > > On Mon, Sep 19, 2016 at 9:22 PM, Francis Ouellette wrote: > > Hi Miguel, > > > > I?m CCing docktester .. I think Junjun or Brian will be best to answer this ? > > I think a bit more RAM would be OK, so could do: m4.10xlarge (10 CPU and 160 GB RAM). > > > > Would that be good Brian? > > > > @bffo > > > > > > -- > > B.F. Francis Ouellette http://oicr.on.ca/person/francis-ouellette > > > > > > > >> On Sep 19, 2016, at 3:09 PM, Zhibin wrote: > >> > >> Jo Miguel, > >> > >> I am not familiar with Sanger pipeline. You should launch instances based on the number > of CPUs and memory you need. > >> > >> Best, > >> > >> Zhibin > >> > >> On Mon, Sep 19, 2016 at 3:05 PM, Miguel Vazquez wrote: > >> Hello again, > >> > >> What image will you suggest to run the Sanger pipeline? I'm not very used to AWS and I > wouldn't want to burn through your credit accidentally. I was thinking of r3.4xlarge > that has 16 cores, 122GB memmory and 1x320 (SSD), would that be a good choice? > >> > >> Best > >> > >> Miguel > >> > >> On Mon, Sep 19, 2016 at 8:42 PM, Miguel Vazquez wrote: > >> Thanks Zhibin > >> Best regards > >> Miguel > > > > > > > > _______________________________________________ > > docktesters mailing list > > docktesters at lists.icgc.org > > https://lists.icgc.org/mailman/listinfo/docktesters > > _______________________________________________ > docktesters mailing list > docktesters at lists.icgc.org > https://lists.icgc.org/mailman/listinfo/docktesters > -- @fiamh Skype: ohofmann +44 795 621 5540 From Junjun.Zhang at oicr.on.ca Tue Sep 20 10:21:47 2016 From: Junjun.Zhang at oicr.on.ca (Junjun Zhang) Date: Tue, 20 Sep 2016 14:21:47 +0000 Subject: [DOCKTESTERS] Amazon account In-Reply-To: References: <27512884B2D81B41AAB7BB266248F240C099E23C@exmb2.ad.oicr.on.ca> <2C84FF4CF2F0A04EB7691F988A717B47CB65E809@exmb2.ad.oicr.on.ca> , Message-ID: <42F77FE4-3AA4-4AF9-9503-3B753DAC6635@oicr.on.ca> I was only thinking about making this docker image for the testing group so it's more efficient to do our work. Junjun > On Sep 20, 2016, at 9:44 AM, Oliver Hofmann wrote: > > I'll second that. A lot of this is specific to the ICGC samples as > well (data access, etc.) whereas I expect many end users will want to > just run this on their own WGS data. > > Oliver > > On 20 September 2016 at 09:43:02, Brian O'Connor > (brian.oconnor at oicr.on.ca) wrote: >> Hi Junjun, >> >> Great to hear this! >> >> I would recommend against trying to make this a docker in docker. It?s something to be >> avoided because it really causes problems running in various environments. >> >> Maybe a well commented bash script? I think the instructions are long but really we expect >> these workflows to run in a lot of different environments and it?s better to explain how >> it works so users can customize for their environment. >> >> What do you all think? >> >> Brian >> >>> On Sep 19, 2016, at 11:02 PM, Junjun Zhang wrote: >>> >>> Good news, both Miguel and myself have Sanger pipeline running on AWS and Collab respectively. >>> >>> Here is the documentation on all steps we went through to get things set up: https://docs.google.com/document/d/1EPo2Wgh-WJz75GdykgTI1fpm89yIdoGGHAyVlJ9PbcA/edit >>> >>> As you can see there are quite some steps to go through, does it make sense to build a docker >> image for setting up testing environment? >>> >>> It's kind of like docker in docker, is that OK? >>> >>> Junjun >>> >>> >>> From: docktesters-bounces+junjun.zhang=oicr.on.ca at lists.icgc.org [docktesters-bounces+junjun.zhang=oicr.on.ca at lists.icgc.org] >> on behalf of Denis Yuen [Denis.Yuen at oicr.on.ca] >>> Sent: Monday, September 19, 2016 3:39 PM >>> To: Miguel Vazquez >>> Cc: docktesters at lists.icgc.org >>> Subject: Re: [DOCKTESTERS] Amazon account >>> >>> Hi, >>> >>> Quoting myself from an email since it is applicable here too >>> >>> Hi, >>> Sounds reasonable, the hardware requirements listed at https://github.com/ICGC-TCGA-PanCancer/CGP-Somatic-Docker#hardware-requirements >> match my recollection and a r3.4xlarge matches that handily in terms of RAM and CPU >>> >>> The only thing I would check would be to make sure that the working directory (where you >> run Dockstore) is in a large 1TB volume. The workflow should be able to overwhelm 320 GB >> if that's all you have, causing it to crash. >>> >>> When we were running for Pan-cancer, we sometimes used lvm to merge all ephemeral drives >> on an AWS instance into one larger drive. >>> But for testing, it would probably be simpler just to use one large EBS volume. >>> >>> Denis Yuen >>> Bioinformatics Software Developer >>> >>> Ontario Institute for Cancer Research >>> MaRS Centre >>> 661 University Avenue >>> Suite 510 >>> Toronto, Ontario, Canada M5G 0A3 >>> Toll-free: 1-866-678-6427 >>> Twitter: @OICR_news >>> www.oicr.on.ca >>> This message and any attachments may contain confidential and/or privileged information >> for the sole use of the intended recipient. Any review or distribution by anyone other >> than the person for whom it was originally intended is strictly prohibited. If you have >> received this message in error, please contact the sender and delete all copies. Opinions, >> conclusions or other information contained in this message may not be that of the organization. >>> From: docktesters-bounces+denis.yuen=oicr.on.ca at lists.icgc.org [docktesters-bounces+denis.yuen=oicr.on.ca at lists.icgc.org] >> on behalf of Miguel Vazquez [mikisvaz at gmail.com] >>> Sent: September 19, 2016 3:26 PM >>> To: Francis Ouellette >>> Cc: docktesters at lists.icgc.org; Zhibin >>> Subject: Re: [DOCKTESTERS] Amazon account >>> >>> Thanks Francis. >>> >>> BTW Brian and Junjun, I think I might not have enough disk space in the instance you got >> for me, gtdownload croaks: >>> >>> Error: The system *might* run out of disk space before all downloads are complete, Downloading >> will continue until less than 1.00 GB is available. >>> >>> and does not seem to download anything. >>> >>> I took the liberty to make a directory in /mn/, which has 95GB avai. but it does not seem >> to change things. Excuse my ignorance, but how big are these files? >>> >>> Miguel >>> >>> On Mon, Sep 19, 2016 at 9:22 PM, Francis Ouellette wrote: >>> Hi Miguel, >>> >>> I?m CCing docktester .. I think Junjun or Brian will be best to answer this ? >>> I think a bit more RAM would be OK, so could do: m4.10xlarge (10 CPU and 160 GB RAM). >>> >>> Would that be good Brian? >>> >>> @bffo >>> >>> >>> -- >>> B.F. Francis Ouellette http://oicr.on.ca/person/francis-ouellette >>> >>> >>> >>>> On Sep 19, 2016, at 3:09 PM, Zhibin wrote: >>>> >>>> Jo Miguel, >>>> >>>> I am not familiar with Sanger pipeline. You should launch instances based on the number >> of CPUs and memory you need. >>>> >>>> Best, >>>> >>>> Zhibin >>>> >>>> On Mon, Sep 19, 2016 at 3:05 PM, Miguel Vazquez wrote: >>>> Hello again, >>>> >>>> What image will you suggest to run the Sanger pipeline? I'm not very used to AWS and I >> wouldn't want to burn through your credit accidentally. I was thinking of r3.4xlarge >> that has 16 cores, 122GB memmory and 1x320 (SSD), would that be a good choice? >>>> >>>> Best >>>> >>>> Miguel >>>> >>>> On Mon, Sep 19, 2016 at 8:42 PM, Miguel Vazquez wrote: >>>> Thanks Zhibin >>>> Best regards >>>> Miguel >>> >>> >>> >>> _______________________________________________ >>> docktesters mailing list >>> docktesters at lists.icgc.org >>> https://lists.icgc.org/mailman/listinfo/docktesters >> >> _______________________________________________ >> docktesters mailing list >> docktesters at lists.icgc.org >> https://lists.icgc.org/mailman/listinfo/docktesters > > -- > @fiamh > Skype: ohofmann > +44 795 621 5540 From mikisvaz at gmail.com Tue Sep 20 10:22:00 2016 From: mikisvaz at gmail.com (Miguel Vazquez) Date: Tue, 20 Sep 2016 16:22:00 +0200 Subject: [DOCKTESTERS] Amazon account In-Reply-To: References: <27512884B2D81B41AAB7BB266248F240C099E23C@exmb2.ad.oicr.on.ca> <2C84FF4CF2F0A04EB7691F988A717B47CB65E809@exmb2.ad.oicr.on.ca> Message-ID: Hi all, I think there are three scripting or systematizing efforts that would help 1) Setting environment up to running the dockerstore. Junjun suggested docker inside docker, which might be a bit convoluted, but a preset virtual machine or AWS AIM would be very suitable. Brian's script would be the script that provisions such a VM, and Vagrant would be a possible way to program this if this technology plays well with VM vendors 2) Downloading the samples and preparing the Dockerstore.json files to run and produce the results in standard places 3) Downloading the released version of the files and comparing with the results of the test. This could be as simple as retrieving the list of SNVs and indels and measuring the overlaps. There is also the issue of launching the instances, issuing the jobs, monitoring completion, and possibly gathering results files for validation prior to turning them down. Point 1) is fairly easy with the documentation we have already. Point 2) is almost 25% done, we still have 3 other dockerstore workflows to setup op, and also drivers for the ICGC client and GNOS client. Point 3) might not be that hard either once the files are gathered and organized. The moving parts here that would require specific drivers I think are: - The code to provision VM images, Vagrant for instance, though it is really just running a script - The different VM technologies: AWS, Collaboratory, etc - The 4 different pipeline: Sanger, Broad, DKFZ, BWA - The 2 downloading tools: ICGC and GNOS - The several different result files: SNV, Indels, SV, etc The effort required to set all this infrastructure up might be a bit of an overkill though. On the other hand the results might be a deliverable piece of work that might have more reach than just these tests. Maybe we can discuss this on our next meeting. Best M On Tue, Sep 20, 2016 at 3:42 PM, Brian O'Connor wrote: > Hi Junjun, > > Great to hear this! > > I would recommend against trying to make this a docker in docker. It?s > something to be avoided because it really causes problems running in > various environments. > > Maybe a well commented bash script? I think the instructions are long but > really we expect these workflows to run in a lot of different environments > and it?s better to explain how it works so users can customize for their > environment. > > What do you all think? > > Brian > > > On Sep 19, 2016, at 11:02 PM, Junjun Zhang > wrote: > > > > Good news, both Miguel and myself have Sanger pipeline running on AWS > and Collab respectively. > > > > Here is the documentation on all steps we went through to get things set > up: https://docs.google.com/document/d/1EPo2Wgh- > WJz75GdykgTI1fpm89yIdoGGHAyVlJ9PbcA/edit > > > > As you can see there are quite some steps to go through, does it make > sense to build a docker image for setting up testing environment? > > > > It's kind of like docker in docker, is that OK? > > > > Junjun > > > > > > From: docktesters-bounces+junjun.zhang=oicr.on.ca at lists.icgc.org > [docktesters-bounces+junjun.zhang=oicr.on.ca at lists.icgc.org] on behalf of > Denis Yuen [Denis.Yuen at oicr.on.ca] > > Sent: Monday, September 19, 2016 3:39 PM > > To: Miguel Vazquez > > Cc: docktesters at lists.icgc.org > > Subject: Re: [DOCKTESTERS] Amazon account > > > > Hi, > > > > Quoting myself from an email since it is applicable here too > > > > Hi, > > Sounds reasonable, the hardware requirements listed at > https://github.com/ICGC-TCGA-PanCancer/CGP-Somatic-Docker# > hardware-requirements match my recollection and a r3.4xlarge matches that > handily in terms of RAM and CPU > > > > The only thing I would check would be to make sure that the working > directory (where you run Dockstore) is in a large 1TB volume. The workflow > should be able to overwhelm 320 GB if that's all you have, causing it to > crash. > > > > When we were running for Pan-cancer, we sometimes used lvm to merge all > ephemeral drives on an AWS instance into one larger drive. > > But for testing, it would probably be simpler just to use one large EBS > volume. > > > > Denis Yuen > > Bioinformatics Software Developer > > > > Ontario Institute for Cancer Research > > MaRS Centre > > 661 University Avenue > > Suite 510 > > Toronto, Ontario, Canada M5G 0A3 > > Toll-free: 1-866-678-6427 > > Twitter: @OICR_news > > www.oicr.on.ca > > This message and any attachments may contain confidential and/or > privileged information for the sole use of the intended recipient. Any > review or distribution by anyone other than the person for whom it was > originally intended is strictly prohibited. If you have received this > message in error, please contact the sender and delete all copies. > Opinions, conclusions or other information contained in this message may > not be that of the organization. > > From: docktesters-bounces+denis.yuen=oicr.on.ca at lists.icgc.org > [docktesters-bounces+denis.yuen=oicr.on.ca at lists.icgc.org] on behalf of > Miguel Vazquez [mikisvaz at gmail.com] > > Sent: September 19, 2016 3:26 PM > > To: Francis Ouellette > > Cc: docktesters at lists.icgc.org; Zhibin > > Subject: Re: [DOCKTESTERS] Amazon account > > > > Thanks Francis. > > > > BTW Brian and Junjun, I think I might not have enough disk space in the > instance you got for me, gtdownload croaks: > > > > Error: The system *might* run out of disk space before all downloads > are complete, Downloading will continue until less than 1.00 GB is > available. > > > > and does not seem to download anything. > > > > I took the liberty to make a directory in /mn/, which has 95GB avai. but > it does not seem to change things. Excuse my ignorance, but how big are > these files? > > > > Miguel > > > > On Mon, Sep 19, 2016 at 9:22 PM, Francis Ouellette > wrote: > > Hi Miguel, > > > > I?m CCing docktester .. I think Junjun or Brian will be best to answer > this ? > > I think a bit more RAM would be OK, so could do: m4.10xlarge (10 CPU > and 160 GB RAM). > > > > Would that be good Brian? > > > > @bffo > > > > > > -- > > B.F. Francis Ouellette http://oicr.on.ca/person/ > francis-ouellette > > > > > > > >> On Sep 19, 2016, at 3:09 PM, Zhibin wrote: > >> > >> Jo Miguel, > >> > >> I am not familiar with Sanger pipeline. You should launch instances > based on the number of CPUs and memory you need. > >> > >> Best, > >> > >> Zhibin > >> > >> On Mon, Sep 19, 2016 at 3:05 PM, Miguel Vazquez > wrote: > >> Hello again, > >> > >> What image will you suggest to run the Sanger pipeline? I'm not very > used to AWS and I wouldn't want to burn through your credit accidentally. I > was thinking of r3.4xlarge that has 16 cores, 122GB memmory and 1x320 > (SSD), would that be a good choice? > >> > >> Best > >> > >> Miguel > >> > >> On Mon, Sep 19, 2016 at 8:42 PM, Miguel Vazquez > wrote: > >> Thanks Zhibin > >> Best regards > >> Miguel > > > > > > > > _______________________________________________ > > docktesters mailing list > > docktesters at lists.icgc.org > > https://lists.icgc.org/mailman/listinfo/docktesters > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From miguel.vazquez at cnio.es Tue Sep 20 10:24:20 2016 From: miguel.vazquez at cnio.es (Miguel Vazquez) Date: Tue, 20 Sep 2016 16:24:20 +0200 Subject: [DOCKTESTERS] Amazon account In-Reply-To: References: <27512884B2D81B41AAB7BB266248F240C099E23C@exmb2.ad.oicr.on.ca> <2C84FF4CF2F0A04EB7691F988A717B47CB65E809@exmb2.ad.oicr.on.ca> Message-ID: I'm resending this. I used the wrong email again and it bounced. Apologies On Tue, Sep 20, 2016 at 4:22 PM, Miguel Vazquez wrote: > Hi all, > > I think there are three scripting or systematizing efforts that would help > > 1) Setting environment up to running the dockerstore. Junjun suggested > docker inside docker, which might be a bit convoluted, but a preset virtual > machine or AWS AIM would be very suitable. Brian's script would be the > script that provisions such a VM, and Vagrant would be a possible way to > program this if this technology plays well with VM vendors > > 2) Downloading the samples and preparing the Dockerstore.json files to run > and produce the results in standard places > > 3) Downloading the released version of the files and comparing with the > results of the test. This could be as simple as retrieving the list of SNVs > and indels and measuring the overlaps. > > There is also the issue of launching the instances, issuing the jobs, > monitoring completion, and possibly gathering results files for validation > prior to turning them down. > > Point 1) is fairly easy with the documentation we have already. Point 2) > is almost 25% done, we still have 3 other dockerstore workflows to setup > op, and also drivers for the ICGC client and GNOS client. Point 3) might > not be that hard either once the files are gathered and organized. > > The moving parts here that would require specific drivers I think are: > - The code to provision VM images, Vagrant for instance, though it is > really just running a script > - The different VM technologies: AWS, Collaboratory, etc > - The 4 different pipeline: Sanger, Broad, DKFZ, BWA > - The 2 downloading tools: ICGC and GNOS > - The several different result files: SNV, Indels, SV, etc > > The effort required to set all this infrastructure up might be a bit of an > overkill though. On the other hand the results might be a deliverable piece > of work that might have more reach than just these tests. Maybe we can > discuss this on our next meeting. > > Best > > M > > > > On Tue, Sep 20, 2016 at 3:42 PM, Brian O'Connor > wrote: > >> Hi Junjun, >> >> Great to hear this! >> >> I would recommend against trying to make this a docker in docker. It?s >> something to be avoided because it really causes problems running in >> various environments. >> >> Maybe a well commented bash script? I think the instructions are long >> but really we expect these workflows to run in a lot of different >> environments and it?s better to explain how it works so users can customize >> for their environment. >> >> What do you all think? >> >> Brian >> >> > On Sep 19, 2016, at 11:02 PM, Junjun Zhang >> wrote: >> > >> > Good news, both Miguel and myself have Sanger pipeline running on AWS >> and Collab respectively. >> > >> > Here is the documentation on all steps we went through to get things >> set up: https://docs.google.com/document/d/1EPo2Wgh-WJz75GdykgTI1fpm >> 89yIdoGGHAyVlJ9PbcA/edit >> > >> > As you can see there are quite some steps to go through, does it make >> sense to build a docker image for setting up testing environment? >> > >> > It's kind of like docker in docker, is that OK? >> > >> > Junjun >> > >> > >> > From: docktesters-bounces+junjun.zhang=oicr.on.ca at lists.icgc.org >> [docktesters-bounces+junjun.zhang=oicr.on.ca at lists.icgc.org] on behalf >> of Denis Yuen [Denis.Yuen at oicr.on.ca] >> > Sent: Monday, September 19, 2016 3:39 PM >> > To: Miguel Vazquez >> > Cc: docktesters at lists.icgc.org >> > Subject: Re: [DOCKTESTERS] Amazon account >> > >> > Hi, >> > >> > Quoting myself from an email since it is applicable here too >> > >> > Hi, >> > Sounds reasonable, the hardware requirements listed at >> https://github.com/ICGC-TCGA-PanCancer/CGP-Somatic-Docker#ha >> rdware-requirements match my recollection and a r3.4xlarge matches that >> handily in terms of RAM and CPU >> > >> > The only thing I would check would be to make sure that the working >> directory (where you run Dockstore) is in a large 1TB volume. The workflow >> should be able to overwhelm 320 GB if that's all you have, causing it to >> crash. >> > >> > When we were running for Pan-cancer, we sometimes used lvm to merge all >> ephemeral drives on an AWS instance into one larger drive. >> > But for testing, it would probably be simpler just to use one large EBS >> volume. >> > >> > Denis Yuen >> > Bioinformatics Software Developer >> > >> > Ontario Institute for Cancer Research >> > MaRS Centre >> > 661 University Avenue >> > Suite 510 >> > Toronto, Ontario, Canada M5G 0A3 >> > Toll-free: 1-866-678-6427 >> > Twitter: @OICR_news >> > www.oicr.on.ca >> > This message and any attachments may contain confidential and/or >> privileged information for the sole use of the intended recipient. Any >> review or distribution by anyone other than the person for whom it was >> originally intended is strictly prohibited. If you have received this >> message in error, please contact the sender and delete all copies. >> Opinions, conclusions or other information contained in this message may >> not be that of the organization. >> > From: docktesters-bounces+denis.yuen=oicr.on.ca at lists.icgc.org >> [docktesters-bounces+denis.yuen=oicr.on.ca at lists.icgc.org] on behalf of >> Miguel Vazquez [mikisvaz at gmail.com] >> > Sent: September 19, 2016 3:26 PM >> > To: Francis Ouellette >> > Cc: docktesters at lists.icgc.org; Zhibin >> > Subject: Re: [DOCKTESTERS] Amazon account >> > >> > Thanks Francis. >> > >> > BTW Brian and Junjun, I think I might not have enough disk space in the >> instance you got for me, gtdownload croaks: >> > >> > Error: The system *might* run out of disk space before all downloads >> are complete, Downloading will continue until less than 1.00 GB is >> available. >> > >> > and does not seem to download anything. >> > >> > I took the liberty to make a directory in /mn/, which has 95GB avai. >> but it does not seem to change things. Excuse my ignorance, but how big are >> these files? >> > >> > Miguel >> > >> > On Mon, Sep 19, 2016 at 9:22 PM, Francis Ouellette >> wrote: >> > Hi Miguel, >> > >> > I?m CCing docktester .. I think Junjun or Brian will be best to answer >> this ? >> > I think a bit more RAM would be OK, so could do: m4.10xlarge (10 CPU >> and 160 GB RAM). >> > >> > Would that be good Brian? >> > >> > @bffo >> > >> > >> > -- >> > B.F. Francis Ouellette http://oicr.on.ca/person/franc >> is-ouellette >> > >> > >> > >> >> On Sep 19, 2016, at 3:09 PM, Zhibin wrote: >> >> >> >> Jo Miguel, >> >> >> >> I am not familiar with Sanger pipeline. You should launch instances >> based on the number of CPUs and memory you need. >> >> >> >> Best, >> >> >> >> Zhibin >> >> >> >> On Mon, Sep 19, 2016 at 3:05 PM, Miguel Vazquez >> wrote: >> >> Hello again, >> >> >> >> What image will you suggest to run the Sanger pipeline? I'm not very >> used to AWS and I wouldn't want to burn through your credit accidentally. I >> was thinking of r3.4xlarge that has 16 cores, 122GB memmory and 1x320 >> (SSD), would that be a good choice? >> >> >> >> Best >> >> >> >> Miguel >> >> >> >> On Mon, Sep 19, 2016 at 8:42 PM, Miguel Vazquez >> wrote: >> >> Thanks Zhibin >> >> Best regards >> >> Miguel >> > >> > >> > >> > _______________________________________________ >> > docktesters mailing list >> > docktesters at lists.icgc.org >> > https://lists.icgc.org/mailman/listinfo/docktesters >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Denis.Yuen at oicr.on.ca Tue Sep 20 10:48:27 2016 From: Denis.Yuen at oicr.on.ca (Denis Yuen) Date: Tue, 20 Sep 2016 14:48:27 +0000 Subject: [DOCKTESTERS] Amazon account In-Reply-To: References: <27512884B2D81B41AAB7BB266248F240C099E23C@exmb2.ad.oicr.on.ca> <2C84FF4CF2F0A04EB7691F988A717B47CB65E809@exmb2.ad.oicr.on.ca> , Message-ID: <27512884B2D81B41AAB7BB266248F240C099E2A3@exmb2.ad.oicr.on.ca> Hi, An AMI/Vagrant script would make sense. I like Ansible too as well and we have some re-usable code here that was used to construct the VMs for the pan-cancer run that could be forked/stripped down to create a testing VM https://github.com/ICGC-TCGA-PanCancer/container-host-bag/tree/bcf5c074f69914ab9542ff8e2ef2607612cd05f7 (you'll probably want just the common, install-docker, java, and workflow roles for example). Docker in Docker would be complicated and with the restrictions that cwltool places on running containers, I wouldn't be surprised if there was some incompatibility. Denis Yuen Bioinformatics Software Developer Ontario Institute for Cancer Research MaRS Centre 661 University Avenue Suite 510 Toronto, Ontario, Canada M5G 0A3 Toll-free: 1-866-678-6427 Twitter: @OICR_news www.oicr.on.ca This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization. ________________________________ From: Miguel Vazquez [mikisvaz at gmail.com] Sent: September 20, 2016 10:22 AM To: Brian O'Connor Cc: Junjun Zhang; Denis Yuen; docktesters at lists.icgc.org Subject: Re: [DOCKTESTERS] Amazon account Hi all, I think there are three scripting or systematizing efforts that would help 1) Setting environment up to running the dockerstore. Junjun suggested docker inside docker, which might be a bit convoluted, but a preset virtual machine or AWS AIM would be very suitable. Brian's script would be the script that provisions such a VM, and Vagrant would be a possible way to program this if this technology plays well with VM vendors 2) Downloading the samples and preparing the Dockerstore.json files to run and produce the results in standard places 3) Downloading the released version of the files and comparing with the results of the test. This could be as simple as retrieving the list of SNVs and indels and measuring the overlaps. There is also the issue of launching the instances, issuing the jobs, monitoring completion, and possibly gathering results files for validation prior to turning them down. Point 1) is fairly easy with the documentation we have already. Point 2) is almost 25% done, we still have 3 other dockerstore workflows to setup op, and also drivers for the ICGC client and GNOS client. Point 3) might not be that hard either once the files are gathered and organized. The moving parts here that would require specific drivers I think are: - The code to provision VM images, Vagrant for instance, though it is really just running a script - The different VM technologies: AWS, Collaboratory, etc - The 4 different pipeline: Sanger, Broad, DKFZ, BWA - The 2 downloading tools: ICGC and GNOS - The several different result files: SNV, Indels, SV, etc The effort required to set all this infrastructure up might be a bit of an overkill though. On the other hand the results might be a deliverable piece of work that might have more reach than just these tests. Maybe we can discuss this on our next meeting. Best M On Tue, Sep 20, 2016 at 3:42 PM, Brian O'Connor > wrote: Hi Junjun, Great to hear this! I would recommend against trying to make this a docker in docker. It?s something to be avoided because it really causes problems running in various environments. Maybe a well commented bash script? I think the instructions are long but really we expect these workflows to run in a lot of different environments and it?s better to explain how it works so users can customize for their environment. What do you all think? Brian > On Sep 19, 2016, at 11:02 PM, Junjun Zhang > wrote: > > Good news, both Miguel and myself have Sanger pipeline running on AWS and Collab respectively. > > Here is the documentation on all steps we went through to get things set up: https://docs.google.com/document/d/1EPo2Wgh-WJz75GdykgTI1fpm89yIdoGGHAyVlJ9PbcA/edit > > As you can see there are quite some steps to go through, does it make sense to build a docker image for setting up testing environment? > > It's kind of like docker in docker, is that OK? > > Junjun > > > From: docktesters-bounces+junjun.zhang=oicr.on.ca at lists.icgc.org [docktesters-bounces+junjun.zhang=oicr.on.ca at lists.icgc.org] on behalf of Denis Yuen [Denis.Yuen at oicr.on.ca] > Sent: Monday, September 19, 2016 3:39 PM > To: Miguel Vazquez > Cc: docktesters at lists.icgc.org > Subject: Re: [DOCKTESTERS] Amazon account > > Hi, > > Quoting myself from an email since it is applicable here too > > Hi, > Sounds reasonable, the hardware requirements listed at https://github.com/ICGC-TCGA-PanCancer/CGP-Somatic-Docker#hardware-requirements match my recollection and a r3.4xlarge matches that handily in terms of RAM and CPU > > The only thing I would check would be to make sure that the working directory (where you run Dockstore) is in a large 1TB volume. The workflow should be able to overwhelm 320 GB if that's all you have, causing it to crash. > > When we were running for Pan-cancer, we sometimes used lvm to merge all ephemeral drives on an AWS instance into one larger drive. > But for testing, it would probably be simpler just to use one large EBS volume. > > Denis Yuen > Bioinformatics Software Developer > > Ontario Institute for Cancer Research > MaRS Centre > 661 University Avenue > Suite 510 > Toronto, Ontario, Canada M5G 0A3 > Toll-free: 1-866-678-6427 > Twitter: @OICR_news > www.oicr.on.ca > This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization. > From: docktesters-bounces+denis.yuen=oicr.on.ca at lists.icgc.org [docktesters-bounces+denis.yuen=oicr.on.ca at lists.icgc.org] on behalf of Miguel Vazquez [mikisvaz at gmail.com] > Sent: September 19, 2016 3:26 PM > To: Francis Ouellette > Cc: docktesters at lists.icgc.org; Zhibin > Subject: Re: [DOCKTESTERS] Amazon account > > Thanks Francis. > > BTW Brian and Junjun, I think I might not have enough disk space in the instance you got for me, gtdownload croaks: > > Error: The system *might* run out of disk space before all downloads are complete, Downloading will continue until less than 1.00 GB is available. > > and does not seem to download anything. > > I took the liberty to make a directory in /mn/, which has 95GB avai. but it does not seem to change things. Excuse my ignorance, but how big are these files? > > Miguel > > On Mon, Sep 19, 2016 at 9:22 PM, Francis Ouellette > wrote: > Hi Miguel, > > I?m CCing docktester .. I think Junjun or Brian will be best to answer this ? > I think a bit more RAM would be OK, so could do: m4.10xlarge (10 CPU and 160 GB RAM). > > Would that be good Brian? > > @bffo > > > -- > B.F. Francis Ouellette http://oicr.on.ca/person/francis-ouellette > > > >> On Sep 19, 2016, at 3:09 PM, Zhibin > wrote: >> >> Jo Miguel, >> >> I am not familiar with Sanger pipeline. You should launch instances based on the number of CPUs and memory you need. >> >> Best, >> >> Zhibin >> >> On Mon, Sep 19, 2016 at 3:05 PM, Miguel Vazquez > wrote: >> Hello again, >> >> What image will you suggest to run the Sanger pipeline? I'm not very used to AWS and I wouldn't want to burn through your credit accidentally. I was thinking of r3.4xlarge that has 16 cores, 122GB memmory and 1x320 (SSD), would that be a good choice? >> >> Best >> >> Miguel >> >> On Mon, Sep 19, 2016 at 8:42 PM, Miguel Vazquez > wrote: >> Thanks Zhibin >> Best regards >> Miguel > > > > _______________________________________________ > docktesters mailing list > docktesters at lists.icgc.org > https://lists.icgc.org/mailman/listinfo/docktesters -------------- next part -------------- An HTML attachment was scrubbed... URL: From Junjun.Zhang at oicr.on.ca Tue Sep 20 11:09:31 2016 From: Junjun.Zhang at oicr.on.ca (Junjun Zhang) Date: Tue, 20 Sep 2016 15:09:31 +0000 Subject: [DOCKTESTERS] Amazon account In-Reply-To: <27512884B2D81B41AAB7BB266248F240C099E2A3@exmb2.ad.oicr.on.ca> References: <27512884B2D81B41AAB7BB266248F240C099E23C@exmb2.ad.oicr.on.ca> <2C84FF4CF2F0A04EB7691F988A717B47CB65E809@exmb2.ad.oicr.on.ca> , , <27512884B2D81B41AAB7BB266248F240C099E2A3@exmb2.ad.oicr.on.ca> Message-ID: Thanks for sharing the thoughts and ansible code. I will just do the docker image as a learning exercise. Just want to get my hands thirty. If docker in docker is so bad at least I know first hand and understand why. Junjun On Sep 20, 2016, at 10:48 AM, Denis Yuen > wrote: Hi, An AMI/Vagrant script would make sense. I like Ansible too as well and we have some re-usable code here that was used to construct the VMs for the pan-cancer run that could be forked/stripped down to create a testing VM https://github.com/ICGC-TCGA-PanCancer/container-host-bag/tree/bcf5c074f69914ab9542ff8e2ef2607612cd05f7 (you'll probably want just the common, install-docker, java, and workflow roles for example). Docker in Docker would be complicated and with the restrictions that cwltool places on running containers, I wouldn't be surprised if there was some incompatibility. Denis Yuen Bioinformatics Software Developer Ontario Institute for Cancer Research MaRS Centre 661 University Avenue Suite 510 Toronto, Ontario, Canada M5G 0A3 Toll-free: 1-866-678-6427 Twitter: @OICR_news www.oicr.on.ca This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization. ________________________________ From: Miguel Vazquez [mikisvaz at gmail.com] Sent: September 20, 2016 10:22 AM To: Brian O'Connor Cc: Junjun Zhang; Denis Yuen; docktesters at lists.icgc.org Subject: Re: [DOCKTESTERS] Amazon account Hi all, I think there are three scripting or systematizing efforts that would help 1) Setting environment up to running the dockerstore. Junjun suggested docker inside docker, which might be a bit convoluted, but a preset virtual machine or AWS AIM would be very suitable. Brian's script would be the script that provisions such a VM, and Vagrant would be a possible way to program this if this technology plays well with VM vendors 2) Downloading the samples and preparing the Dockerstore.json files to run and produce the results in standard places 3) Downloading the released version of the files and comparing with the results of the test. This could be as simple as retrieving the list of SNVs and indels and measuring the overlaps. There is also the issue of launching the instances, issuing the jobs, monitoring completion, and possibly gathering results files for validation prior to turning them down. Point 1) is fairly easy with the documentation we have already. Point 2) is almost 25% done, we still have 3 other dockerstore workflows to setup op, and also drivers for the ICGC client and GNOS client. Point 3) might not be that hard either once the files are gathered and organized. The moving parts here that would require specific drivers I think are: - The code to provision VM images, Vagrant for instance, though it is really just running a script - The different VM technologies: AWS, Collaboratory, etc - The 4 different pipeline: Sanger, Broad, DKFZ, BWA - The 2 downloading tools: ICGC and GNOS - The several different result files: SNV, Indels, SV, etc The effort required to set all this infrastructure up might be a bit of an overkill though. On the other hand the results might be a deliverable piece of work that might have more reach than just these tests. Maybe we can discuss this on our next meeting. Best M On Tue, Sep 20, 2016 at 3:42 PM, Brian O'Connor > wrote: Hi Junjun, Great to hear this! I would recommend against trying to make this a docker in docker. It?s something to be avoided because it really causes problems running in various environments. Maybe a well commented bash script? I think the instructions are long but really we expect these workflows to run in a lot of different environments and it?s better to explain how it works so users can customize for their environment. What do you all think? Brian > On Sep 19, 2016, at 11:02 PM, Junjun Zhang > wrote: > > Good news, both Miguel and myself have Sanger pipeline running on AWS and Collab respectively. > > Here is the documentation on all steps we went through to get things set up: https://docs.google.com/document/d/1EPo2Wgh-WJz75GdykgTI1fpm89yIdoGGHAyVlJ9PbcA/edit > > As you can see there are quite some steps to go through, does it make sense to build a docker image for setting up testing environment? > > It's kind of like docker in docker, is that OK? > > Junjun > > > From: docktesters-bounces+junjun.zhang=oicr.on.ca at lists.icgc.org [docktesters-bounces+junjun.zhang=oicr.on.ca at lists.icgc.org] on behalf of Denis Yuen [Denis.Yuen at oicr.on.ca] > Sent: Monday, September 19, 2016 3:39 PM > To: Miguel Vazquez > Cc: docktesters at lists.icgc.org > Subject: Re: [DOCKTESTERS] Amazon account > > Hi, > > Quoting myself from an email since it is applicable here too > > Hi, > Sounds reasonable, the hardware requirements listed at https://github.com/ICGC-TCGA-PanCancer/CGP-Somatic-Docker#hardware-requirements match my recollection and a r3.4xlarge matches that handily in terms of RAM and CPU > > The only thing I would check would be to make sure that the working directory (where you run Dockstore) is in a large 1TB volume. The workflow should be able to overwhelm 320 GB if that's all you have, causing it to crash. > > When we were running for Pan-cancer, we sometimes used lvm to merge all ephemeral drives on an AWS instance into one larger drive. > But for testing, it would probably be simpler just to use one large EBS volume. > > Denis Yuen > Bioinformatics Software Developer > > Ontario Institute for Cancer Research > MaRS Centre > 661 University Avenue > Suite 510 > Toronto, Ontario, Canada M5G 0A3 > Toll-free: 1-866-678-6427 > Twitter: @OICR_news > www.oicr.on.ca > This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization. > From: docktesters-bounces+denis.yuen=oicr.on.ca at lists.icgc.org [docktesters-bounces+denis.yuen=oicr.on.ca at lists.icgc.org] on behalf of Miguel Vazquez [mikisvaz at gmail.com] > Sent: September 19, 2016 3:26 PM > To: Francis Ouellette > Cc: docktesters at lists.icgc.org; Zhibin > Subject: Re: [DOCKTESTERS] Amazon account > > Thanks Francis. > > BTW Brian and Junjun, I think I might not have enough disk space in the instance you got for me, gtdownload croaks: > > Error: The system *might* run out of disk space before all downloads are complete, Downloading will continue until less than 1.00 GB is available. > > and does not seem to download anything. > > I took the liberty to make a directory in /mn/, which has 95GB avai. but it does not seem to change things. Excuse my ignorance, but how big are these files? > > Miguel > > On Mon, Sep 19, 2016 at 9:22 PM, Francis Ouellette > wrote: > Hi Miguel, > > I?m CCing docktester .. I think Junjun or Brian will be best to answer this ? > I think a bit more RAM would be OK, so could do: m4.10xlarge (10 CPU and 160 GB RAM). > > Would that be good Brian? > > @bffo > > > -- > B.F. Francis Ouellette http://oicr.on.ca/person/francis-ouellette > > > >> On Sep 19, 2016, at 3:09 PM, Zhibin > wrote: >> >> Jo Miguel, >> >> I am not familiar with Sanger pipeline. You should launch instances based on the number of CPUs and memory you need. >> >> Best, >> >> Zhibin >> >> On Mon, Sep 19, 2016 at 3:05 PM, Miguel Vazquez > wrote: >> Hello again, >> >> What image will you suggest to run the Sanger pipeline? I'm not very used to AWS and I wouldn't want to burn through your credit accidentally. I was thinking of r3.4xlarge that has 16 cores, 122GB memmory and 1x320 (SSD), would that be a good choice? >> >> Best >> >> Miguel >> >> On Mon, Sep 19, 2016 at 8:42 PM, Miguel Vazquez > wrote: >> Thanks Zhibin >> Best regards >> Miguel > > > > _______________________________________________ > docktesters mailing list > docktesters at lists.icgc.org > https://lists.icgc.org/mailman/listinfo/docktesters -------------- next part -------------- An HTML attachment was scrubbed... URL: From mikisvaz at gmail.com Tue Sep 20 14:55:07 2016 From: mikisvaz at gmail.com (Miguel Vazquez) Date: Tue, 20 Sep 2016 20:55:07 +0200 Subject: [DOCKTESTERS] Amazon account In-Reply-To: References: <27512884B2D81B41AAB7BB266248F240C099E23C@exmb2.ad.oicr.on.ca> <2C84FF4CF2F0A04EB7691F988A717B47CB65E809@exmb2.ad.oicr.on.ca> <27512884B2D81B41AAB7BB266248F240C099E2A3@exmb2.ad.oicr.on.ca> Message-ID: Just a heads up, the process failed. The complete log is bellow, but I think this is the culprit: Error while running job: Error collecting output for parameter 'somatic_cnv_tar_gz': Did not find output file with glob pattern: '['*.somatic.cnv.tar.gz']' I wrote something like this in Dockerstore.json "somatic_cnv_tar_gz": { "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.cnv.tar.gz", "class": "File" } I've replace those entries with this "somatic_cnv_tar_gz": { "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/DONOR.somatic.cnv.tar.gz", "class": "File" } so that the glob work. I'm trying again. I'll update the documentation Best Miguel ------------------ Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_25.stderr ----------------------------------------------------------------------- Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_56.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_54 Job ID: 335639174 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_54.e335639174 Updated: Tue Sep 20 03:55:15 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_54.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_54.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_13 Job ID: 335639178 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_13.e335639178 Updated: Tue Sep 20 12:07:55 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_13.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_13.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_17 Job ID: 335639179 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_17.e335639179 Updated: Tue Sep 20 12:05:07 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_17.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_17.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_15 Job ID: 335639180 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_15.e335639180 ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_48 Job ID: 335639020 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_48.e335639020 Updated: Tue Sep 20 05:54:57 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_48.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_48.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_50 Job ID: 335639025 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_50.e335639025 Updated: Tue Sep 20 04:48:39 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_50.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_50.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_52 Job ID: 335639111 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_52.e335639111 Updated: Tue Sep 20 05:05:25 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_52.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_52.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_56 Job ID: 335639173 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_56.e335639173 Updated: Tue Sep 20 03:39:33 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_56.sh Command exit code: 0 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_34.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_34.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_38 Job ID: 335638783 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_38.e335638783 Updated: Tue Sep 20 06:49:18 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_38.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_38.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_42 Job ID: 335638805 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_42.e335638805 Updated: Tue Sep 20 06:07:49 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_42.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_42.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_46 Job ID: 335638826 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_46.e335638826 Updated: Tue Sep 20 05:40:42 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_46.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_46.stderr ----------------------------------------------------------------------- Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_unpackRef_NA_10.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_22 Job ID: 335638775 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_22.e335638775 Updated: Tue Sep 20 09:32:19 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_22.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_22.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_28 Job ID: 335638776 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_28.e335638776 Updated: Tue Sep 20 08:57:31 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_28.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_28.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_32 Job ID: 335638777 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_32.e335638777 Updated: Tue Sep 20 08:12:44 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_32.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_32.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_34 Job ID: 335638778 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_34.e335638778 Updated: Tue Sep 20 08:24:35 UTC 2016 Job Name: s58_unpackRef_NA_9 Job ID: 331891142 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_unpackRef_NA_9.e331891142 Updated: Tue Sep 20 00:39:16 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_unpackRef_NA_9.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_unpackRef_NA_9.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_verifyBamHomChk_control_6 Job ID: 331891143 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_verifyBamHomChk_control_6.e331891143 Updated: Tue Sep 20 00:44:52 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_verifyBamHomChk_control_6.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_verifyBamHomChk_control_6.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_basFileGenerate_control_11 Job ID: 332292910 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_basFileGenerate_control_11.e332292910 Updated: Tue Sep 20 01:20:39 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_basFileGenerate_control_11.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_basFileGenerate_control_11.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_unpackRef_NA_10 Job ID: 332292911 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_unpackRef_NA_10.e332292911 Updated: Tue Sep 20 00:44:57 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_unpackRef_NA_10.sh Command exit code: 0 Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_start_0.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_start_0.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_mark_start_1 Job ID: 331890603 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_mark_start_1.e331890603 Updated: Tue Sep 20 00:38:10 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_mark_start_1.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_mark_start_1.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_prepBam_control_3 Job ID: 331890831 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_prepBam_control_3.e331890831 Updated: Tue Sep 20 00:38:11 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_prepBam_control_3.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_prepBam_control_3.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_prepBam_tumour_2 Job ID: 331890832 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_prepBam_tumour_2.e331890832 Updated: Tue Sep 20 00:38:11 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_prepBam_tumour_2.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_prepBam_tumour_2.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_61.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_BRASS_input_99 Job ID: 379374477 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_BRASS_input_99.o379374477 Updated: Tue Sep 20 16:49:15 UTC 2016 Contents Excerpt: [V] 18 0.49745MB/s 1781.56 [V] 19 0.525041MB/s 1879.07 [V] 20 0.552722MB/s 1976.44 [V] 21 0.579942MB/s 2072.21 [V] 22 0.607543MB/s 2169.2 [V] 23 0.635118MB/s 2266.04 [V] 24264262 [V] MemUsage(size=71.1484,rss=10.9336,peak=291.977) wall clock time 02:57:24:31175299 11827.06user 310.09system 2:59:40elapsed 112%CPU (0avgtext+0avgdata 4265632maxresident)k 117507424inputs+14421104outputs (84major+234838minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_BRASS_input_99.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_merge_59 Job ID: 379374478 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.o379374478 Updated: Tue Sep 20 13:51:15 UTC 2016 Contents Excerpt: 87.14user 5.10system 1:41.25elapsed 91%CPU (0avgtext+0avgdata 66448maxresident)k 2720952inputs+4360560outputs (5major+7600minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.stdout ----------------------------------------------------------------------- % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 54.9M 100 54.9M 0 0 1016k 0 0:00:55 0:00:55 --:--:-- 1047k % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 174k 100 174k 0 0 174k 0 0:00:01 0:00:01 --:--:-- 567k [2016/09/20 16:49:15] | Output for stderr due to workflow run failure: ----------------------------------------------------------------------- Job Name: s58_start_0 Job ID: 331890362 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_start_0.e331890362 Updated: Tue Sep 20 00:38:10 UTC 2016 Contents Excerpt: File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_renameSampleFile_208.o373317274 Updated: Tue Sep 20 12:08:37 UTC 2016 Contents Excerpt: Modified command: cp /var/spool/cwl/b02b4bba-6e66-44fb-a48f-38c309aaaac5.genotype.tar.gz /var/spool/cwl/b02b4bba-6e66-44fb-a48f-38c309aaaac5.csc_0-0-0.20160920.somatic.genotype.tar.gz Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_renameSampleFile_208.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_57 Job ID: 373317275 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_57.o373317275 Updated: Tue Sep 20 13:29:27 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr23.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.23.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 4798.51user 50.73system 1:20:50elapsed 99%CPU (0avgtext+0avgdata 3115856maxresident)k 9833328inputs+56328outputs (0major+199552minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_57.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_ASCAT_allele_count_60 Job ID: 379374473 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_60.o379374473 Updated: Tue Sep 20 15:34:45 UTC 2016 Contents Excerpt: Errors from command: /opt/wtsi-cgp/bin/alleleCounter -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam -o /var/spool/cwl/0/ascat/tmpAscat/allele_count/b02b4bba-6e66-44fb-a48f-38c309aaaac5.allct -l /var/spool/cwl/reference_files/ascat/SnpLocus.tsv -m 20 5928.09user 101.55system 1:45:10elapsed 95%CPU (0avgtext+0avgdata 2345888maxresident)k 221140208inputs+43144outputs (37major+169349minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_60.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_ASCAT_allele_count_61 Job ID: 379374475 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_61.o379374475 Updated: Tue Sep 20 14:58:41 UTC 2016 Contents Excerpt: Errors from command: /opt/wtsi-cgp/bin/alleleCounter -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam -o /var/spool/cwl/0/ascat/tmpAscat/allele_count/8c0354eb-6a3e-4a98-b41c-f8add599884c.allct -l /var/spool/cwl/reference_files/ascat/SnpLocus.tsv -m 20 3864.82user 67.24system 1:09:07elapsed 94%CPU (0avgtext+0avgdata 2350544maxresident)k 157460240inputs+43120outputs (57major+167795minor)pagefaults 0swaps 11476.37user 140.61system 6:48:23elapsed 47%CPU (0avgtext+0avgdata 3035728maxresident)k 7380072inputs+56816outputs (0major+196640minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_39.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_41 Job ID: 335639489 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_41.o335639489 Updated: Tue Sep 20 07:35:04 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr15.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.15.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 9429.90user 117.09system 5:54:22elapsed 44%CPU (0avgtext+0avgdata 2739152maxresident)k 5273744inputs+51000outputs (0major+177355minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_41.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_45 Job ID: 335639845 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_45.o335639845 Updated: Tue Sep 20 07:29:41 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr17.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.17.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 9231.30user 116.04system 5:49:00elapsed 44%CPU (0avgtext+0avgdata 2540400maxresident)k 5255296inputs+46736outputs (0major+165277minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_45.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_43 Job ID: 335639853 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_43.o335639853 Updated: Tue Sep 20 08:28:45 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr16.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.16.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 11465.31user 146.48system 6:48:03elapsed 47%CPU (0avgtext+0avgdata 2945712maxresident)k 6906080inputs+54432outputs (0major+190932minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_43.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_renameSampleFile_208 Job ID: 373317274 ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_33 Job ID: 335639420 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_33.o335639420 Updated: Tue Sep 20 10:42:41 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr11.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.11.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 18904.62user 233.41system 9:02:00elapsed 58%CPU (0avgtext+0avgdata 4537600maxresident)k 15888800inputs+86400outputs (0major+292553minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_33.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_35 Job ID: 335639430 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_35.o335639430 Updated: Tue Sep 20 10:03:48 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr12.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.12.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 16584.76user 210.26system 8:23:07elapsed 55%CPU (0avgtext+0avgdata 4373600maxresident)k 12917040inputs+82896outputs (0major+281480minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_35.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_37 Job ID: 335639431 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_37.o335639431 Updated: Tue Sep 20 08:26:17 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr13.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.13.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 11361.18user 138.30system 6:45:36elapsed 47%CPU (0avgtext+0avgdata 3301008maxresident)k 7418080inputs+62192outputs (0major+212951minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_37.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_39 Job ID: 335639452 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_39.o335639452 Updated: Tue Sep 20 08:29:04 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr14.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.14.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam Updated: Tue Sep 20 11:02:29 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr7.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.7.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 20088.69user 242.69system 9:21:48elapsed 60%CPU (0avgtext+0avgdata 5281504maxresident)k 18604808inputs+96776outputs (0major+339332minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_25.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_27 Job ID: 335639400 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_27.o335639400 Updated: Tue Sep 20 11:02:53 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr8.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.8.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 20108.48user 243.42system 9:22:11elapsed 60%CPU (0avgtext+0avgdata 5228912maxresident)k 17295080inputs+95440outputs (0major+335764minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_27.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_29 Job ID: 335639401 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_29.o335639401 Updated: Tue Sep 20 09:18:32 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr9.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.9.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 13962.23user 175.03system 7:37:51elapsed 51%CPU (0avgtext+0avgdata 3971872maxresident)k 12246072inputs+72144outputs (0major+255173minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_29.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_31 Job ID: 335639417 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_31.o335639417 Updated: Tue Sep 20 10:11:08 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr10.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.10.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 17052.42user 207.86system 8:30:26elapsed 56%CPU (0avgtext+0avgdata 4504144maxresident)k 13931760inputs+85488outputs (0major+289717minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_31.stdout ----------------------------------------------------------------------- 23593416inputs+121608outputs (0major+421477minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_17.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_15 Job ID: 335639180 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_15.o335639180 Updated: Tue Sep 20 12:08:37 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr2.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.2.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 24021.20user 275.32system 10:27:56elapsed 64%CPU (0avgtext+0avgdata 7851136maxresident)k 24358016inputs+146264outputs (0major+499924minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_15.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_19 Job ID: 335639200 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_19.o335639200 Updated: Tue Sep 20 11:57:43 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr4.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.4.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 23336.68user 273.00system 10:17:02elapsed 63%CPU (0avgtext+0avgdata 6501344maxresident)k 22397816inputs+120192outputs (0major+416448minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_19.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_23 Job ID: 335639375 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_23.o335639375 Updated: Tue Sep 20 11:14:37 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr6.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.6.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 20846.11user 251.83system 9:33:55elapsed 61%CPU (0avgtext+0avgdata 5765024maxresident)k 19462064inputs+106080outputs (0major+369701minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_23.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_25 Job ID: 335639387 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_25.o335639387 ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_56 Job ID: 335639173 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_56.o335639173 Updated: Tue Sep 20 03:39:33 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr22.txt -o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.22.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam 2810.79user 34.33system 1:58:52elapsed 39%CPU (0avgtext+0avgdata 1250144maxresident)k 1243552inputs+22208outputs (0major+82726minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_56.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_54 Job ID: 335639174 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_54.o335639174 Updated: Tue Sep 20 03:55:15 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr21.txt -o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.21.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam 3187.08user 39.68system 2:14:34elapsed 39%CPU (0avgtext+0avgdata 1302656maxresident)k 1689216inputs+23256outputs (0major+86038minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_54.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_58 Job ID: 335639178 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_58.o335639178 Updated: Tue Sep 20 04:41:10 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr23.txt -o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.23.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam 4375.73user 53.14system 3:00:29elapsed 40%CPU (0avgtext+0avgdata 3123136maxresident)k 4325272inputs+56240outputs (0major+199643minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_58.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_17 Job ID: 335639179 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_17.o335639179 Updated: Tue Sep 20 12:05:07 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr3.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.3.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 23819.53user 283.10system 10:24:27elapsed 64%CPU (0avgtext+0avgdata 6576048maxresident)k Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr17.txt -o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.17.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam 5945.65user 71.96system 4:00:01elapsed 41%CPU (0avgtext+0avgdata 2544496maxresident)k 5572568inputs+46720outputs (0major+163875minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_46.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_48 Job ID: 335639020 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_48.o335639020 Updated: Tue Sep 20 05:54:57 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr18.txt -o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.18.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam 6337.11user 77.66system 4:14:16elapsed 42%CPU (0avgtext+0avgdata 2647504maxresident)k 5337616inputs+48704outputs (0major+170347minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_48.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_50 Job ID: 335639025 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_50.o335639025 Updated: Tue Sep 20 04:48:39 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr19.txt -o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.19.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam 4542.91user 55.47system 3:07:58elapsed 40%CPU (0avgtext+0avgdata 1995904maxresident)k 3514080inputs+36192outputs (0major+129470minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_50.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_52 Job ID: 335639111 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_52.o335639111 Updated: Tue Sep 20 05:05:25 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr20.txt -o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.20.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam 4979.15user 61.39system 3:24:44elapsed 41%CPU (0avgtext+0avgdata 2102832maxresident)k 3653168inputs+38272outputs (0major+136206minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_52.stdout ----------------------------------------------------------------------- -6a3e-4a98-b41c-f8add599884c.11.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam 11287.76user 142.04system 6:43:55elapsed 47%CPU (0avgtext+0avgdata 4543376maxresident)k 9747344inputs+86048outputs (0major+289230minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_34.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_38 Job ID: 335638783 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_38.o335638783 Updated: Tue Sep 20 06:49:18 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr13.txt -o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.13.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam 7981.44user 98.27system 5:08:39elapsed 43%CPU (0avgtext+0avgdata 3310512maxresident)k 6948640inputs+62176outputs (7major+211942minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_38.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_42 Job ID: 335638805 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_42.o335638805 Updated: Tue Sep 20 06:07:49 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr15.txt -o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.15.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam 6705.59user 83.09system 4:27:09elapsed 42%CPU (0avgtext+0avgdata 2746816maxresident)k 6146600inputs+50992outputs (0major+176574minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_42.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_46 Job ID: 379374477 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_cgpPindel_input_70.e379374477 Updated: Tue Sep 20 13:50:00 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_cgpPindel_input_70.sh Output from command: /usr/bin/perl /opt/wtsi-cgp/bin/pindel_input_gen.pl -b /var/lib/cwl/stg33415604-d4eb-49aa-8f81-345b6fb2a6f3/fdcb1bd7cffca69d15383ca9566c58e0.bam -o /var/spool/cwl/0/pindel/tmpPindel/8c0354eb-6a3e-4a98-b41c-f8add599884c -t 4 -e /var/spool/cwl/reference_files/brass/ucscHiDepth_0.01_mrg1000_no_exon_coreChrs.bed.gz [SeqWare Pipeline] ERROR [2016/09/20 13:50:00] | The exit value was 25 Command exit code: 1 Output from command: /usr/bin/perl /opt/wtsi-cgp/bin/pindel_input_gen.pl -b /var/lib/cwl/stg33415604-d4eb-49aa-8f81-345b6fb2a6f3/fdcb1bd7cffca69d15383ca9566c58e0.bam -o /var/spool/cwl/0/pindel/tmpPindel/8c0354eb-6a3e-4a98-b41c-f8add599884c -t 4 -e /var/spool/cwl/reference_files/brass/ucscHiDepth_0.01_mrg1000_no_exon_coreChrs.bed.gz Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_cgpPindel_input_70.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_merge_59 Job ID: 379374478 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.e379374478 Updated: Tue Sep 20 13:51:15 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.stderr ----------------------------------------------------------------------- The method 'do_run' exited abnormally so the Runner will terminate here! Return value was: 15 [WARNING] command: seqware bundle launch --dir /home/seqware/CGP-Somatic-Docker/target/Workflow_Bundle_CgpSomaticCore_0.0.0_SeqWare_1.1.1/ --engine whitestar-parallel --ini /var/spool/cwl/workflow.ini --no-metadata exited with code: 15 Error while running job: Error collecting output for parameter 'somatic_cnv_tar_gz': Did not find output file with glob pattern: '['*.somatic.cnv.tar.gz']' [job temp319312608049643386.cwl] completed permanentFail Final process status is permanentFail Workflow error, try again with --debug for more information: Process status is ['permanentFail'] stdout : java.lang.RuntimeException: problems running command: cwltool --enable-dev --non-strict --enable-net --outdir /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/outputs/ --tmpdir-prefix /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/working/ /tmp/1474331255066-0/temp319312608049643386.cwl /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/workflow_params.json ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ f f: command not found ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ df Filesystem 1K-blocks Used Available Use% Mounted on udev 62947280 12 62947268 1% /dev tmpfs 12590448 364 12590084 1% /run /dev/xvda1 8115168 6093092 1586800 80% / none 4 0 4 0% /sys/fs/cgroup none 5120 0 5120 0% /run/lock none 62952228 0 62952228 0% /run/shm none 102400 0 102400 0% /run/user /dev/xvdb 1031992064 303267080 676279800 31% /mnt/1TB ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ df -h Filesystem Size Used Avail Use% Mounted on udev 61G 12K 61G 1% /dev tmpfs 13G 364K 13G 1% /run /dev/xvda1 7.8G 5.9G 1.6G 80% / none 4.0K 0 4.0K 0% /sys/fs/cgroup none 5.0M 0 5.0M 0% /run/lock none 61G 0 61G 0% /run/shm none 100M 0 100M 0% /run/user /dev/xvdb 985G 290G 645G 31% /mnt/1TB ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ vi Dockstore.json { "bbFrom": { "bbFrom": { "path": " https://s3-eu-west-1.amazonaws.com/wtsi-pancancer/reference/GRCh37d5_battenberg.tar.gz ", "class": "File" }, "refFrom": { "path": " https://s3-eu-west-1.amazonaws.com/wtsi-pancancer/reference/GRCh37d5_CGP_refBundle.tar.gz ", "class": "File" }, "tumor": { "path": "/home/ubuntu/DockerTest-Miguel/data/7875b5196f6b8b52847f99bf370aada0.bam", "class": "File" }, "normal": { "path": "/home/ubuntu/DockerTest-Miguel/data/fdcb1bd7cffca69d15383ca9566c58e0.bam", "class": "File" }, "somatic_sv_tar_gz": { "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.sv.tar.gz", "class": "File" }, "somatic_snv_mnv_tar_gz": { "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.snv.mnv.tar.gz", "class": "File" }, "somatic_verifyBamId_tar_gz": { "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.verifyBamId.tar.gz", "class": "File" }, "somatic_cnv_tar_gz": { "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.cnv.tar.gz", "class": "File" }, "somatic_imputeCounts_tar_gz": { "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.imputeCounts.tar.gz", "class": "File" }, "somatic_genotype_tar_gz": { "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.genotype.tar.gz", "class": "File" }, "somatic_indel_tar_gz": { "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.indel.tar.gz", "class": "File" } } ~ ~ ~ ~ ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ l results/ ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ vi Dockstore.json ^C Updated: Tue Sep 20 13:51:15 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.stderr ----------------------------------------------------------------------- The method 'do_run' exited abnormally so the Runner will terminate here! Return value was: 15 [WARNING] command: seqware bundle launch --dir /home/seqware/CGP-Somatic-Docker/target/Workflow_Bundle_CgpSomaticCore_0.0.0_SeqWare_1.1.1/ --engine whitestar-parallel --ini /var/spool/cwl/workflow.ini --no-metadata exited with code: 15 Error while running job: Error collecting output for parameter 'somatic_cnv_tar_gz': Did not find output file with glob pattern: '['*.somatic.cnv.tar.gz']' [job temp319312608049643386.cwl] completed permanentFail Final process status is permanentFail Workflow error, try again with --debug for more information: Process status is ['permanentFail'] stdout : java.lang.RuntimeException: problems running command: cwltool --enable-dev --non-strict --enable-net --outdir /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/outputs/ --tmpdir-prefix /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/working/ /tmp/1474331255066-0/temp319312608049643386.cwl /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/workflow_params.json ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ f f: command not found ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ df Filesystem 1K-blocks Used Available Use% Mounted on udev 62947280 12 62947268 1% /dev tmpfs 12590448 364 12590084 1% /run /dev/xvda1 8115168 6093092 1586800 80% / none 4 0 4 0% /sys/fs/cgroup none 5120 0 5120 0% /run/lock none 62952228 0 62952228 0% /run/shm none 102400 0 102400 0% /run/user /dev/xvdb 1031992064 303267080 676279800 31% /mnt/1TB ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ df -h Filesystem Size Used Avail Use% Mounted on udev 61G 12K 61G 1% /dev tmpfs 13G 364K 13G 1% /run /dev/xvda1 7.8G 5.9G 1.6G 80% / none 4.0K 0 4.0K 0% /sys/fs/cgroup none 5.0M 0 5.0M 0% /run/lock none 61G 0 61G 0% /run/shm none 100M 0 100M 0% /run/user /dev/xvdb 985G 290G 645G 31% /mnt/1TB ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ vi Dockstore.json { Output from command: /opt/wtsi-cgp/bin/alleleCounter -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam -o /var/spool/cwl/0/ascat/tmpAscat/allele_count/b02b4bba-6e66-44fb-a48f-38c309aaaac5.allct -l /var/spool/cwl/reference_files/ascat/SnpLocus.tsv -m 20 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_60.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_ASCAT_allele_count_61 Job ID: 379374475 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_61.e379374475 Updated: Tue Sep 20 14:58:41 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_61.sh Command exit code: 0 Output from command: /opt/wtsi-cgp/bin/alleleCounter -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam -o /var/spool/cwl/0/ascat/tmpAscat/allele_count/8c0354eb-6a3e-4a98-b41c-f8add599884c.allct -l /var/spool/cwl/reference_files/ascat/SnpLocus.tsv -m 20 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_61.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_cgpPindel_input_70 Job ID: 379374477 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_cgpPindel_input_70.e379374477 Updated: Tue Sep 20 13:50:00 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_cgpPindel_input_70.sh Output from command: /usr/bin/perl /opt/wtsi-cgp/bin/pindel_input_gen.pl -b /var/lib/cwl/stg33415604-d4eb-49aa-8f81-345b6fb2a6f3/fdcb1bd7cffca69d15383ca9566c58e0.bam -o /var/spool/cwl/0/pindel/tmpPindel/8c0354eb-6a3e-4a98-b41c-f8add599884c -t 4 -e /var/spool/cwl/reference_files/brass/ucscHiDepth_0.01_mrg1000_no_exon_coreChrs.bed.gz [SeqWare Pipeline] ERROR [2016/09/20 13:50:00] | The exit value was 25 Command exit code: 1 Output from command: /usr/bin/perl /opt/wtsi-cgp/bin/pindel_input_gen.pl -b /var/lib/cwl/stg33415604-d4eb-49aa-8f81-345b6fb2a6f3/fdcb1bd7cffca69d15383ca9566c58e0.bam -o /var/spool/cwl/0/pindel/tmpPindel/8c0354eb-6a3e-4a98-b41c-f8add599884c -t 4 -e /var/spool/cwl/reference_files/brass/ucscHiDepth_0.01_mrg1000_no_exon_coreChrs.bed.gz Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_cgpPindel_input_70.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_merge_59 Job ID: 379374478 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.e379374478 Updated: Tue Sep 20 13:51:15 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.stderr ----------------------------------------------------------------------- The method 'do_run' exited abnormally so the Runner will terminate here! Return value was: 15 [WARNING] command: seqware bundle launch --dir /home/seqware/CGP-Somatic-Docker/target/Workflow_Bundle_CgpSomaticCore_0.0.0_SeqWare_1.1.1/ --engine whitestar-parallel --ini /var/spool/cwl/workflow.ini --no-metadata exited with code: 15 Error while running job: Error collecting output for parameter 'somatic_cnv_tar_gz': Did not find output file with glob pattern: '['*.somatic.cnv.tar.gz']' [job temp319312608049643386.cwl] completed permanentFail Final process status is permanentFail Workflow error, try again with --debug for more information: Process status is ['permanentFail'] stdout : java.lang.RuntimeException: problems running command: cwltool --enable-dev --non-strict --enable-net --outdir /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/outputs/ --tmpdir-prefix /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/working/ /tmp/1474331255066-0/temp319312608049643386.cwl /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/workflow_params.json -------------- next part -------------- An HTML attachment was scrubbed... URL: From Denis.Yuen at oicr.on.ca Tue Sep 20 15:11:27 2016 From: Denis.Yuen at oicr.on.ca (Denis Yuen) Date: Tue, 20 Sep 2016 19:11:27 +0000 Subject: [DOCKTESTERS] Amazon account In-Reply-To: References: <27512884B2D81B41AAB7BB266248F240C099E23C@exmb2.ad.oicr.on.ca> <2C84FF4CF2F0A04EB7691F988A717B47CB65E809@exmb2.ad.oicr.on.ca> <27512884B2D81B41AAB7BB266248F240C099E2A3@exmb2.ad.oicr.on.ca> , Message-ID: <27512884B2D81B41AAB7BB266248F240C099E397@exmb2.ad.oicr.on.ca> Hi, That's really just saying that cwltool was unable to find the output. Changing the entry will just save the output somewhere else. The real problem is probably in the section: ---- bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_cgpPindel_input_70.sh Output from command: /usr/bin/perl /opt/wtsi-cgp/bin/pindel_input_gen.pl -b /var/lib/cwl/stg33415604-d4eb-49aa-8f81-345b6fb2a6f3/fdcb1bd7cffca69d15383ca9566c58e0.bam -o /var/spool/cwl/0/pindel/tmpPindel/8c0354eb-6a3e-4a98-b41c-f8add599884c -t 4 -e /var/spool/cwl/reference_files/brass/ucscHiDepth_0.01_mrg1000_no_exon_coreChrs.bed.gz [SeqWare Pipeline] ERROR [2016/09/20 13:50:00] | The exit value was 25 Command exit code: 1 Output from command: /usr/bin/perl /opt/wtsi-cgp/bin/pindel_input_gen.pl -b /var/lib/cwl/stg33415604-d4eb-49aa-8f81-345b6fb2a6f3/fdcb1bd7cffca69d15383ca9566c58e0.bam -o /var/spool/cwl/0/pindel/tmpPindel/8c0354eb-6a3e-4a98-b41c-f8add599884c -t 4 -e /var/spool/cwl/reference_files/brass/ucscHiDepth_0.01_mrg1000_no_exon_coreChrs.bed.gz ---- That says that pindel failed, but there doesn't appear to be any more explanation as to why. Denis Yuen Bioinformatics Software Developer Ontario Institute for Cancer Research MaRS Centre 661 University Avenue Suite 510 Toronto, Ontario, Canada M5G 0A3 Toll-free: 1-866-678-6427 Twitter: @OICR_news www.oicr.on.ca This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization. ________________________________ From: Miguel Vazquez [mikisvaz at gmail.com] Sent: September 20, 2016 2:55 PM To: Junjun Zhang Cc: Denis Yuen; Brian O'Connor; docktesters at lists.icgc.org Subject: Re: [DOCKTESTERS] Amazon account Just a heads up, the process failed. The complete log is bellow, but I think this is the culprit: Error while running job: Error collecting output for parameter 'somatic_cnv_tar_gz': Did not find output file with glob pattern: '['*.somatic.cnv.tar.gz']' I wrote something like this in Dockerstore.json "somatic_cnv_tar_gz": { "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.cnv.tar.gz", "class": "File" } I've replace those entries with this "somatic_cnv_tar_gz": { "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/DONOR.somatic.cnv.tar.gz", "class": "File" } so that the glob work. I'm trying again. I'll update the documentation Best Miguel ------------------ Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_25.stderr ----------------------------------------------------------------------- Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_56.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_54 Job ID: 335639174 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_54.e335639174 Updated: Tue Sep 20 03:55:15 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_54.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_54.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_13 Job ID: 335639178 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_13.e335639178 Updated: Tue Sep 20 12:07:55 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_13.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_13.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_17 Job ID: 335639179 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_17.e335639179 Updated: Tue Sep 20 12:05:07 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_17.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_17.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_15 Job ID: 335639180 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_15.e335639180 ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_48 Job ID: 335639020 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_48.e335639020 Updated: Tue Sep 20 05:54:57 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_48.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_48.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_50 Job ID: 335639025 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_50.e335639025 Updated: Tue Sep 20 04:48:39 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_50.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_50.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_52 Job ID: 335639111 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_52.e335639111 Updated: Tue Sep 20 05:05:25 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_52.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_52.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_56 Job ID: 335639173 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_56.e335639173 Updated: Tue Sep 20 03:39:33 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_56.sh Command exit code: 0 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_34.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_34.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_38 Job ID: 335638783 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_38.e335638783 Updated: Tue Sep 20 06:49:18 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_38.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_38.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_42 Job ID: 335638805 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_42.e335638805 Updated: Tue Sep 20 06:07:49 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_42.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_42.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_46 Job ID: 335638826 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_46.e335638826 Updated: Tue Sep 20 05:40:42 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_46.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_46.stderr ----------------------------------------------------------------------- Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_unpackRef_NA_10.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_22 Job ID: 335638775 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_22.e335638775 Updated: Tue Sep 20 09:32:19 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_22.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_22.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_28 Job ID: 335638776 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_28.e335638776 Updated: Tue Sep 20 08:57:31 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_28.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_28.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_32 Job ID: 335638777 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_32.e335638777 Updated: Tue Sep 20 08:12:44 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_32.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_32.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_34 Job ID: 335638778 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_34.e335638778 Updated: Tue Sep 20 08:24:35 UTC 2016 Job Name: s58_unpackRef_NA_9 Job ID: 331891142 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_unpackRef_NA_9.e331891142 Updated: Tue Sep 20 00:39:16 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_unpackRef_NA_9.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_unpackRef_NA_9.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_verifyBamHomChk_control_6 Job ID: 331891143 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_verifyBamHomChk_control_6.e331891143 Updated: Tue Sep 20 00:44:52 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_verifyBamHomChk_control_6.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_verifyBamHomChk_control_6.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_basFileGenerate_control_11 Job ID: 332292910 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_basFileGenerate_control_11.e332292910 Updated: Tue Sep 20 01:20:39 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_basFileGenerate_control_11.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_basFileGenerate_control_11.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_unpackRef_NA_10 Job ID: 332292911 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_unpackRef_NA_10.e332292911 Updated: Tue Sep 20 00:44:57 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_unpackRef_NA_10.sh Command exit code: 0 Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_start_0.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_start_0.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_mark_start_1 Job ID: 331890603 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_mark_start_1.e331890603 Updated: Tue Sep 20 00:38:10 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_mark_start_1.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_mark_start_1.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_prepBam_control_3 Job ID: 331890831 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_prepBam_control_3.e331890831 Updated: Tue Sep 20 00:38:11 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_prepBam_control_3.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_prepBam_control_3.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_prepBam_tumour_2 Job ID: 331890832 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_prepBam_tumour_2.e331890832 Updated: Tue Sep 20 00:38:11 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_prepBam_tumour_2.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_prepBam_tumour_2.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_61.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_BRASS_input_99 Job ID: 379374477 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_BRASS_input_99.o379374477 Updated: Tue Sep 20 16:49:15 UTC 2016 Contents Excerpt: [V] 18 0.49745MB/s 1781.56 [V] 19 0.525041MB/s 1879.07 [V] 20 0.552722MB/s 1976.44 [V] 21 0.579942MB/s 2072.21 [V] 22 0.607543MB/s 2169.2 [V] 23 0.635118MB/s 2266.04 [V] 24264262 [V] MemUsage(size=71.1484,rss=10.9336,peak=291.977) wall clock time 02:57:24:31175299 11827.06user 310.09system 2:59:40elapsed 112%CPU (0avgtext+0avgdata 4265632maxresident)k 117507424inputs+14421104outputs (84major+234838minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_BRASS_input_99.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_merge_59 Job ID: 379374478 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.o379374478 Updated: Tue Sep 20 13:51:15 UTC 2016 Contents Excerpt: 87.14user 5.10system 1:41.25elapsed 91%CPU (0avgtext+0avgdata 66448maxresident)k 2720952inputs+4360560outputs (5major+7600minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.stdout ----------------------------------------------------------------------- % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 54.9M 100 54.9M 0 0 1016k 0 0:00:55 0:00:55 --:--:-- 1047k % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 174k 100 174k 0 0 174k 0 0:00:01 0:00:01 --:--:-- 567k [2016/09/20 16:49:15] | Output for stderr due to workflow run failure: ----------------------------------------------------------------------- Job Name: s58_start_0 Job ID: 331890362 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_start_0.e331890362 Updated: Tue Sep 20 00:38:10 UTC 2016 Contents Excerpt: File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_renameSampleFile_208.o373317274 Updated: Tue Sep 20 12:08:37 UTC 2016 Contents Excerpt: Modified command: cp /var/spool/cwl/b02b4bba-6e66-44fb-a48f-38c309aaaac5.genotype.tar.gz /var/spool/cwl/b02b4bba-6e66-44fb-a48f-38c309aaaac5.csc_0-0-0.20160920.somatic.genotype.tar.gz Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_renameSampleFile_208.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_57 Job ID: 373317275 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_57.o373317275 Updated: Tue Sep 20 13:29:27 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr23.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.23.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 4798.51user 50.73system 1:20:50elapsed 99%CPU (0avgtext+0avgdata 3115856maxresident)k 9833328inputs+56328outputs (0major+199552minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_57.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_ASCAT_allele_count_60 Job ID: 379374473 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_60.o379374473 Updated: Tue Sep 20 15:34:45 UTC 2016 Contents Excerpt: Errors from command: /opt/wtsi-cgp/bin/alleleCounter -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam -o /var/spool/cwl/0/ascat/tmpAscat/allele_count/b02b4bba-6e66-44fb-a48f-38c309aaaac5.allct -l /var/spool/cwl/reference_files/ascat/SnpLocus.tsv -m 20 5928.09user 101.55system 1:45:10elapsed 95%CPU (0avgtext+0avgdata 2345888maxresident)k 221140208inputs+43144outputs (37major+169349minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_60.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_ASCAT_allele_count_61 Job ID: 379374475 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_61.o379374475 Updated: Tue Sep 20 14:58:41 UTC 2016 Contents Excerpt: Errors from command: /opt/wtsi-cgp/bin/alleleCounter -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam -o /var/spool/cwl/0/ascat/tmpAscat/allele_count/8c0354eb-6a3e-4a98-b41c-f8add599884c.allct -l /var/spool/cwl/reference_files/ascat/SnpLocus.tsv -m 20 3864.82user 67.24system 1:09:07elapsed 94%CPU (0avgtext+0avgdata 2350544maxresident)k 157460240inputs+43120outputs (57major+167795minor)pagefaults 0swaps 11476.37user 140.61system 6:48:23elapsed 47%CPU (0avgtext+0avgdata 3035728maxresident)k 7380072inputs+56816outputs (0major+196640minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_39.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_41 Job ID: 335639489 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_41.o335639489 Updated: Tue Sep 20 07:35:04 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr15.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.15.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 9429.90user 117.09system 5:54:22elapsed 44%CPU (0avgtext+0avgdata 2739152maxresident)k 5273744inputs+51000outputs (0major+177355minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_41.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_45 Job ID: 335639845 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_45.o335639845 Updated: Tue Sep 20 07:29:41 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr17.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.17.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 9231.30user 116.04system 5:49:00elapsed 44%CPU (0avgtext+0avgdata 2540400maxresident)k 5255296inputs+46736outputs (0major+165277minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_45.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_43 Job ID: 335639853 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_43.o335639853 Updated: Tue Sep 20 08:28:45 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr16.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.16.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 11465.31user 146.48system 6:48:03elapsed 47%CPU (0avgtext+0avgdata 2945712maxresident)k 6906080inputs+54432outputs (0major+190932minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_43.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_renameSampleFile_208 Job ID: 373317274 ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_33 Job ID: 335639420 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_33.o335639420 Updated: Tue Sep 20 10:42:41 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr11.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.11.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 18904.62user 233.41system 9:02:00elapsed 58%CPU (0avgtext+0avgdata 4537600maxresident)k 15888800inputs+86400outputs (0major+292553minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_33.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_35 Job ID: 335639430 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_35.o335639430 Updated: Tue Sep 20 10:03:48 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr12.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.12.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 16584.76user 210.26system 8:23:07elapsed 55%CPU (0avgtext+0avgdata 4373600maxresident)k 12917040inputs+82896outputs (0major+281480minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_35.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_37 Job ID: 335639431 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_37.o335639431 Updated: Tue Sep 20 08:26:17 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr13.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.13.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 11361.18user 138.30system 6:45:36elapsed 47%CPU (0avgtext+0avgdata 3301008maxresident)k 7418080inputs+62192outputs (0major+212951minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_37.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_39 Job ID: 335639452 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_39.o335639452 Updated: Tue Sep 20 08:29:04 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr14.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.14.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam Updated: Tue Sep 20 11:02:29 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr7.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.7.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 20088.69user 242.69system 9:21:48elapsed 60%CPU (0avgtext+0avgdata 5281504maxresident)k 18604808inputs+96776outputs (0major+339332minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_25.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_27 Job ID: 335639400 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_27.o335639400 Updated: Tue Sep 20 11:02:53 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr8.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.8.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 20108.48user 243.42system 9:22:11elapsed 60%CPU (0avgtext+0avgdata 5228912maxresident)k 17295080inputs+95440outputs (0major+335764minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_27.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_29 Job ID: 335639401 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_29.o335639401 Updated: Tue Sep 20 09:18:32 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr9.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.9.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 13962.23user 175.03system 7:37:51elapsed 51%CPU (0avgtext+0avgdata 3971872maxresident)k 12246072inputs+72144outputs (0major+255173minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_29.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_31 Job ID: 335639417 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_31.o335639417 Updated: Tue Sep 20 10:11:08 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr10.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.10.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 17052.42user 207.86system 8:30:26elapsed 56%CPU (0avgtext+0avgdata 4504144maxresident)k 13931760inputs+85488outputs (0major+289717minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_31.stdout ----------------------------------------------------------------------- 23593416inputs+121608outputs (0major+421477minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_17.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_15 Job ID: 335639180 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_15.o335639180 Updated: Tue Sep 20 12:08:37 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr2.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.2.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 24021.20user 275.32system 10:27:56elapsed 64%CPU (0avgtext+0avgdata 7851136maxresident)k 24358016inputs+146264outputs (0major+499924minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_15.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_19 Job ID: 335639200 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_19.o335639200 Updated: Tue Sep 20 11:57:43 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr4.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.4.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 23336.68user 273.00system 10:17:02elapsed 63%CPU (0avgtext+0avgdata 6501344maxresident)k 22397816inputs+120192outputs (0major+416448minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_19.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_23 Job ID: 335639375 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_23.o335639375 Updated: Tue Sep 20 11:14:37 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr6.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.6.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 20846.11user 251.83system 9:33:55elapsed 61%CPU (0avgtext+0avgdata 5765024maxresident)k 19462064inputs+106080outputs (0major+369701minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_23.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_25 Job ID: 335639387 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_25.o335639387 ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_56 Job ID: 335639173 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_56.o335639173 Updated: Tue Sep 20 03:39:33 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr22.txt -o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.22.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam 2810.79user 34.33system 1:58:52elapsed 39%CPU (0avgtext+0avgdata 1250144maxresident)k 1243552inputs+22208outputs (0major+82726minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_56.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_54 Job ID: 335639174 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_54.o335639174 Updated: Tue Sep 20 03:55:15 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr21.txt -o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.21.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam 3187.08user 39.68system 2:14:34elapsed 39%CPU (0avgtext+0avgdata 1302656maxresident)k 1689216inputs+23256outputs (0major+86038minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_54.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_58 Job ID: 335639178 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_58.o335639178 Updated: Tue Sep 20 04:41:10 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr23.txt -o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.23.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam 4375.73user 53.14system 3:00:29elapsed 40%CPU (0avgtext+0avgdata 3123136maxresident)k 4325272inputs+56240outputs (0major+199643minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_58.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_17 Job ID: 335639179 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_17.o335639179 Updated: Tue Sep 20 12:05:07 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr3.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.3.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 23819.53user 283.10system 10:24:27elapsed 64%CPU (0avgtext+0avgdata 6576048maxresident)k Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr17.txt -o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.17.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam 5945.65user 71.96system 4:00:01elapsed 41%CPU (0avgtext+0avgdata 2544496maxresident)k 5572568inputs+46720outputs (0major+163875minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_46.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_48 Job ID: 335639020 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_48.o335639020 Updated: Tue Sep 20 05:54:57 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr18.txt -o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.18.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam 6337.11user 77.66system 4:14:16elapsed 42%CPU (0avgtext+0avgdata 2647504maxresident)k 5337616inputs+48704outputs (0major+170347minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_48.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_50 Job ID: 335639025 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_50.o335639025 Updated: Tue Sep 20 04:48:39 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr19.txt -o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.19.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam 4542.91user 55.47system 3:07:58elapsed 40%CPU (0avgtext+0avgdata 1995904maxresident)k 3514080inputs+36192outputs (0major+129470minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_50.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_52 Job ID: 335639111 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_52.o335639111 Updated: Tue Sep 20 05:05:25 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr20.txt -o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.20.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam 4979.15user 61.39system 3:24:44elapsed 41%CPU (0avgtext+0avgdata 2102832maxresident)k 3653168inputs+38272outputs (0major+136206minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_52.stdout ----------------------------------------------------------------------- -6a3e-4a98-b41c-f8add599884c.11.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam 11287.76user 142.04system 6:43:55elapsed 47%CPU (0avgtext+0avgdata 4543376maxresident)k 9747344inputs+86048outputs (0major+289230minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_34.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_38 Job ID: 335638783 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_38.o335638783 Updated: Tue Sep 20 06:49:18 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr13.txt -o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.13.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam 7981.44user 98.27system 5:08:39elapsed 43%CPU (0avgtext+0avgdata 3310512maxresident)k 6948640inputs+62176outputs (7major+211942minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_38.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_42 Job ID: 335638805 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_42.o335638805 Updated: Tue Sep 20 06:07:49 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr15.txt -o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.15.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam 6705.59user 83.09system 4:27:09elapsed 42%CPU (0avgtext+0avgdata 2746816maxresident)k 6146600inputs+50992outputs (0major+176574minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_42.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_46 Job ID: 379374477 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_cgpPindel_input_70.e379374477 Updated: Tue Sep 20 13:50:00 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_cgpPindel_input_70.sh Output from command: /usr/bin/perl /opt/wtsi-cgp/bin/pindel_input_gen.pl -b /var/lib/cwl/stg33415604-d4eb-49aa-8f81-345b6fb2a6f3/fdcb1bd7cffca69d15383ca9566c58e0.bam -o /var/spool/cwl/0/pindel/tmpPindel/8c0354eb-6a3e-4a98-b41c-f8add599884c -t 4 -e /var/spool/cwl/reference_files/brass/ucscHiDepth_0.01_mrg1000_no_exon_coreChrs.bed.gz [SeqWare Pipeline] ERROR [2016/09/20 13:50:00] | The exit value was 25 Command exit code: 1 Output from command: /usr/bin/perl /opt/wtsi-cgp/bin/pindel_input_gen.pl -b /var/lib/cwl/stg33415604-d4eb-49aa-8f81-345b6fb2a6f3/fdcb1bd7cffca69d15383ca9566c58e0.bam -o /var/spool/cwl/0/pindel/tmpPindel/8c0354eb-6a3e-4a98-b41c-f8add599884c -t 4 -e /var/spool/cwl/reference_files/brass/ucscHiDepth_0.01_mrg1000_no_exon_coreChrs.bed.gz Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_cgpPindel_input_70.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_merge_59 Job ID: 379374478 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.e379374478 Updated: Tue Sep 20 13:51:15 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.stderr ----------------------------------------------------------------------- The method 'do_run' exited abnormally so the Runner will terminate here! Return value was: 15 [WARNING] command: seqware bundle launch --dir /home/seqware/CGP-Somatic-Docker/target/Workflow_Bundle_CgpSomaticCore_0.0.0_SeqWare_1.1.1/ --engine whitestar-parallel --ini /var/spool/cwl/workflow.ini --no-metadata exited with code: 15 Error while running job: Error collecting output for parameter 'somatic_cnv_tar_gz': Did not find output file with glob pattern: '['*.somatic.cnv.tar.gz']' [job temp319312608049643386.cwl] completed permanentFail Final process status is permanentFail Workflow error, try again with --debug for more information: Process status is ['permanentFail'] stdout : java.lang.RuntimeException: problems running command: cwltool --enable-dev --non-strict --enable-net --outdir /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/outputs/ --tmpdir-prefix /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/working/ /tmp/1474331255066-0/temp319312608049643386.cwl /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/workflow_params.json ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ f f: command not found ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ df Filesystem 1K-blocks Used Available Use% Mounted on udev 62947280 12 62947268 1% /dev tmpfs 12590448 364 12590084 1% /run /dev/xvda1 8115168 6093092 1586800 80% / none 4 0 4 0% /sys/fs/cgroup none 5120 0 5120 0% /run/lock none 62952228 0 62952228 0% /run/shm none 102400 0 102400 0% /run/user /dev/xvdb 1031992064 303267080 676279800 31% /mnt/1TB ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ df -h Filesystem Size Used Avail Use% Mounted on udev 61G 12K 61G 1% /dev tmpfs 13G 364K 13G 1% /run /dev/xvda1 7.8G 5.9G 1.6G 80% / none 4.0K 0 4.0K 0% /sys/fs/cgroup none 5.0M 0 5.0M 0% /run/lock none 61G 0 61G 0% /run/shm none 100M 0 100M 0% /run/user /dev/xvdb 985G 290G 645G 31% /mnt/1TB ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ vi Dockstore.json { "bbFrom": { "bbFrom": { "path": "https://s3-eu-west-1.amazonaws.com/wtsi-pancancer/reference/GRCh37d5_battenberg.tar.gz", "class": "File" }, "refFrom": { "path": "https://s3-eu-west-1.amazonaws.com/wtsi-pancancer/reference/GRCh37d5_CGP_refBundle.tar.gz", "class": "File" }, "tumor": { "path": "/home/ubuntu/DockerTest-Miguel/data/7875b5196f6b8b52847f99bf370aada0.bam", "class": "File" }, "normal": { "path": "/home/ubuntu/DockerTest-Miguel/data/fdcb1bd7cffca69d15383ca9566c58e0.bam", "class": "File" }, "somatic_sv_tar_gz": { "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.sv.tar.gz", "class": "File" }, "somatic_snv_mnv_tar_gz": { "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.snv.mnv.tar.gz", "class": "File" }, "somatic_verifyBamId_tar_gz": { "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.verifyBamId.tar.gz", "class": "File" }, "somatic_cnv_tar_gz": { "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.cnv.tar.gz", "class": "File" }, "somatic_imputeCounts_tar_gz": { "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.imputeCounts.tar.gz", "class": "File" }, "somatic_genotype_tar_gz": { "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.genotype.tar.gz", "class": "File" }, "somatic_indel_tar_gz": { "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.indel.tar.gz", "class": "File" } } ~ ~ ~ ~ ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ l results/ ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ vi Dockstore.json ^C Updated: Tue Sep 20 13:51:15 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.stderr ----------------------------------------------------------------------- The method 'do_run' exited abnormally so the Runner will terminate here! Return value was: 15 [WARNING] command: seqware bundle launch --dir /home/seqware/CGP-Somatic-Docker/target/Workflow_Bundle_CgpSomaticCore_0.0.0_SeqWare_1.1.1/ --engine whitestar-parallel --ini /var/spool/cwl/workflow.ini --no-metadata exited with code: 15 Error while running job: Error collecting output for parameter 'somatic_cnv_tar_gz': Did not find output file with glob pattern: '['*.somatic.cnv.tar.gz']' [job temp319312608049643386.cwl] completed permanentFail Final process status is permanentFail Workflow error, try again with --debug for more information: Process status is ['permanentFail'] stdout : java.lang.RuntimeException: problems running command: cwltool --enable-dev --non-strict --enable-net --outdir /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/outputs/ --tmpdir-prefix /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/working/ /tmp/1474331255066-0/temp319312608049643386.cwl /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/workflow_params.json ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ f f: command not found ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ df Filesystem 1K-blocks Used Available Use% Mounted on udev 62947280 12 62947268 1% /dev tmpfs 12590448 364 12590084 1% /run /dev/xvda1 8115168 6093092 1586800 80% / none 4 0 4 0% /sys/fs/cgroup none 5120 0 5120 0% /run/lock none 62952228 0 62952228 0% /run/shm none 102400 0 102400 0% /run/user /dev/xvdb 1031992064 303267080 676279800 31% /mnt/1TB ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ df -h Filesystem Size Used Avail Use% Mounted on udev 61G 12K 61G 1% /dev tmpfs 13G 364K 13G 1% /run /dev/xvda1 7.8G 5.9G 1.6G 80% / none 4.0K 0 4.0K 0% /sys/fs/cgroup none 5.0M 0 5.0M 0% /run/lock none 61G 0 61G 0% /run/shm none 100M 0 100M 0% /run/user /dev/xvdb 985G 290G 645G 31% /mnt/1TB ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ vi Dockstore.json { Output from command: /opt/wtsi-cgp/bin/alleleCounter -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam -o /var/spool/cwl/0/ascat/tmpAscat/allele_count/b02b4bba-6e66-44fb-a48f-38c309aaaac5.allct -l /var/spool/cwl/reference_files/ascat/SnpLocus.tsv -m 20 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_60.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_ASCAT_allele_count_61 Job ID: 379374475 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_61.e379374475 Updated: Tue Sep 20 14:58:41 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_61.sh Command exit code: 0 Output from command: /opt/wtsi-cgp/bin/alleleCounter -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam -o /var/spool/cwl/0/ascat/tmpAscat/allele_count/8c0354eb-6a3e-4a98-b41c-f8add599884c.allct -l /var/spool/cwl/reference_files/ascat/SnpLocus.tsv -m 20 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_61.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_cgpPindel_input_70 Job ID: 379374477 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_cgpPindel_input_70.e379374477 Updated: Tue Sep 20 13:50:00 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_cgpPindel_input_70.sh Output from command: /usr/bin/perl /opt/wtsi-cgp/bin/pindel_input_gen.pl -b /var/lib/cwl/stg33415604-d4eb-49aa-8f81-345b6fb2a6f3/fdcb1bd7cffca69d15383ca9566c58e0.bam -o /var/spool/cwl/0/pindel/tmpPindel/8c0354eb-6a3e-4a98-b41c-f8add599884c -t 4 -e /var/spool/cwl/reference_files/brass/ucscHiDepth_0.01_mrg1000_no_exon_coreChrs.bed.gz [SeqWare Pipeline] ERROR [2016/09/20 13:50:00] | The exit value was 25 Command exit code: 1 Output from command: /usr/bin/perl /opt/wtsi-cgp/bin/pindel_input_gen.pl -b /var/lib/cwl/stg33415604-d4eb-49aa-8f81-345b6fb2a6f3/fdcb1bd7cffca69d15383ca9566c58e0.bam -o /var/spool/cwl/0/pindel/tmpPindel/8c0354eb-6a3e-4a98-b41c-f8add599884c -t 4 -e /var/spool/cwl/reference_files/brass/ucscHiDepth_0.01_mrg1000_no_exon_coreChrs.bed.gz Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_cgpPindel_input_70.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_merge_59 Job ID: 379374478 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.e379374478 Updated: Tue Sep 20 13:51:15 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.stderr ----------------------------------------------------------------------- The method 'do_run' exited abnormally so the Runner will terminate here! Return value was: 15 [WARNING] command: seqware bundle launch --dir /home/seqware/CGP-Somatic-Docker/target/Workflow_Bundle_CgpSomaticCore_0.0.0_SeqWare_1.1.1/ --engine whitestar-parallel --ini /var/spool/cwl/workflow.ini --no-metadata exited with code: 15 Error while running job: Error collecting output for parameter 'somatic_cnv_tar_gz': Did not find output file with glob pattern: '['*.somatic.cnv.tar.gz']' [job temp319312608049643386.cwl] completed permanentFail Final process status is permanentFail Workflow error, try again with --debug for more information: Process status is ['permanentFail'] stdout : java.lang.RuntimeException: problems running command: cwltool --enable-dev --non-strict --enable-net --outdir /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/outputs/ --tmpdir-prefix /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/working/ /tmp/1474331255066-0/temp319312608049643386.cwl /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/workflow_params.json -------------- next part -------------- An HTML attachment was scrubbed... URL: From mikisvaz at gmail.com Tue Sep 20 15:15:28 2016 From: mikisvaz at gmail.com (Miguel Vazquez) Date: Tue, 20 Sep 2016 21:15:28 +0200 Subject: [DOCKTESTERS] Amazon account In-Reply-To: <27512884B2D81B41AAB7BB266248F240C099E397@exmb2.ad.oicr.on.ca> References: <27512884B2D81B41AAB7BB266248F240C099E23C@exmb2.ad.oicr.on.ca> <2C84FF4CF2F0A04EB7691F988A717B47CB65E809@exmb2.ad.oicr.on.ca> <27512884B2D81B41AAB7BB266248F240C099E2A3@exmb2.ad.oicr.on.ca> <27512884B2D81B41AAB7BB266248F240C099E397@exmb2.ad.oicr.on.ca> Message-ID: Well, that's a bummer. Any ideas? On Sep 20, 2016 9:11 PM, "Denis Yuen" wrote: > Hi, > That's really just saying that cwltool was unable to find the output. > Changing the entry will just save the output somewhere else. > > The real problem is probably in the section: > ---- > bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_cgpPindel_input_70.sh > > Output from command: /usr/bin/perl /opt/wtsi-cgp/bin/pindel_input_gen.pl > > -b /var/lib/cwl/stg33415604-d4eb-49aa-8f81-345b6fb2a6f3/ > fdcb1bd7cffca69d15383ca9566c58e0.bam -o /var/spool/cwl/0/pindel/ > tmpPindel/8c0354eb-6a3e-4a98-b41c-f8add599884c -t 4 -e > /var/spool/cwl/reference_files/brass/ucscHiDepth_0.01_ > mrg1000_no_exon_coreChrs.bed.gz > > [SeqWare Pipeline] ERROR [2016/09/20 13:50:00] | The exit value was 25 > Command exit code: 1 > > Output from command: /usr/bin/perl /opt/wtsi-cgp/bin/pindel_input_gen.pl > > -b /var/lib/cwl/stg33415604-d4eb-49aa-8f81-345b6fb2a6f3/ > fdcb1bd7cffca69d15383ca9566c58e0.bam -o /var/spool/cwl/0/pindel/ > tmpPindel/8c0354eb-6a3e-4a98-b41c-f8add599884c -t 4 -e > /var/spool/cwl/reference_files/brass/ucscHiDepth_0.01_ > mrg1000_no_exon_coreChrs.bed.gz > ---- > > That says that pindel failed, but there doesn't appear to be any more > explanation as to why. > > > *Denis Yuen* > Bioinformatics Software Developer > > > *Ontario* *Institute* *for* *Cancer* *Research* > MaRS Centre > 661 University Avenue > Suite 510 > Toronto, Ontario, Canada M5G 0A3 > > Toll-free: 1-866-678-6427 > Twitter: @OICR_news > *www.oicr.on.ca * > > This message and any attachments may contain confidential and/or > privileged information for the sole use of the intended recipient. Any > review or distribution by anyone other than the person for whom it was > originally intended is strictly prohibited. If you have received this > message in error, please contact the sender and delete all copies. > Opinions, conclusions or other information contained in this message may > not be that of the organization. > ------------------------------ > *From:* Miguel Vazquez [mikisvaz at gmail.com] > *Sent:* September 20, 2016 2:55 PM > *To:* Junjun Zhang > *Cc:* Denis Yuen; Brian O'Connor; docktesters at lists.icgc.org > *Subject:* Re: [DOCKTESTERS] Amazon account > > Just a heads up, the process failed. > > The complete log is bellow, but I think this is the culprit: > > Error while running job: Error collecting output for parameter > 'somatic_cnv_tar_gz': Did not find output file with glob pattern: > '['*.somatic.cnv.tar.gz']' > > I wrote something like this in Dockerstore.json > > "somatic_cnv_tar_gz": { > "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic. > cnv.tar.gz", > "class": "File" > } > > I've replace those entries with this > > "somatic_cnv_tar_gz": { > "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/DONOR. > somatic.cnv.tar.gz", > "class": "File" > } > > so that the glob work. I'm trying again. I'll update the documentation > > Best > > Miguel > > > > > > ------------------ > > > > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_tumour_25.stderr > ----------------------------------------------------------------------- > > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_control_56.stderr > ----------------------------------------------------------------------- > > ----------------------------------------------------------------------- > Job Name: s58_bbAllele_control_54 > Job ID: 335639174 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_control_54.e335639174 > Updated: Tue Sep 20 03:55:15 UTC 2016 > Contents Excerpt: > Command run: > bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_control_54.sh > Command exit code: 0 > > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_control_54.stderr > ----------------------------------------------------------------------- > > ----------------------------------------------------------------------- > Job Name: s58_bbAllele_tumour_13 > Job ID: 335639178 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_tumour_13.e335639178 > Updated: Tue Sep 20 12:07:55 UTC 2016 > Contents Excerpt: > Command run: > bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_tumour_13.sh > Command exit code: 0 > > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_tumour_13.stderr > ----------------------------------------------------------------------- > > ----------------------------------------------------------------------- > Job Name: s58_bbAllele_tumour_17 > Job ID: 335639179 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_tumour_17.e335639179 > Updated: Tue Sep 20 12:05:07 UTC 2016 > Contents Excerpt: > Command run: > bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_tumour_17.sh > Command exit code: 0 > > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_tumour_17.stderr > ----------------------------------------------------------------------- > > ----------------------------------------------------------------------- > Job Name: s58_bbAllele_tumour_15 > Job ID: 335639180 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_tumour_15.e335639180 > ----------------------------------------------------------------------- > Job Name: s58_bbAllele_control_48 > Job ID: 335639020 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_control_48.e335639020 > Updated: Tue Sep 20 05:54:57 UTC 2016 > Contents Excerpt: > Command run: > bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_control_48.sh > Command exit code: 0 > > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_control_48.stderr > ----------------------------------------------------------------------- > > ----------------------------------------------------------------------- > Job Name: s58_bbAllele_control_50 > Job ID: 335639025 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_control_50.e335639025 > Updated: Tue Sep 20 04:48:39 UTC 2016 > Contents Excerpt: > Command run: > bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_control_50.sh > Command exit code: 0 > > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_control_50.stderr > ----------------------------------------------------------------------- > > ----------------------------------------------------------------------- > Job Name: s58_bbAllele_control_52 > Job ID: 335639111 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_control_52.e335639111 > Updated: Tue Sep 20 05:05:25 UTC 2016 > Contents Excerpt: > Command run: > bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_control_52.sh > Command exit code: 0 > > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_control_52.stderr > ----------------------------------------------------------------------- > > ----------------------------------------------------------------------- > Job Name: s58_bbAllele_control_56 > Job ID: 335639173 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_control_56.e335639173 > Updated: Tue Sep 20 03:39:33 UTC 2016 > Contents Excerpt: > Command run: > bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_control_56.sh > Command exit code: 0 > Contents Excerpt: > Command run: > bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_control_34.sh > Command exit code: 0 > > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_control_34.stderr > ----------------------------------------------------------------------- > > ----------------------------------------------------------------------- > Job Name: s58_bbAllele_control_38 > Job ID: 335638783 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_control_38.e335638783 > Updated: Tue Sep 20 06:49:18 UTC 2016 > Contents Excerpt: > Command run: > bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_control_38.sh > Command exit code: 0 > > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_control_38.stderr > ----------------------------------------------------------------------- > > ----------------------------------------------------------------------- > Job Name: s58_bbAllele_control_42 > Job ID: 335638805 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_control_42.e335638805 > Updated: Tue Sep 20 06:07:49 UTC 2016 > Contents Excerpt: > Command run: > bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_control_42.sh > Command exit code: 0 > > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_control_42.stderr > ----------------------------------------------------------------------- > > ----------------------------------------------------------------------- > Job Name: s58_bbAllele_control_46 > Job ID: 335638826 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_control_46.e335638826 > Updated: Tue Sep 20 05:40:42 UTC 2016 > Contents Excerpt: > Command run: > bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_control_46.sh > Command exit code: 0 > > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_control_46.stderr > ----------------------------------------------------------------------- > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_unpackRef_NA_10.stderr > ----------------------------------------------------------------------- > > ----------------------------------------------------------------------- > Job Name: s58_bbAllele_control_22 > Job ID: 335638775 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_control_22.e335638775 > Updated: Tue Sep 20 09:32:19 UTC 2016 > Contents Excerpt: > Command run: > bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_control_22.sh > Command exit code: 0 > > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_control_22.stderr > ----------------------------------------------------------------------- > > ----------------------------------------------------------------------- > Job Name: s58_bbAllele_control_28 > Job ID: 335638776 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_control_28.e335638776 > Updated: Tue Sep 20 08:57:31 UTC 2016 > Contents Excerpt: > Command run: > bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_control_28.sh > Command exit code: 0 > > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_control_28.stderr > ----------------------------------------------------------------------- > > ----------------------------------------------------------------------- > Job Name: s58_bbAllele_control_32 > Job ID: 335638777 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_control_32.e335638777 > Updated: Tue Sep 20 08:12:44 UTC 2016 > Contents Excerpt: > Command run: > bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_control_32.sh > Command exit code: 0 > > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_control_32.stderr > ----------------------------------------------------------------------- > > ----------------------------------------------------------------------- > Job Name: s58_bbAllele_control_34 > Job ID: 335638778 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_control_34.e335638778 > Updated: Tue Sep 20 08:24:35 UTC 2016 > Job Name: s58_unpackRef_NA_9 > Job ID: 331891142 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_unpackRef_NA_9.e331891142 > Updated: Tue Sep 20 00:39:16 UTC 2016 > Contents Excerpt: > Command run: > bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_unpackRef_NA_9.sh > Command exit code: 0 > > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_unpackRef_NA_9.stderr > ----------------------------------------------------------------------- > > ----------------------------------------------------------------------- > Job Name: s58_verifyBamHomChk_control_6 > Job ID: 331891143 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_verifyBamHomChk_control_6.e331891143 > Updated: Tue Sep 20 00:44:52 UTC 2016 > Contents Excerpt: > Command run: > bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_verifyBamHomChk_control_6.sh > Command exit code: 0 > > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_verifyBamHomChk_control_6.stderr > ----------------------------------------------------------------------- > > ----------------------------------------------------------------------- > Job Name: s58_basFileGenerate_control_11 > Job ID: 332292910 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_basFileGenerate_control_11.e332292910 > Updated: Tue Sep 20 01:20:39 UTC 2016 > Contents Excerpt: > Command run: > bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_basFileGenerate_control_11.sh > Command exit code: 0 > > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_basFileGenerate_control_11.stderr > ----------------------------------------------------------------------- > > ----------------------------------------------------------------------- > Job Name: s58_unpackRef_NA_10 > Job ID: 332292911 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_unpackRef_NA_10.e332292911 > Updated: Tue Sep 20 00:44:57 UTC 2016 > Contents Excerpt: > Command run: > bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_unpackRef_NA_10.sh > Command exit code: 0 > Command run: > bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_start_0.sh > Command exit code: 0 > > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_start_0.stderr > ----------------------------------------------------------------------- > > ----------------------------------------------------------------------- > Job Name: s58_mark_start_1 > Job ID: 331890603 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_mark_start_1.e331890603 > Updated: Tue Sep 20 00:38:10 UTC 2016 > Contents Excerpt: > Command run: > bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_mark_start_1.sh > Command exit code: 0 > > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_mark_start_1.stderr > ----------------------------------------------------------------------- > > ----------------------------------------------------------------------- > Job Name: s58_prepBam_control_3 > Job ID: 331890831 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_prepBam_control_3.e331890831 > Updated: Tue Sep 20 00:38:11 UTC 2016 > Contents Excerpt: > Command run: > bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_prepBam_control_3.sh > Command exit code: 0 > > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_prepBam_control_3.stderr > ----------------------------------------------------------------------- > > ----------------------------------------------------------------------- > Job Name: s58_prepBam_tumour_2 > Job ID: 331890832 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_prepBam_tumour_2.e331890832 > Updated: Tue Sep 20 00:38:11 UTC 2016 > Contents Excerpt: > Command run: > bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_prepBam_tumour_2.sh > Command exit code: 0 > > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_prepBam_tumour_2.stderr > ----------------------------------------------------------------------- > > ----------------------------------------------------------------------- > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_ASCAT_allele_count_61.stdout > ----------------------------------------------------------------------- > > ----------------------------------------------------------------------- > Job Name: s58_BRASS_input_99 > Job ID: 379374477 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_BRASS_input_99.o379374477 > Updated: Tue Sep 20 16:49:15 UTC 2016 > Contents Excerpt: > [V] 18 0.49745MB/s 1781.56 > [V] 19 0.525041MB/s 1879.07 > [V] 20 0.552722MB/s 1976.44 > [V] 21 0.579942MB/s 2072.21 > [V] 22 0.607543MB/s 2169.2 > [V] 23 0.635118MB/s 2266.04 > [V] 24264262 > [V] MemUsage(size=71.1484,rss=10.9336,peak=291.977) wall clock time > 02:57:24:31175299 > 11827.06user 310.09system 2:59:40elapsed 112%CPU (0avgtext+0avgdata > 4265632maxresident)k > 117507424inputs+14421104outputs (84major+234838minor)pagefaults 0swaps > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_BRASS_input_99.stdout > ----------------------------------------------------------------------- > > ----------------------------------------------------------------------- > Job Name: s58_bbAllele_merge_59 > Job ID: 379374478 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_merge_59.o379374478 > Updated: Tue Sep 20 13:51:15 UTC 2016 > Contents Excerpt: > 87.14user 5.10system 1:41.25elapsed 91%CPU (0avgtext+0avgdata > 66448maxresident)k > 2720952inputs+4360560outputs (5major+7600minor)pagefaults 0swaps > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_merge_59.stdout > ----------------------------------------------------------------------- > > > % Total % Received % Xferd Average Speed Time Time Time > Current > Dload Upload Total Spent Left > Speed > 0 0 0 0 0 0 0 0 --:--:-- --:--:-- > --:--:-- 0 > 100 54.9M 100 54.9M 0 0 1016k 0 0:00:55 0:00:55 --:--:-- > 1047k > % Total % Received % Xferd Average Speed Time Time Time > Current > Dload Upload Total Spent Left > Speed > 0 0 0 0 0 0 0 0 --:--:-- --:--:-- > --:--:-- 0 > 100 174k 100 174k 0 0 174k 0 0:00:01 0:00:01 --:--:-- > 567k > [2016/09/20 16:49:15] | Output for stderr due to workflow run failure: > ----------------------------------------------------------------------- > Job Name: s58_start_0 > Job ID: 331890362 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_start_0.e331890362 > Updated: Tue Sep 20 00:38:10 UTC 2016 > Contents Excerpt: > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_renameSampleFile_208.o373317274 > Updated: Tue Sep 20 12:08:37 UTC 2016 > Contents Excerpt: > Modified command: cp /var/spool/cwl/b02b4bba-6e66-44fb-a48f-38c309aaaac5.genotype.tar.gz > /var/spool/cwl/b02b4bba-6e66-44fb-a48f-38c309aaaac5.csc_0- > 0-0.20160920.somatic.genotype.tar.gz > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_renameSampleFile_208.stdout > ----------------------------------------------------------------------- > > ----------------------------------------------------------------------- > Job Name: s58_bbAllele_tumour_57 > Job ID: 373317275 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_tumour_57.o373317275 > Updated: Tue Sep 20 13:29:27 UTC 2016 > Contents Excerpt: > Modified command: alleleCounter -l /var/spool/cwl/reference_ > files/battenberg/1000genomesloci/1000genomesloci2012_chr23.txt -o > /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.23.tsv -b > /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam > 4798.51user 50.73system 1:20:50elapsed 99%CPU (0avgtext+0avgdata > 3115856maxresident)k > 9833328inputs+56328outputs (0major+199552minor)pagefaults 0swaps > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_tumour_57.stdout > ----------------------------------------------------------------------- > > ----------------------------------------------------------------------- > Job Name: s58_ASCAT_allele_count_60 > Job ID: 379374473 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_ASCAT_allele_count_60.o379374473 > Updated: Tue Sep 20 15:34:45 UTC 2016 > Contents Excerpt: > > Errors from command: /opt/wtsi-cgp/bin/alleleCounter -b /var/spool/cwl/ > 7875b5196f6b8b52847f99bf370aada0.bam -o /var/spool/cwl/0/ascat/ > tmpAscat/allele_count/b02b4bba-6e66-44fb-a48f-38c309aaaac5.allct -l > /var/spool/cwl/reference_files/ascat/SnpLocus.tsv -m 20 > > 5928.09user 101.55system 1:45:10elapsed 95%CPU (0avgtext+0avgdata > 2345888maxresident)k > 221140208inputs+43144outputs (37major+169349minor)pagefaults 0swaps > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_ASCAT_allele_count_60.stdout > ----------------------------------------------------------------------- > > ----------------------------------------------------------------------- > Job Name: s58_ASCAT_allele_count_61 > Job ID: 379374475 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_ASCAT_allele_count_61.o379374475 > Updated: Tue Sep 20 14:58:41 UTC 2016 > Contents Excerpt: > > Errors from command: /opt/wtsi-cgp/bin/alleleCounter -b /var/spool/cwl/ > fdcb1bd7cffca69d15383ca9566c58e0.bam -o /var/spool/cwl/0/ascat/ > tmpAscat/allele_count/8c0354eb-6a3e-4a98-b41c-f8add599884c.allct -l > /var/spool/cwl/reference_files/ascat/SnpLocus.tsv -m 20 > > 3864.82user 67.24system 1:09:07elapsed 94%CPU (0avgtext+0avgdata > 2350544maxresident)k > 157460240inputs+43120outputs (57major+167795minor)pagefaults 0swaps > 11476.37user 140.61system 6:48:23elapsed 47%CPU (0avgtext+0avgdata > 3035728maxresident)k > 7380072inputs+56816outputs (0major+196640minor)pagefaults 0swaps > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_tumour_39.stdout > ----------------------------------------------------------------------- > > ----------------------------------------------------------------------- > Job Name: s58_bbAllele_tumour_41 > Job ID: 335639489 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_tumour_41.o335639489 > Updated: Tue Sep 20 07:35:04 UTC 2016 > Contents Excerpt: > Modified command: alleleCounter -l /var/spool/cwl/reference_ > files/battenberg/1000genomesloci/1000genomesloci2012_chr15.txt -o > /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.15.tsv -b > /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam > 9429.90user 117.09system 5:54:22elapsed 44%CPU (0avgtext+0avgdata > 2739152maxresident)k > 5273744inputs+51000outputs (0major+177355minor)pagefaults 0swaps > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_tumour_41.stdout > ----------------------------------------------------------------------- > > ----------------------------------------------------------------------- > Job Name: s58_bbAllele_tumour_45 > Job ID: 335639845 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_tumour_45.o335639845 > Updated: Tue Sep 20 07:29:41 UTC 2016 > Contents Excerpt: > Modified command: alleleCounter -l /var/spool/cwl/reference_ > files/battenberg/1000genomesloci/1000genomesloci2012_chr17.txt -o > /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.17.tsv -b > /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam > 9231.30user 116.04system 5:49:00elapsed 44%CPU (0avgtext+0avgdata > 2540400maxresident)k > 5255296inputs+46736outputs (0major+165277minor)pagefaults 0swaps > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_tumour_45.stdout > ----------------------------------------------------------------------- > > ----------------------------------------------------------------------- > Job Name: s58_bbAllele_tumour_43 > Job ID: 335639853 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_tumour_43.o335639853 > Updated: Tue Sep 20 08:28:45 UTC 2016 > Contents Excerpt: > Modified command: alleleCounter -l /var/spool/cwl/reference_ > files/battenberg/1000genomesloci/1000genomesloci2012_chr16.txt -o > /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.16.tsv -b > /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam > 11465.31user 146.48system 6:48:03elapsed 47%CPU (0avgtext+0avgdata > 2945712maxresident)k > 6906080inputs+54432outputs (0major+190932minor)pagefaults 0swaps > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_tumour_43.stdout > ----------------------------------------------------------------------- > > ----------------------------------------------------------------------- > Job Name: s58_renameSampleFile_208 > Job ID: 373317274 > > ----------------------------------------------------------------------- > Job Name: s58_bbAllele_tumour_33 > Job ID: 335639420 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_tumour_33.o335639420 > Updated: Tue Sep 20 10:42:41 UTC 2016 > Contents Excerpt: > Modified command: alleleCounter -l /var/spool/cwl/reference_ > files/battenberg/1000genomesloci/1000genomesloci2012_chr11.txt -o > /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.11.tsv -b > /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam > 18904.62user 233.41system 9:02:00elapsed 58%CPU (0avgtext+0avgdata > 4537600maxresident)k > 15888800inputs+86400outputs (0major+292553minor)pagefaults 0swaps > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_tumour_33.stdout > ----------------------------------------------------------------------- > > ----------------------------------------------------------------------- > Job Name: s58_bbAllele_tumour_35 > Job ID: 335639430 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_tumour_35.o335639430 > Updated: Tue Sep 20 10:03:48 UTC 2016 > Contents Excerpt: > Modified command: alleleCounter -l /var/spool/cwl/reference_ > files/battenberg/1000genomesloci/1000genomesloci2012_chr12.txt -o > /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.12.tsv -b > /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam > 16584.76user 210.26system 8:23:07elapsed 55%CPU (0avgtext+0avgdata > 4373600maxresident)k > 12917040inputs+82896outputs (0major+281480minor)pagefaults 0swaps > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_tumour_35.stdout > ----------------------------------------------------------------------- > > ----------------------------------------------------------------------- > Job Name: s58_bbAllele_tumour_37 > Job ID: 335639431 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_tumour_37.o335639431 > Updated: Tue Sep 20 08:26:17 UTC 2016 > Contents Excerpt: > Modified command: alleleCounter -l /var/spool/cwl/reference_ > files/battenberg/1000genomesloci/1000genomesloci2012_chr13.txt -o > /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.13.tsv -b > /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam > 11361.18user 138.30system 6:45:36elapsed 47%CPU (0avgtext+0avgdata > 3301008maxresident)k > 7418080inputs+62192outputs (0major+212951minor)pagefaults 0swaps > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_tumour_37.stdout > ----------------------------------------------------------------------- > > ----------------------------------------------------------------------- > Job Name: s58_bbAllele_tumour_39 > Job ID: 335639452 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_tumour_39.o335639452 > Updated: Tue Sep 20 08:29:04 UTC 2016 > Contents Excerpt: > Modified command: alleleCounter -l /var/spool/cwl/reference_ > files/battenberg/1000genomesloci/1000genomesloci2012_chr14.txt -o > /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.14.tsv -b > /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam > Updated: Tue Sep 20 11:02:29 UTC 2016 > Contents Excerpt: > Modified command: alleleCounter -l /var/spool/cwl/reference_ > files/battenberg/1000genomesloci/1000genomesloci2012_chr7.txt -o > /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.7.tsv -b > /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam > 20088.69user 242.69system 9:21:48elapsed 60%CPU (0avgtext+0avgdata > 5281504maxresident)k > 18604808inputs+96776outputs (0major+339332minor)pagefaults 0swaps > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_tumour_25.stdout > ----------------------------------------------------------------------- > > ----------------------------------------------------------------------- > Job Name: s58_bbAllele_tumour_27 > Job ID: 335639400 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_tumour_27.o335639400 > Updated: Tue Sep 20 11:02:53 UTC 2016 > Contents Excerpt: > Modified command: alleleCounter -l /var/spool/cwl/reference_ > files/battenberg/1000genomesloci/1000genomesloci2012_chr8.txt -o > /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.8.tsv -b > /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam > 20108.48user 243.42system 9:22:11elapsed 60%CPU (0avgtext+0avgdata > 5228912maxresident)k > 17295080inputs+95440outputs (0major+335764minor)pagefaults 0swaps > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_tumour_27.stdout > ----------------------------------------------------------------------- > > ----------------------------------------------------------------------- > Job Name: s58_bbAllele_tumour_29 > Job ID: 335639401 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_tumour_29.o335639401 > Updated: Tue Sep 20 09:18:32 UTC 2016 > Contents Excerpt: > Modified command: alleleCounter -l /var/spool/cwl/reference_ > files/battenberg/1000genomesloci/1000genomesloci2012_chr9.txt -o > /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.9.tsv -b > /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam > 13962.23user 175.03system 7:37:51elapsed 51%CPU (0avgtext+0avgdata > 3971872maxresident)k > 12246072inputs+72144outputs (0major+255173minor)pagefaults 0swaps > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_tumour_29.stdout > ----------------------------------------------------------------------- > > ----------------------------------------------------------------------- > Job Name: s58_bbAllele_tumour_31 > Job ID: 335639417 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_tumour_31.o335639417 > Updated: Tue Sep 20 10:11:08 UTC 2016 > Contents Excerpt: > Modified command: alleleCounter -l /var/spool/cwl/reference_ > files/battenberg/1000genomesloci/1000genomesloci2012_chr10.txt -o > /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.10.tsv -b > /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam > 17052.42user 207.86system 8:30:26elapsed 56%CPU (0avgtext+0avgdata > 4504144maxresident)k > 13931760inputs+85488outputs (0major+289717minor)pagefaults 0swaps > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_tumour_31.stdout > ----------------------------------------------------------------------- > 23593416inputs+121608outputs (0major+421477minor)pagefaults 0swaps > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_tumour_17.stdout > ----------------------------------------------------------------------- > > ----------------------------------------------------------------------- > Job Name: s58_bbAllele_tumour_15 > Job ID: 335639180 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_tumour_15.o335639180 > Updated: Tue Sep 20 12:08:37 UTC 2016 > Contents Excerpt: > Modified command: alleleCounter -l /var/spool/cwl/reference_ > files/battenberg/1000genomesloci/1000genomesloci2012_chr2.txt -o > /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.2.tsv -b > /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam > 24021.20user 275.32system 10:27:56elapsed 64%CPU (0avgtext+0avgdata > 7851136maxresident)k > 24358016inputs+146264outputs (0major+499924minor)pagefaults 0swaps > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_tumour_15.stdout > ----------------------------------------------------------------------- > > ----------------------------------------------------------------------- > Job Name: s58_bbAllele_tumour_19 > Job ID: 335639200 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_tumour_19.o335639200 > Updated: Tue Sep 20 11:57:43 UTC 2016 > Contents Excerpt: > Modified command: alleleCounter -l /var/spool/cwl/reference_ > files/battenberg/1000genomesloci/1000genomesloci2012_chr4.txt -o > /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.4.tsv -b > /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam > 23336.68user 273.00system 10:17:02elapsed 63%CPU (0avgtext+0avgdata > 6501344maxresident)k > 22397816inputs+120192outputs (0major+416448minor)pagefaults 0swaps > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_tumour_19.stdout > ----------------------------------------------------------------------- > > ----------------------------------------------------------------------- > Job Name: s58_bbAllele_tumour_23 > Job ID: 335639375 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_tumour_23.o335639375 > Updated: Tue Sep 20 11:14:37 UTC 2016 > Contents Excerpt: > Modified command: alleleCounter -l /var/spool/cwl/reference_ > files/battenberg/1000genomesloci/1000genomesloci2012_chr6.txt -o > /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.6.tsv -b > /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam > 20846.11user 251.83system 9:33:55elapsed 61%CPU (0avgtext+0avgdata > 5765024maxresident)k > 19462064inputs+106080outputs (0major+369701minor)pagefaults 0swaps > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_tumour_23.stdout > ----------------------------------------------------------------------- > > ----------------------------------------------------------------------- > Job Name: s58_bbAllele_tumour_25 > Job ID: 335639387 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_tumour_25.o335639387 > ----------------------------------------------------------------------- > Job Name: s58_bbAllele_control_56 > Job ID: 335639173 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_control_56.o335639173 > Updated: Tue Sep 20 03:39:33 UTC 2016 > Contents Excerpt: > Modified command: alleleCounter -l /var/spool/cwl/reference_ > files/battenberg/1000genomesloci/1000genomesloci2012_chr22.txt -o > /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.22.tsv -b > /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam > 2810.79user 34.33system 1:58:52elapsed 39%CPU (0avgtext+0avgdata > 1250144maxresident)k > 1243552inputs+22208outputs (0major+82726minor)pagefaults 0swaps > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_control_56.stdout > ----------------------------------------------------------------------- > > ----------------------------------------------------------------------- > Job Name: s58_bbAllele_control_54 > Job ID: 335639174 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_control_54.o335639174 > Updated: Tue Sep 20 03:55:15 UTC 2016 > Contents Excerpt: > Modified command: alleleCounter -l /var/spool/cwl/reference_ > files/battenberg/1000genomesloci/1000genomesloci2012_chr21.txt -o > /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.21.tsv -b > /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam > 3187.08user 39.68system 2:14:34elapsed 39%CPU (0avgtext+0avgdata > 1302656maxresident)k > 1689216inputs+23256outputs (0major+86038minor)pagefaults 0swaps > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_control_54.stdout > ----------------------------------------------------------------------- > > ----------------------------------------------------------------------- > Job Name: s58_bbAllele_control_58 > Job ID: 335639178 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_control_58.o335639178 > Updated: Tue Sep 20 04:41:10 UTC 2016 > Contents Excerpt: > Modified command: alleleCounter -l /var/spool/cwl/reference_ > files/battenberg/1000genomesloci/1000genomesloci2012_chr23.txt -o > /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.23.tsv -b > /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam > 4375.73user 53.14system 3:00:29elapsed 40%CPU (0avgtext+0avgdata > 3123136maxresident)k > 4325272inputs+56240outputs (0major+199643minor)pagefaults 0swaps > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_control_58.stdout > ----------------------------------------------------------------------- > > ----------------------------------------------------------------------- > Job Name: s58_bbAllele_tumour_17 > Job ID: 335639179 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_tumour_17.o335639179 > Updated: Tue Sep 20 12:05:07 UTC 2016 > Contents Excerpt: > Modified command: alleleCounter -l /var/spool/cwl/reference_ > files/battenberg/1000genomesloci/1000genomesloci2012_chr3.txt -o > /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.3.tsv -b > /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam > 23819.53user 283.10system 10:24:27elapsed 64%CPU (0avgtext+0avgdata > 6576048maxresident)k > Contents Excerpt: > Modified command: alleleCounter -l /var/spool/cwl/reference_ > files/battenberg/1000genomesloci/1000genomesloci2012_chr17.txt -o > /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.17.tsv -b > /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam > 5945.65user 71.96system 4:00:01elapsed 41%CPU (0avgtext+0avgdata > 2544496maxresident)k > 5572568inputs+46720outputs (0major+163875minor)pagefaults 0swaps > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_control_46.stdout > ----------------------------------------------------------------------- > > ----------------------------------------------------------------------- > Job Name: s58_bbAllele_control_48 > Job ID: 335639020 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_control_48.o335639020 > Updated: Tue Sep 20 05:54:57 UTC 2016 > Contents Excerpt: > Modified command: alleleCounter -l /var/spool/cwl/reference_ > files/battenberg/1000genomesloci/1000genomesloci2012_chr18.txt -o > /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.18.tsv -b > /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam > 6337.11user 77.66system 4:14:16elapsed 42%CPU (0avgtext+0avgdata > 2647504maxresident)k > 5337616inputs+48704outputs (0major+170347minor)pagefaults 0swaps > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_control_48.stdout > ----------------------------------------------------------------------- > > ----------------------------------------------------------------------- > Job Name: s58_bbAllele_control_50 > Job ID: 335639025 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_control_50.o335639025 > Updated: Tue Sep 20 04:48:39 UTC 2016 > Contents Excerpt: > Modified command: alleleCounter -l /var/spool/cwl/reference_ > files/battenberg/1000genomesloci/1000genomesloci2012_chr19.txt -o > /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.19.tsv -b > /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam > 4542.91user 55.47system 3:07:58elapsed 40%CPU (0avgtext+0avgdata > 1995904maxresident)k > 3514080inputs+36192outputs (0major+129470minor)pagefaults 0swaps > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_control_50.stdout > ----------------------------------------------------------------------- > > ----------------------------------------------------------------------- > Job Name: s58_bbAllele_control_52 > Job ID: 335639111 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_control_52.o335639111 > Updated: Tue Sep 20 05:05:25 UTC 2016 > Contents Excerpt: > Modified command: alleleCounter -l /var/spool/cwl/reference_ > files/battenberg/1000genomesloci/1000genomesloci2012_chr20.txt -o > /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.20.tsv -b > /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam > 4979.15user 61.39system 3:24:44elapsed 41%CPU (0avgtext+0avgdata > 2102832maxresident)k > 3653168inputs+38272outputs (0major+136206minor)pagefaults 0swaps > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_control_52.stdout > ----------------------------------------------------------------------- > > > > > > > > > > > > > > > -6a3e-4a98-b41c-f8add599884c.11.tsv -b /var/spool/cwl/ > fdcb1bd7cffca69d15383ca9566c58e0.bam > 11287.76user 142.04system 6:43:55elapsed 47%CPU (0avgtext+0avgdata > 4543376maxresident)k > 9747344inputs+86048outputs (0major+289230minor)pagefaults 0swaps > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_control_34.stdout > ----------------------------------------------------------------------- > > ----------------------------------------------------------------------- > Job Name: s58_bbAllele_control_38 > Job ID: 335638783 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_control_38.o335638783 > Updated: Tue Sep 20 06:49:18 UTC 2016 > Contents Excerpt: > Modified command: alleleCounter -l /var/spool/cwl/reference_ > files/battenberg/1000genomesloci/1000genomesloci2012_chr13.txt -o > /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.13.tsv -b > /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam > 7981.44user 98.27system 5:08:39elapsed 43%CPU (0avgtext+0avgdata > 3310512maxresident)k > 6948640inputs+62176outputs (7major+211942minor)pagefaults 0swaps > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_control_38.stdout > ----------------------------------------------------------------------- > > ----------------------------------------------------------------------- > Job Name: s58_bbAllele_control_42 > Job ID: 335638805 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_control_42.o335638805 > Updated: Tue Sep 20 06:07:49 UTC 2016 > Contents Excerpt: > Modified command: alleleCounter -l /var/spool/cwl/reference_ > files/battenberg/1000genomesloci/1000genomesloci2012_chr15.txt -o > /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.15.tsv -b > /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam > 6705.59user 83.09system 4:27:09elapsed 42%CPU (0avgtext+0avgdata > 2746816maxresident)k > 6146600inputs+50992outputs (0major+176574minor)pagefaults 0swaps > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_control_42.stdout > ----------------------------------------------------------------------- > > ----------------------------------------------------------------------- > Job Name: s58_bbAllele_control_46 > Job ID: 379374477 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_cgpPindel_input_70.e379374477 > Updated: Tue Sep 20 13:50:00 UTC 2016 > Contents Excerpt: > Command run: > bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_cgpPindel_input_70.sh > > Output from command: /usr/bin/perl /opt/wtsi-cgp/bin/pindel_input_gen.pl > > -b /var/lib/cwl/stg33415604-d4eb-49aa-8f81-345b6fb2a6f3/ > fdcb1bd7cffca69d15383ca9566c58e0.bam -o /var/spool/cwl/0/pindel/ > tmpPindel/8c0354eb-6a3e-4a98-b41c-f8add599884c -t 4 -e > /var/spool/cwl/reference_files/brass/ucscHiDepth_0.01_ > mrg1000_no_exon_coreChrs.bed.gz > > [SeqWare Pipeline] ERROR [2016/09/20 13:50:00] | The exit value was 25 > Command exit code: 1 > > Output from command: /usr/bin/perl /opt/wtsi-cgp/bin/pindel_input_gen.pl > > -b /var/lib/cwl/stg33415604-d4eb-49aa-8f81-345b6fb2a6f3/ > fdcb1bd7cffca69d15383ca9566c58e0.bam -o /var/spool/cwl/0/pindel/ > tmpPindel/8c0354eb-6a3e-4a98-b41c-f8add599884c -t 4 -e > /var/spool/cwl/reference_files/brass/ucscHiDepth_0.01_ > mrg1000_no_exon_coreChrs.bed.gz > > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_cgpPindel_input_70.stderr > ----------------------------------------------------------------------- > > ----------------------------------------------------------------------- > Job Name: s58_bbAllele_merge_59 > Job ID: 379374478 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_merge_59.e379374478 > Updated: Tue Sep 20 13:51:15 UTC 2016 > Contents Excerpt: > Command run: > bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_merge_59.sh > Command exit code: 0 > > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_merge_59.stderr > ----------------------------------------------------------------------- > > > The method 'do_run' exited abnormally so the Runner will terminate here! > Return value was: 15 > > [WARNING] command: seqware bundle launch --dir /home/seqware/CGP-Somatic- > Docker/target/Workflow_Bundle_CgpSomaticCore_0.0.0_SeqWare_1.1.1/ > --engine whitestar-parallel --ini /var/spool/cwl/workflow.ini --no-metadata > exited with code: 15 > Error while running job: Error collecting output for parameter > 'somatic_cnv_tar_gz': Did not find output file with glob pattern: > '['*.somatic.cnv.tar.gz']' > [job temp319312608049643386.cwl] completed permanentFail > Final process status is permanentFail > Workflow error, try again with --debug for more information: > Process status is ['permanentFail'] > > stdout : > java.lang.RuntimeException: problems running command: cwltool --enable-dev > --non-strict --enable-net --outdir /mnt/1TB/work/DockerTest- > Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/outputs/ > --tmpdir-prefix /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/ > launcher-780ac637-b999-4a70-8ab7-79b51c64f428/working/ > /tmp/1474331255066-0/temp319312608049643386.cwl /mnt/1TB/work/DockerTest- > Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70- > 8ab7-79b51c64f428/workflow_params.json > ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ f > f: command not found > ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ df > Filesystem 1K-blocks Used Available Use% Mounted on > udev 62947280 12 62947268 1% /dev > tmpfs 12590448 364 12590084 1% /run > /dev/xvda1 8115168 6093092 1586800 80% / > none 4 0 4 0% /sys/fs/cgroup > none 5120 0 5120 0% /run/lock > none 62952228 0 62952228 0% /run/shm > none 102400 0 102400 0% /run/user > /dev/xvdb 1031992064 303267080 676279800 31% /mnt/1TB > ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ df -h > Filesystem Size Used Avail Use% Mounted on > udev 61G 12K 61G 1% /dev > tmpfs 13G 364K 13G 1% /run > /dev/xvda1 7.8G 5.9G 1.6G 80% / > none 4.0K 0 4.0K 0% /sys/fs/cgroup > none 5.0M 0 5.0M 0% /run/lock > none 61G 0 61G 0% /run/shm > none 100M 0 100M 0% /run/user > /dev/xvdb 985G 290G 645G 31% /mnt/1TB > ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ vi Dockstore.json > { > "bbFrom": { > "bbFrom": { > "path": "https://s3-eu-west-1.amazonaws.com/wtsi-pancancer/ > reference/GRCh37d5_battenberg.tar.gz > > ", > "class": "File" > }, > "refFrom": { > "path": "https://s3-eu-west-1.amazonaws.com/wtsi-pancancer/ > reference/GRCh37d5_CGP_refBundle.tar.gz > > ", > "class": "File" > }, > "tumor": { > "path": "/home/ubuntu/DockerTest-Miguel/data/ > 7875b5196f6b8b52847f99bf370aada0.bam", > "class": "File" > }, > "normal": { > "path": "/home/ubuntu/DockerTest-Miguel/data/ > fdcb1bd7cffca69d15383ca9566c58e0.bam", > "class": "File" > }, > "somatic_sv_tar_gz": { > "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic. > sv.tar.gz", > "class": "File" > }, > "somatic_snv_mnv_tar_gz": { > "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic. > snv.mnv.tar.gz", > "class": "File" > }, > "somatic_verifyBamId_tar_gz": { > "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic. > verifyBamId.tar.gz", > "class": "File" > }, > "somatic_cnv_tar_gz": { > "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic. > cnv.tar.gz", > "class": "File" > }, > "somatic_imputeCounts_tar_gz": { > "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic. > imputeCounts.tar.gz", > "class": "File" > }, > "somatic_genotype_tar_gz": { > "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic. > genotype.tar.gz", > "class": "File" > }, > "somatic_indel_tar_gz": { > "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic. > indel.tar.gz", > "class": "File" > } > } > ~ > ~ > ~ > ~ > ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ l results/ > ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ vi Dockstore.json ^C > Updated: Tue Sep 20 13:51:15 UTC 2016 > Contents Excerpt: > Command run: > bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_merge_59.sh > Command exit code: 0 > > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_merge_59.stderr > ----------------------------------------------------------------------- > > > The method 'do_run' exited abnormally so the Runner will terminate here! > Return value was: 15 > > [WARNING] command: seqware bundle launch --dir /home/seqware/CGP-Somatic- > Docker/target/Workflow_Bundle_CgpSomaticCore_0.0.0_SeqWare_1.1.1/ > --engine whitestar-parallel --ini /var/spool/cwl/workflow.ini --no-metadata > exited with code: 15 > Error while running job: Error collecting output for parameter > 'somatic_cnv_tar_gz': Did not find output file with glob pattern: > '['*.somatic.cnv.tar.gz']' > [job temp319312608049643386.cwl] completed permanentFail > Final process status is permanentFail > Workflow error, try again with --debug for more information: > Process status is ['permanentFail'] > > stdout : > java.lang.RuntimeException: problems running command: cwltool --enable-dev > --non-strict --enable-net --outdir /mnt/1TB/work/DockerTest- > Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/outputs/ > --tmpdir-prefix /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/ > launcher-780ac637-b999-4a70-8ab7-79b51c64f428/working/ > /tmp/1474331255066-0/temp319312608049643386.cwl /mnt/1TB/work/DockerTest- > Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70- > 8ab7-79b51c64f428/workflow_params.json > ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ f > f: command not found > ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ df > Filesystem 1K-blocks Used Available Use% Mounted on > udev 62947280 12 62947268 1% /dev > tmpfs 12590448 364 12590084 1% /run > /dev/xvda1 8115168 6093092 1586800 80% / > none 4 0 4 0% /sys/fs/cgroup > none 5120 0 5120 0% /run/lock > none 62952228 0 62952228 0% /run/shm > none 102400 0 102400 0% /run/user > /dev/xvdb 1031992064 303267080 676279800 31% /mnt/1TB > ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ df -h > Filesystem Size Used Avail Use% Mounted on > udev 61G 12K 61G 1% /dev > tmpfs 13G 364K 13G 1% /run > /dev/xvda1 7.8G 5.9G 1.6G 80% / > none 4.0K 0 4.0K 0% /sys/fs/cgroup > none 5.0M 0 5.0M 0% /run/lock > none 61G 0 61G 0% /run/shm > none 100M 0 100M 0% /run/user > /dev/xvdb 985G 290G 645G 31% /mnt/1TB > ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ vi Dockstore.json > > { > > Output from command: /opt/wtsi-cgp/bin/alleleCounter -b /var/spool/cwl/ > 7875b5196f6b8b52847f99bf370aada0.bam -o /var/spool/cwl/0/ascat/ > tmpAscat/allele_count/b02b4bba-6e66-44fb-a48f-38c309aaaac5.allct -l > /var/spool/cwl/reference_files/ascat/SnpLocus.tsv -m 20 > > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_ASCAT_allele_count_60.stderr > ----------------------------------------------------------------------- > > ----------------------------------------------------------------------- > Job Name: s58_ASCAT_allele_count_61 > Job ID: 379374475 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_ASCAT_allele_count_61.e379374475 > Updated: Tue Sep 20 14:58:41 UTC 2016 > Contents Excerpt: > Command run: > bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_ASCAT_allele_count_61.sh > Command exit code: 0 > > Output from command: /opt/wtsi-cgp/bin/alleleCounter -b /var/spool/cwl/ > fdcb1bd7cffca69d15383ca9566c58e0.bam -o /var/spool/cwl/0/ascat/ > tmpAscat/allele_count/8c0354eb-6a3e-4a98-b41c-f8add599884c.allct -l > /var/spool/cwl/reference_files/ascat/SnpLocus.tsv -m 20 > > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_ASCAT_allele_count_61.stderr > ----------------------------------------------------------------------- > > ----------------------------------------------------------------------- > Job Name: s58_cgpPindel_input_70 > Job ID: 379374477 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_cgpPindel_input_70.e379374477 > Updated: Tue Sep 20 13:50:00 UTC 2016 > Contents Excerpt: > Command run: > bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_cgpPindel_input_70.sh > > Output from command: /usr/bin/perl /opt/wtsi-cgp/bin/pindel_input_gen.pl > > -b /var/lib/cwl/stg33415604-d4eb-49aa-8f81-345b6fb2a6f3/ > fdcb1bd7cffca69d15383ca9566c58e0.bam -o /var/spool/cwl/0/pindel/ > tmpPindel/8c0354eb-6a3e-4a98-b41c-f8add599884c -t 4 -e > /var/spool/cwl/reference_files/brass/ucscHiDepth_0.01_ > mrg1000_no_exon_coreChrs.bed.gz > > [SeqWare Pipeline] ERROR [2016/09/20 13:50:00] | The exit value was 25 > Command exit code: 1 > > Output from command: /usr/bin/perl /opt/wtsi-cgp/bin/pindel_input_gen.pl > > -b /var/lib/cwl/stg33415604-d4eb-49aa-8f81-345b6fb2a6f3/ > fdcb1bd7cffca69d15383ca9566c58e0.bam -o /var/spool/cwl/0/pindel/ > tmpPindel/8c0354eb-6a3e-4a98-b41c-f8add599884c -t 4 -e > /var/spool/cwl/reference_files/brass/ucscHiDepth_0.01_ > mrg1000_no_exon_coreChrs.bed.gz > > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_cgpPindel_input_70.stderr > ----------------------------------------------------------------------- > > ----------------------------------------------------------------------- > Job Name: s58_bbAllele_merge_59 > Job ID: 379374478 > File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_merge_59.e379374478 > Updated: Tue Sep 20 13:51:15 UTC 2016 > Contents Excerpt: > Command run: > bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_merge_59.sh > Command exit code: 0 > > > Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/ > generated-scripts/s58_bbAllele_merge_59.stderr > ----------------------------------------------------------------------- > > > The method 'do_run' exited abnormally so the Runner will terminate here! > Return value was: 15 > > [WARNING] command: seqware bundle launch --dir /home/seqware/CGP-Somatic- > Docker/target/Workflow_Bundle_CgpSomaticCore_0.0.0_SeqWare_1.1.1/ > --engine whitestar-parallel --ini /var/spool/cwl/workflow.ini --no-metadata > exited with code: 15 > Error while running job: Error collecting output for parameter > 'somatic_cnv_tar_gz': Did not find output file with glob pattern: > '['*.somatic.cnv.tar.gz']' > [job temp319312608049643386.cwl] completed permanentFail > Final process status is permanentFail > Workflow error, try again with --debug for more information: > Process status is ['permanentFail'] > > stdout : > java.lang.RuntimeException: problems running command: cwltool --enable-dev > --non-strict --enable-net --outdir /mnt/1TB/work/DockerTest- > Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/outputs/ > --tmpdir-prefix /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/ > launcher-780ac637-b999-4a70-8ab7-79b51c64f428/working/ > /tmp/1474331255066-0/temp319312608049643386.cwl /mnt/1TB/work/DockerTest- > Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70- > 8ab7-79b51c64f428/workflow_params.json > > > 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URL: From Denis.Yuen at oicr.on.ca Tue Sep 20 15:20:47 2016 From: Denis.Yuen at oicr.on.ca (Denis Yuen) Date: Tue, 20 Sep 2016 19:20:47 +0000 Subject: [DOCKTESTERS] Amazon account In-Reply-To: References: <27512884B2D81B41AAB7BB266248F240C099E23C@exmb2.ad.oicr.on.ca> <2C84FF4CF2F0A04EB7691F988A717B47CB65E809@exmb2.ad.oicr.on.ca> <27512884B2D81B41AAB7BB266248F240C099E2A3@exmb2.ad.oicr.on.ca> <27512884B2D81B41AAB7BB266248F240C099E397@exmb2.ad.oicr.on.ca>, Message-ID: <27512884B2D81B41AAB7BB266248F240C099E3B6@exmb2.ad.oicr.on.ca> I think there are a few pieces of information that could be useful. Look in this ticket https://github.com/ICGC-TCGA-PanCancer/CGP-Somatic-Docker/issues/5 there's a section that starts with "docker run -i", this will let me see if there's anything obviously strange with the call to Docker. Failing that, I think we'll have to see what exit code 25 denotes for Pindel. ________________________________ From: Miguel Vazquez [mikisvaz at gmail.com] Sent: September 20, 2016 3:15 PM To: Denis Yuen Cc: docktesters at lists.icgc.org; Brian O'Connor; Junjun Zhang Subject: RE: [DOCKTESTERS] Amazon account Well, that's a bummer. Any ideas? On Sep 20, 2016 9:11 PM, "Denis Yuen" > wrote: Hi, That's really just saying that cwltool was unable to find the output. Changing the entry will just save the output somewhere else. The real problem is probably in the section: ---- bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_cgpPindel_input_70.sh Output from command: /usr/bin/perl /opt/wtsi-cgp/bin/pindel_input_gen.pl -b /var/lib/cwl/stg33415604-d4eb-49aa-8f81-345b6fb2a6f3/fdcb1bd7cffca69d15383ca9566c58e0.bam -o /var/spool/cwl/0/pindel/tmpPindel/8c0354eb-6a3e-4a98-b41c-f8add599884c -t 4 -e /var/spool/cwl/reference_files/brass/ucscHiDepth_0.01_mrg1000_no_exon_coreChrs.bed.gz [SeqWare Pipeline] ERROR [2016/09/20 13:50:00] | The exit value was 25 Command exit code: 1 Output from command: /usr/bin/perl /opt/wtsi-cgp/bin/pindel_input_gen.pl -b /var/lib/cwl/stg33415604-d4eb-49aa-8f81-345b6fb2a6f3/fdcb1bd7cffca69d15383ca9566c58e0.bam -o /var/spool/cwl/0/pindel/tmpPindel/8c0354eb-6a3e-4a98-b41c-f8add599884c -t 4 -e /var/spool/cwl/reference_files/brass/ucscHiDepth_0.01_mrg1000_no_exon_coreChrs.bed.gz ---- That says that pindel failed, but there doesn't appear to be any more explanation as to why. Denis Yuen Bioinformatics Software Developer Ontario Institute for Cancer Research MaRS Centre 661 University Avenue Suite 510 Toronto, Ontario, Canada M5G 0A3 Toll-free: 1-866-678-6427 Twitter: @OICR_news www.oicr.on.ca This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization. ________________________________ From: Miguel Vazquez [mikisvaz at gmail.com] Sent: September 20, 2016 2:55 PM To: Junjun Zhang Cc: Denis Yuen; Brian O'Connor; docktesters at lists.icgc.org Subject: Re: [DOCKTESTERS] Amazon account Just a heads up, the process failed. The complete log is bellow, but I think this is the culprit: Error while running job: Error collecting output for parameter 'somatic_cnv_tar_gz': Did not find output file with glob pattern: '['*.somatic.cnv.tar.gz']' I wrote something like this in Dockerstore.json "somatic_cnv_tar_gz": { "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.cnv.tar.gz", "class": "File" } I've replace those entries with this "somatic_cnv_tar_gz": { "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/DONOR.somatic.cnv.tar.gz", "class": "File" } so that the glob work. I'm trying again. I'll update the documentation Best Miguel ------------------ Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_25.stderr ----------------------------------------------------------------------- Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_56.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_54 Job ID: 335639174 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_54.e335639174 Updated: Tue Sep 20 03:55:15 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_54.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_54.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_13 Job ID: 335639178 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_13.e335639178 Updated: Tue Sep 20 12:07:55 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_13.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_13.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_17 Job ID: 335639179 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_17.e335639179 Updated: Tue Sep 20 12:05:07 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_17.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_17.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_15 Job ID: 335639180 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_15.e335639180 ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_48 Job ID: 335639020 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_48.e335639020 Updated: Tue Sep 20 05:54:57 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_48.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_48.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_50 Job ID: 335639025 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_50.e335639025 Updated: Tue Sep 20 04:48:39 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_50.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_50.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_52 Job ID: 335639111 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_52.e335639111 Updated: Tue Sep 20 05:05:25 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_52.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_52.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_56 Job ID: 335639173 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_56.e335639173 Updated: Tue Sep 20 03:39:33 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_56.sh Command exit code: 0 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_34.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_34.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_38 Job ID: 335638783 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_38.e335638783 Updated: Tue Sep 20 06:49:18 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_38.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_38.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_42 Job ID: 335638805 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_42.e335638805 Updated: Tue Sep 20 06:07:49 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_42.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_42.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_46 Job ID: 335638826 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_46.e335638826 Updated: Tue Sep 20 05:40:42 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_46.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_46.stderr ----------------------------------------------------------------------- Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_unpackRef_NA_10.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_22 Job ID: 335638775 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_22.e335638775 Updated: Tue Sep 20 09:32:19 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_22.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_22.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_28 Job ID: 335638776 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_28.e335638776 Updated: Tue Sep 20 08:57:31 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_28.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_28.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_32 Job ID: 335638777 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_32.e335638777 Updated: Tue Sep 20 08:12:44 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_32.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_32.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_34 Job ID: 335638778 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_34.e335638778 Updated: Tue Sep 20 08:24:35 UTC 2016 Job Name: s58_unpackRef_NA_9 Job ID: 331891142 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_unpackRef_NA_9.e331891142 Updated: Tue Sep 20 00:39:16 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_unpackRef_NA_9.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_unpackRef_NA_9.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_verifyBamHomChk_control_6 Job ID: 331891143 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_verifyBamHomChk_control_6.e331891143 Updated: Tue Sep 20 00:44:52 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_verifyBamHomChk_control_6.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_verifyBamHomChk_control_6.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_basFileGenerate_control_11 Job ID: 332292910 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_basFileGenerate_control_11.e332292910 Updated: Tue Sep 20 01:20:39 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_basFileGenerate_control_11.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_basFileGenerate_control_11.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_unpackRef_NA_10 Job ID: 332292911 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_unpackRef_NA_10.e332292911 Updated: Tue Sep 20 00:44:57 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_unpackRef_NA_10.sh Command exit code: 0 Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_start_0.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_start_0.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_mark_start_1 Job ID: 331890603 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_mark_start_1.e331890603 Updated: Tue Sep 20 00:38:10 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_mark_start_1.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_mark_start_1.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_prepBam_control_3 Job ID: 331890831 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_prepBam_control_3.e331890831 Updated: Tue Sep 20 00:38:11 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_prepBam_control_3.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_prepBam_control_3.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_prepBam_tumour_2 Job ID: 331890832 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_prepBam_tumour_2.e331890832 Updated: Tue Sep 20 00:38:11 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_prepBam_tumour_2.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_prepBam_tumour_2.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_61.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_BRASS_input_99 Job ID: 379374477 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_BRASS_input_99.o379374477 Updated: Tue Sep 20 16:49:15 UTC 2016 Contents Excerpt: [V] 18 0.49745MB/s 1781.56 [V] 19 0.525041MB/s 1879.07 [V] 20 0.552722MB/s 1976.44 [V] 21 0.579942MB/s 2072.21 [V] 22 0.607543MB/s 2169.2 [V] 23 0.635118MB/s 2266.04 [V] 24264262 [V] MemUsage(size=71.1484,rss=10.9336,peak=291.977) wall clock time 02:57:24:31175299 11827.06user 310.09system 2:59:40elapsed 112%CPU (0avgtext+0avgdata 4265632maxresident)k 117507424inputs+14421104outputs (84major+234838minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_BRASS_input_99.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_merge_59 Job ID: 379374478 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.o379374478 Updated: Tue Sep 20 13:51:15 UTC 2016 Contents Excerpt: 87.14user 5.10system 1:41.25elapsed 91%CPU (0avgtext+0avgdata 66448maxresident)k 2720952inputs+4360560outputs (5major+7600minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.stdout ----------------------------------------------------------------------- % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 54.9M 100 54.9M 0 0 1016k 0 0:00:55 0:00:55 --:--:-- 1047k % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 174k 100 174k 0 0 174k 0 0:00:01 0:00:01 --:--:-- 567k [2016/09/20 16:49:15] | Output for stderr due to workflow run failure: ----------------------------------------------------------------------- Job Name: s58_start_0 Job ID: 331890362 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_start_0.e331890362 Updated: Tue Sep 20 00:38:10 UTC 2016 Contents Excerpt: File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_renameSampleFile_208.o373317274 Updated: Tue Sep 20 12:08:37 UTC 2016 Contents Excerpt: Modified command: cp /var/spool/cwl/b02b4bba-6e66-44fb-a48f-38c309aaaac5.genotype.tar.gz /var/spool/cwl/b02b4bba-6e66-44fb-a48f-38c309aaaac5.csc_0-0-0.20160920.somatic.genotype.tar.gz Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_renameSampleFile_208.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_57 Job ID: 373317275 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_57.o373317275 Updated: Tue Sep 20 13:29:27 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr23.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.23.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 4798.51user 50.73system 1:20:50elapsed 99%CPU (0avgtext+0avgdata 3115856maxresident)k 9833328inputs+56328outputs (0major+199552minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_57.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_ASCAT_allele_count_60 Job ID: 379374473 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_60.o379374473 Updated: Tue Sep 20 15:34:45 UTC 2016 Contents Excerpt: Errors from command: /opt/wtsi-cgp/bin/alleleCounter -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam -o /var/spool/cwl/0/ascat/tmpAscat/allele_count/b02b4bba-6e66-44fb-a48f-38c309aaaac5.allct -l /var/spool/cwl/reference_files/ascat/SnpLocus.tsv -m 20 5928.09user 101.55system 1:45:10elapsed 95%CPU (0avgtext+0avgdata 2345888maxresident)k 221140208inputs+43144outputs (37major+169349minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_60.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_ASCAT_allele_count_61 Job ID: 379374475 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_61.o379374475 Updated: Tue Sep 20 14:58:41 UTC 2016 Contents Excerpt: Errors from command: /opt/wtsi-cgp/bin/alleleCounter -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam -o /var/spool/cwl/0/ascat/tmpAscat/allele_count/8c0354eb-6a3e-4a98-b41c-f8add599884c.allct -l /var/spool/cwl/reference_files/ascat/SnpLocus.tsv -m 20 3864.82user 67.24system 1:09:07elapsed 94%CPU (0avgtext+0avgdata 2350544maxresident)k 157460240inputs+43120outputs (57major+167795minor)pagefaults 0swaps 11476.37user 140.61system 6:48:23elapsed 47%CPU (0avgtext+0avgdata 3035728maxresident)k 7380072inputs+56816outputs (0major+196640minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_39.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_41 Job ID: 335639489 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_41.o335639489 Updated: Tue Sep 20 07:35:04 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr15.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.15.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 9429.90user 117.09system 5:54:22elapsed 44%CPU (0avgtext+0avgdata 2739152maxresident)k 5273744inputs+51000outputs (0major+177355minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_41.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_45 Job ID: 335639845 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_45.o335639845 Updated: Tue Sep 20 07:29:41 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr17.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.17.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 9231.30user 116.04system 5:49:00elapsed 44%CPU (0avgtext+0avgdata 2540400maxresident)k 5255296inputs+46736outputs (0major+165277minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_45.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_43 Job ID: 335639853 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_43.o335639853 Updated: Tue Sep 20 08:28:45 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr16.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.16.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 11465.31user 146.48system 6:48:03elapsed 47%CPU (0avgtext+0avgdata 2945712maxresident)k 6906080inputs+54432outputs (0major+190932minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_43.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_renameSampleFile_208 Job ID: 373317274 ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_33 Job ID: 335639420 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_33.o335639420 Updated: Tue Sep 20 10:42:41 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr11.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.11.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 18904.62user 233.41system 9:02:00elapsed 58%CPU (0avgtext+0avgdata 4537600maxresident)k 15888800inputs+86400outputs (0major+292553minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_33.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_35 Job ID: 335639430 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_35.o335639430 Updated: Tue Sep 20 10:03:48 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr12.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.12.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 16584.76user 210.26system 8:23:07elapsed 55%CPU (0avgtext+0avgdata 4373600maxresident)k 12917040inputs+82896outputs (0major+281480minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_35.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_37 Job ID: 335639431 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_37.o335639431 Updated: Tue Sep 20 08:26:17 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr13.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.13.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 11361.18user 138.30system 6:45:36elapsed 47%CPU (0avgtext+0avgdata 3301008maxresident)k 7418080inputs+62192outputs (0major+212951minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_37.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_39 Job ID: 335639452 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_39.o335639452 Updated: Tue Sep 20 08:29:04 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr14.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.14.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam Updated: Tue Sep 20 11:02:29 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr7.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.7.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 20088.69user 242.69system 9:21:48elapsed 60%CPU (0avgtext+0avgdata 5281504maxresident)k 18604808inputs+96776outputs (0major+339332minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_25.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_27 Job ID: 335639400 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_27.o335639400 Updated: Tue Sep 20 11:02:53 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr8.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.8.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 20108.48user 243.42system 9:22:11elapsed 60%CPU (0avgtext+0avgdata 5228912maxresident)k 17295080inputs+95440outputs (0major+335764minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_27.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_29 Job ID: 335639401 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_29.o335639401 Updated: Tue Sep 20 09:18:32 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr9.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.9.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 13962.23user 175.03system 7:37:51elapsed 51%CPU (0avgtext+0avgdata 3971872maxresident)k 12246072inputs+72144outputs (0major+255173minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_29.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_31 Job ID: 335639417 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_31.o335639417 Updated: Tue Sep 20 10:11:08 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr10.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.10.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 17052.42user 207.86system 8:30:26elapsed 56%CPU (0avgtext+0avgdata 4504144maxresident)k 13931760inputs+85488outputs (0major+289717minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_31.stdout ----------------------------------------------------------------------- 23593416inputs+121608outputs (0major+421477minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_17.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_15 Job ID: 335639180 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_15.o335639180 Updated: Tue Sep 20 12:08:37 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr2.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.2.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 24021.20user 275.32system 10:27:56elapsed 64%CPU (0avgtext+0avgdata 7851136maxresident)k 24358016inputs+146264outputs (0major+499924minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_15.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_19 Job ID: 335639200 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_19.o335639200 Updated: Tue Sep 20 11:57:43 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr4.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.4.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 23336.68user 273.00system 10:17:02elapsed 63%CPU (0avgtext+0avgdata 6501344maxresident)k 22397816inputs+120192outputs (0major+416448minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_19.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_23 Job ID: 335639375 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_23.o335639375 Updated: Tue Sep 20 11:14:37 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr6.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.6.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 20846.11user 251.83system 9:33:55elapsed 61%CPU (0avgtext+0avgdata 5765024maxresident)k 19462064inputs+106080outputs (0major+369701minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_23.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_25 Job ID: 335639387 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_25.o335639387 ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_56 Job ID: 335639173 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_56.o335639173 Updated: Tue Sep 20 03:39:33 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr22.txt -o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.22.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam 2810.79user 34.33system 1:58:52elapsed 39%CPU (0avgtext+0avgdata 1250144maxresident)k 1243552inputs+22208outputs (0major+82726minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_56.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_54 Job ID: 335639174 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_54.o335639174 Updated: Tue Sep 20 03:55:15 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr21.txt -o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.21.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam 3187.08user 39.68system 2:14:34elapsed 39%CPU (0avgtext+0avgdata 1302656maxresident)k 1689216inputs+23256outputs (0major+86038minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_54.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_58 Job ID: 335639178 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_58.o335639178 Updated: Tue Sep 20 04:41:10 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr23.txt -o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.23.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam 4375.73user 53.14system 3:00:29elapsed 40%CPU (0avgtext+0avgdata 3123136maxresident)k 4325272inputs+56240outputs (0major+199643minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_58.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_17 Job ID: 335639179 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_17.o335639179 Updated: Tue Sep 20 12:05:07 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr3.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.3.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 23819.53user 283.10system 10:24:27elapsed 64%CPU (0avgtext+0avgdata 6576048maxresident)k Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr17.txt -o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.17.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam 5945.65user 71.96system 4:00:01elapsed 41%CPU (0avgtext+0avgdata 2544496maxresident)k 5572568inputs+46720outputs (0major+163875minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_46.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_48 Job ID: 335639020 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_48.o335639020 Updated: Tue Sep 20 05:54:57 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr18.txt -o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.18.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam 6337.11user 77.66system 4:14:16elapsed 42%CPU (0avgtext+0avgdata 2647504maxresident)k 5337616inputs+48704outputs (0major+170347minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_48.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_50 Job ID: 335639025 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_50.o335639025 Updated: Tue Sep 20 04:48:39 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr19.txt -o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.19.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam 4542.91user 55.47system 3:07:58elapsed 40%CPU (0avgtext+0avgdata 1995904maxresident)k 3514080inputs+36192outputs (0major+129470minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_50.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_52 Job ID: 335639111 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_52.o335639111 Updated: Tue Sep 20 05:05:25 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr20.txt -o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.20.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam 4979.15user 61.39system 3:24:44elapsed 41%CPU (0avgtext+0avgdata 2102832maxresident)k 3653168inputs+38272outputs (0major+136206minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_52.stdout ----------------------------------------------------------------------- -6a3e-4a98-b41c-f8add599884c.11.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam 11287.76user 142.04system 6:43:55elapsed 47%CPU (0avgtext+0avgdata 4543376maxresident)k 9747344inputs+86048outputs (0major+289230minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_34.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_38 Job ID: 335638783 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_38.o335638783 Updated: Tue Sep 20 06:49:18 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr13.txt -o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.13.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam 7981.44user 98.27system 5:08:39elapsed 43%CPU (0avgtext+0avgdata 3310512maxresident)k 6948640inputs+62176outputs (7major+211942minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_38.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_42 Job ID: 335638805 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_42.o335638805 Updated: Tue Sep 20 06:07:49 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr15.txt -o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.15.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam 6705.59user 83.09system 4:27:09elapsed 42%CPU (0avgtext+0avgdata 2746816maxresident)k 6146600inputs+50992outputs (0major+176574minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_42.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_46 Job ID: 379374477 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_cgpPindel_input_70.e379374477 Updated: Tue Sep 20 13:50:00 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_cgpPindel_input_70.sh Output from command: /usr/bin/perl /opt/wtsi-cgp/bin/pindel_input_gen.pl -b /var/lib/cwl/stg33415604-d4eb-49aa-8f81-345b6fb2a6f3/fdcb1bd7cffca69d15383ca9566c58e0.bam -o /var/spool/cwl/0/pindel/tmpPindel/8c0354eb-6a3e-4a98-b41c-f8add599884c -t 4 -e /var/spool/cwl/reference_files/brass/ucscHiDepth_0.01_mrg1000_no_exon_coreChrs.bed.gz [SeqWare Pipeline] ERROR [2016/09/20 13:50:00] | The exit value was 25 Command exit code: 1 Output from command: /usr/bin/perl /opt/wtsi-cgp/bin/pindel_input_gen.pl -b /var/lib/cwl/stg33415604-d4eb-49aa-8f81-345b6fb2a6f3/fdcb1bd7cffca69d15383ca9566c58e0.bam -o /var/spool/cwl/0/pindel/tmpPindel/8c0354eb-6a3e-4a98-b41c-f8add599884c -t 4 -e /var/spool/cwl/reference_files/brass/ucscHiDepth_0.01_mrg1000_no_exon_coreChrs.bed.gz Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_cgpPindel_input_70.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_merge_59 Job ID: 379374478 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.e379374478 Updated: Tue Sep 20 13:51:15 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.stderr ----------------------------------------------------------------------- The method 'do_run' exited abnormally so the Runner will terminate here! Return value was: 15 [WARNING] command: seqware bundle launch --dir /home/seqware/CGP-Somatic-Docker/target/Workflow_Bundle_CgpSomaticCore_0.0.0_SeqWare_1.1.1/ --engine whitestar-parallel --ini /var/spool/cwl/workflow.ini --no-metadata exited with code: 15 Error while running job: Error collecting output for parameter 'somatic_cnv_tar_gz': Did not find output file with glob pattern: '['*.somatic.cnv.tar.gz']' [job temp319312608049643386.cwl] completed permanentFail Final process status is permanentFail Workflow error, try again with --debug for more information: Process status is ['permanentFail'] stdout : java.lang.RuntimeException: problems running command: cwltool --enable-dev --non-strict --enable-net --outdir /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/outputs/ --tmpdir-prefix /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/working/ /tmp/1474331255066-0/temp319312608049643386.cwl /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/workflow_params.json ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ f f: command not found ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ df Filesystem 1K-blocks Used Available Use% Mounted on udev 62947280 12 62947268 1% /dev tmpfs 12590448 364 12590084 1% /run /dev/xvda1 8115168 6093092 1586800 80% / none 4 0 4 0% /sys/fs/cgroup none 5120 0 5120 0% /run/lock none 62952228 0 62952228 0% /run/shm none 102400 0 102400 0% /run/user /dev/xvdb 1031992064 303267080 676279800 31% /mnt/1TB ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ df -h Filesystem Size Used Avail Use% Mounted on udev 61G 12K 61G 1% /dev tmpfs 13G 364K 13G 1% /run /dev/xvda1 7.8G 5.9G 1.6G 80% / none 4.0K 0 4.0K 0% /sys/fs/cgroup none 5.0M 0 5.0M 0% /run/lock none 61G 0 61G 0% /run/shm none 100M 0 100M 0% /run/user /dev/xvdb 985G 290G 645G 31% /mnt/1TB ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ vi Dockstore.json { "bbFrom": { "bbFrom": { "path": "https://s3-eu-west-1.amazonaws.com/wtsi-pancancer/reference/GRCh37d5_battenberg.tar.gz", "class": "File" }, "refFrom": { "path": "https://s3-eu-west-1.amazonaws.com/wtsi-pancancer/reference/GRCh37d5_CGP_refBundle.tar.gz", "class": "File" }, "tumor": { "path": "/home/ubuntu/DockerTest-Miguel/data/7875b5196f6b8b52847f99bf370aada0.bam", "class": "File" }, "normal": { "path": "/home/ubuntu/DockerTest-Miguel/data/fdcb1bd7cffca69d15383ca9566c58e0.bam", "class": "File" }, "somatic_sv_tar_gz": { "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.sv.tar.gz", "class": "File" }, "somatic_snv_mnv_tar_gz": { "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.snv.mnv.tar.gz", "class": "File" }, "somatic_verifyBamId_tar_gz": { "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.verifyBamId.tar.gz", "class": "File" }, "somatic_cnv_tar_gz": { "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.cnv.tar.gz", "class": "File" }, "somatic_imputeCounts_tar_gz": { "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.imputeCounts.tar.gz", "class": "File" }, "somatic_genotype_tar_gz": { "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.genotype.tar.gz", "class": "File" }, "somatic_indel_tar_gz": { "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.indel.tar.gz", "class": "File" } } ~ ~ ~ ~ ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ l results/ ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ vi Dockstore.json ^C Updated: Tue Sep 20 13:51:15 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.stderr ----------------------------------------------------------------------- The method 'do_run' exited abnormally so the Runner will terminate here! Return value was: 15 [WARNING] command: seqware bundle launch --dir /home/seqware/CGP-Somatic-Docker/target/Workflow_Bundle_CgpSomaticCore_0.0.0_SeqWare_1.1.1/ --engine whitestar-parallel --ini /var/spool/cwl/workflow.ini --no-metadata exited with code: 15 Error while running job: Error collecting output for parameter 'somatic_cnv_tar_gz': Did not find output file with glob pattern: '['*.somatic.cnv.tar.gz']' [job temp319312608049643386.cwl] completed permanentFail Final process status is permanentFail Workflow error, try again with --debug for more information: Process status is ['permanentFail'] stdout : java.lang.RuntimeException: problems running command: cwltool --enable-dev --non-strict --enable-net --outdir /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/outputs/ --tmpdir-prefix /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/working/ /tmp/1474331255066-0/temp319312608049643386.cwl /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/workflow_params.json ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ f f: command not found ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ df Filesystem 1K-blocks Used Available Use% Mounted on udev 62947280 12 62947268 1% /dev tmpfs 12590448 364 12590084 1% /run /dev/xvda1 8115168 6093092 1586800 80% / none 4 0 4 0% /sys/fs/cgroup none 5120 0 5120 0% /run/lock none 62952228 0 62952228 0% /run/shm none 102400 0 102400 0% /run/user /dev/xvdb 1031992064 303267080 676279800 31% /mnt/1TB ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ df -h Filesystem Size Used Avail Use% Mounted on udev 61G 12K 61G 1% /dev tmpfs 13G 364K 13G 1% /run /dev/xvda1 7.8G 5.9G 1.6G 80% / none 4.0K 0 4.0K 0% /sys/fs/cgroup none 5.0M 0 5.0M 0% /run/lock none 61G 0 61G 0% /run/shm none 100M 0 100M 0% /run/user /dev/xvdb 985G 290G 645G 31% /mnt/1TB ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ vi Dockstore.json { Output from command: /opt/wtsi-cgp/bin/alleleCounter -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam -o /var/spool/cwl/0/ascat/tmpAscat/allele_count/b02b4bba-6e66-44fb-a48f-38c309aaaac5.allct -l /var/spool/cwl/reference_files/ascat/SnpLocus.tsv -m 20 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_60.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_ASCAT_allele_count_61 Job ID: 379374475 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_61.e379374475 Updated: Tue Sep 20 14:58:41 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_61.sh Command exit code: 0 Output from command: /opt/wtsi-cgp/bin/alleleCounter -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam -o /var/spool/cwl/0/ascat/tmpAscat/allele_count/8c0354eb-6a3e-4a98-b41c-f8add599884c.allct -l /var/spool/cwl/reference_files/ascat/SnpLocus.tsv -m 20 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_61.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_cgpPindel_input_70 Job ID: 379374477 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_cgpPindel_input_70.e379374477 Updated: Tue Sep 20 13:50:00 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_cgpPindel_input_70.sh Output from command: /usr/bin/perl /opt/wtsi-cgp/bin/pindel_input_gen.pl -b /var/lib/cwl/stg33415604-d4eb-49aa-8f81-345b6fb2a6f3/fdcb1bd7cffca69d15383ca9566c58e0.bam -o /var/spool/cwl/0/pindel/tmpPindel/8c0354eb-6a3e-4a98-b41c-f8add599884c -t 4 -e /var/spool/cwl/reference_files/brass/ucscHiDepth_0.01_mrg1000_no_exon_coreChrs.bed.gz [SeqWare Pipeline] ERROR [2016/09/20 13:50:00] | The exit value was 25 Command exit code: 1 Output from command: /usr/bin/perl /opt/wtsi-cgp/bin/pindel_input_gen.pl -b /var/lib/cwl/stg33415604-d4eb-49aa-8f81-345b6fb2a6f3/fdcb1bd7cffca69d15383ca9566c58e0.bam -o /var/spool/cwl/0/pindel/tmpPindel/8c0354eb-6a3e-4a98-b41c-f8add599884c -t 4 -e /var/spool/cwl/reference_files/brass/ucscHiDepth_0.01_mrg1000_no_exon_coreChrs.bed.gz Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_cgpPindel_input_70.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_merge_59 Job ID: 379374478 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.e379374478 Updated: Tue Sep 20 13:51:15 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.stderr ----------------------------------------------------------------------- The method 'do_run' exited abnormally so the Runner will terminate here! Return value was: 15 [WARNING] command: seqware bundle launch --dir /home/seqware/CGP-Somatic-Docker/target/Workflow_Bundle_CgpSomaticCore_0.0.0_SeqWare_1.1.1/ --engine whitestar-parallel --ini /var/spool/cwl/workflow.ini --no-metadata exited with code: 15 Error while running job: Error collecting output for parameter 'somatic_cnv_tar_gz': Did not find output file with glob pattern: '['*.somatic.cnv.tar.gz']' [job temp319312608049643386.cwl] completed permanentFail Final process status is permanentFail Workflow error, try again with --debug for more information: Process status is ['permanentFail'] stdout : java.lang.RuntimeException: problems running command: cwltool --enable-dev --non-strict --enable-net --outdir /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/outputs/ --tmpdir-prefix /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/working/ /tmp/1474331255066-0/temp319312608049643386.cwl /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/workflow_params.json -------------- next part -------------- An HTML attachment was scrubbed... URL: From Junjun.Zhang at oicr.on.ca Tue Sep 20 16:09:29 2016 From: Junjun.Zhang at oicr.on.ca (Junjun Zhang) Date: Tue, 20 Sep 2016 20:09:29 +0000 Subject: [DOCKTESTERS] Amazon account In-Reply-To: <27512884B2D81B41AAB7BB266248F240C099E3B6@exmb2.ad.oicr.on.ca> References: <27512884B2D81B41AAB7BB266248F240C099E23C@exmb2.ad.oicr.on.ca> <2C84FF4CF2F0A04EB7691F988A717B47CB65E809@exmb2.ad.oicr.on.ca> <27512884B2D81B41AAB7BB266248F240C099E2A3@exmb2.ad.oicr.on.ca> <27512884B2D81B41AAB7BB266248F240C099E397@exmb2.ad.oicr.on.ca>, , <27512884B2D81B41AAB7BB266248F240C099E3B6@exmb2.ad.oicr.on.ca> Message-ID: <2C84FF4CF2F0A04EB7691F988A717B47CB660030@exmb2.ad.oicr.on.ca> My run failed with same error message. ________________________________ From: Denis Yuen Sent: Tuesday, September 20, 2016 3:20 PM To: Miguel Vazquez Cc: docktesters at lists.icgc.org; Brian O'Connor; Junjun Zhang Subject: RE: [DOCKTESTERS] Amazon account I think there are a few pieces of information that could be useful. Look in this ticket https://github.com/ICGC-TCGA-PanCancer/CGP-Somatic-Docker/issues/5 there's a section that starts with "docker run -i", this will let me see if there's anything obviously strange with the call to Docker. Failing that, I think we'll have to see what exit code 25 denotes for Pindel. ________________________________ From: Miguel Vazquez [mikisvaz at gmail.com] Sent: September 20, 2016 3:15 PM To: Denis Yuen Cc: docktesters at lists.icgc.org; Brian O'Connor; Junjun Zhang Subject: RE: [DOCKTESTERS] Amazon account Well, that's a bummer. Any ideas? On Sep 20, 2016 9:11 PM, "Denis Yuen" > wrote: Hi, That's really just saying that cwltool was unable to find the output. Changing the entry will just save the output somewhere else. The real problem is probably in the section: ---- bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_cgpPindel_input_70.sh Output from command: /usr/bin/perl /opt/wtsi-cgp/bin/pindel_input_gen.pl -b /var/lib/cwl/stg33415604-d4eb-49aa-8f81-345b6fb2a6f3/fdcb1bd7cffca69d15383ca9566c58e0.bam -o /var/spool/cwl/0/pindel/tmpPindel/8c0354eb-6a3e-4a98-b41c-f8add599884c -t 4 -e /var/spool/cwl/reference_files/brass/ucscHiDepth_0.01_mrg1000_no_exon_coreChrs.bed.gz [SeqWare Pipeline] ERROR [2016/09/20 13:50:00] | The exit value was 25 Command exit code: 1 Output from command: /usr/bin/perl /opt/wtsi-cgp/bin/pindel_input_gen.pl -b /var/lib/cwl/stg33415604-d4eb-49aa-8f81-345b6fb2a6f3/fdcb1bd7cffca69d15383ca9566c58e0.bam -o /var/spool/cwl/0/pindel/tmpPindel/8c0354eb-6a3e-4a98-b41c-f8add599884c -t 4 -e /var/spool/cwl/reference_files/brass/ucscHiDepth_0.01_mrg1000_no_exon_coreChrs.bed.gz ---- That says that pindel failed, but there doesn't appear to be any more explanation as to why. Denis Yuen Bioinformatics Software Developer Ontario Institute for Cancer Research MaRS Centre 661 University Avenue Suite 510 Toronto, Ontario, Canada M5G 0A3 Toll-free: 1-866-678-6427 Twitter: @OICR_news www.oicr.on.ca This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization. ________________________________ From: Miguel Vazquez [mikisvaz at gmail.com] Sent: September 20, 2016 2:55 PM To: Junjun Zhang Cc: Denis Yuen; Brian O'Connor; docktesters at lists.icgc.org Subject: Re: [DOCKTESTERS] Amazon account Just a heads up, the process failed. The complete log is bellow, but I think this is the culprit: Error while running job: Error collecting output for parameter 'somatic_cnv_tar_gz': Did not find output file with glob pattern: '['*.somatic.cnv.tar.gz']' I wrote something like this in Dockerstore.json "somatic_cnv_tar_gz": { "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.cnv.tar.gz", "class": "File" } I've replace those entries with this "somatic_cnv_tar_gz": { "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/DONOR.somatic.cnv.tar.gz", "class": "File" } so that the glob work. I'm trying again. I'll update the documentation Best Miguel ------------------ Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_25.stderr ----------------------------------------------------------------------- Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_56.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_54 Job ID: 335639174 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_54.e335639174 Updated: Tue Sep 20 03:55:15 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_54.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_54.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_13 Job ID: 335639178 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_13.e335639178 Updated: Tue Sep 20 12:07:55 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_13.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_13.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_17 Job ID: 335639179 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_17.e335639179 Updated: Tue Sep 20 12:05:07 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_17.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_17.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_15 Job ID: 335639180 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_15.e335639180 ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_48 Job ID: 335639020 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_48.e335639020 Updated: Tue Sep 20 05:54:57 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_48.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_48.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_50 Job ID: 335639025 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_50.e335639025 Updated: Tue Sep 20 04:48:39 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_50.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_50.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_52 Job ID: 335639111 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_52.e335639111 Updated: Tue Sep 20 05:05:25 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_52.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_52.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_56 Job ID: 335639173 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_56.e335639173 Updated: Tue Sep 20 03:39:33 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_56.sh Command exit code: 0 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_34.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_34.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_38 Job ID: 335638783 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_38.e335638783 Updated: Tue Sep 20 06:49:18 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_38.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_38.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_42 Job ID: 335638805 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_42.e335638805 Updated: Tue Sep 20 06:07:49 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_42.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_42.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_46 Job ID: 335638826 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_46.e335638826 Updated: Tue Sep 20 05:40:42 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_46.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_46.stderr ----------------------------------------------------------------------- Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_unpackRef_NA_10.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_22 Job ID: 335638775 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_22.e335638775 Updated: Tue Sep 20 09:32:19 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_22.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_22.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_28 Job ID: 335638776 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_28.e335638776 Updated: Tue Sep 20 08:57:31 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_28.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_28.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_32 Job ID: 335638777 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_32.e335638777 Updated: Tue Sep 20 08:12:44 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_32.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_32.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_34 Job ID: 335638778 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_34.e335638778 Updated: Tue Sep 20 08:24:35 UTC 2016 Job Name: s58_unpackRef_NA_9 Job ID: 331891142 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_unpackRef_NA_9.e331891142 Updated: Tue Sep 20 00:39:16 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_unpackRef_NA_9.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_unpackRef_NA_9.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_verifyBamHomChk_control_6 Job ID: 331891143 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_verifyBamHomChk_control_6.e331891143 Updated: Tue Sep 20 00:44:52 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_verifyBamHomChk_control_6.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_verifyBamHomChk_control_6.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_basFileGenerate_control_11 Job ID: 332292910 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_basFileGenerate_control_11.e332292910 Updated: Tue Sep 20 01:20:39 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_basFileGenerate_control_11.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_basFileGenerate_control_11.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_unpackRef_NA_10 Job ID: 332292911 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_unpackRef_NA_10.e332292911 Updated: Tue Sep 20 00:44:57 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_unpackRef_NA_10.sh Command exit code: 0 Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_start_0.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_start_0.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_mark_start_1 Job ID: 331890603 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_mark_start_1.e331890603 Updated: Tue Sep 20 00:38:10 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_mark_start_1.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_mark_start_1.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_prepBam_control_3 Job ID: 331890831 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_prepBam_control_3.e331890831 Updated: Tue Sep 20 00:38:11 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_prepBam_control_3.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_prepBam_control_3.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_prepBam_tumour_2 Job ID: 331890832 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_prepBam_tumour_2.e331890832 Updated: Tue Sep 20 00:38:11 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_prepBam_tumour_2.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_prepBam_tumour_2.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_61.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_BRASS_input_99 Job ID: 379374477 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_BRASS_input_99.o379374477 Updated: Tue Sep 20 16:49:15 UTC 2016 Contents Excerpt: [V] 18 0.49745MB/s 1781.56 [V] 19 0.525041MB/s 1879.07 [V] 20 0.552722MB/s 1976.44 [V] 21 0.579942MB/s 2072.21 [V] 22 0.607543MB/s 2169.2 [V] 23 0.635118MB/s 2266.04 [V] 24264262 [V] MemUsage(size=71.1484,rss=10.9336,peak=291.977) wall clock time 02:57:24:31175299 11827.06user 310.09system 2:59:40elapsed 112%CPU (0avgtext+0avgdata 4265632maxresident)k 117507424inputs+14421104outputs (84major+234838minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_BRASS_input_99.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_merge_59 Job ID: 379374478 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.o379374478 Updated: Tue Sep 20 13:51:15 UTC 2016 Contents Excerpt: 87.14user 5.10system 1:41.25elapsed 91%CPU (0avgtext+0avgdata 66448maxresident)k 2720952inputs+4360560outputs (5major+7600minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.stdout ----------------------------------------------------------------------- % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 54.9M 100 54.9M 0 0 1016k 0 0:00:55 0:00:55 --:--:-- 1047k % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 174k 100 174k 0 0 174k 0 0:00:01 0:00:01 --:--:-- 567k [2016/09/20 16:49:15] | Output for stderr due to workflow run failure: ----------------------------------------------------------------------- Job Name: s58_start_0 Job ID: 331890362 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_start_0.e331890362 Updated: Tue Sep 20 00:38:10 UTC 2016 Contents Excerpt: File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_renameSampleFile_208.o373317274 Updated: Tue Sep 20 12:08:37 UTC 2016 Contents Excerpt: Modified command: cp /var/spool/cwl/b02b4bba-6e66-44fb-a48f-38c309aaaac5.genotype.tar.gz /var/spool/cwl/b02b4bba-6e66-44fb-a48f-38c309aaaac5.csc_0-0-0.20160920.somatic.genotype.tar.gz Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_renameSampleFile_208.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_57 Job ID: 373317275 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_57.o373317275 Updated: Tue Sep 20 13:29:27 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr23.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.23.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 4798.51user 50.73system 1:20:50elapsed 99%CPU (0avgtext+0avgdata 3115856maxresident)k 9833328inputs+56328outputs (0major+199552minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_57.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_ASCAT_allele_count_60 Job ID: 379374473 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_60.o379374473 Updated: Tue Sep 20 15:34:45 UTC 2016 Contents Excerpt: Errors from command: /opt/wtsi-cgp/bin/alleleCounter -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam -o /var/spool/cwl/0/ascat/tmpAscat/allele_count/b02b4bba-6e66-44fb-a48f-38c309aaaac5.allct -l /var/spool/cwl/reference_files/ascat/SnpLocus.tsv -m 20 5928.09user 101.55system 1:45:10elapsed 95%CPU (0avgtext+0avgdata 2345888maxresident)k 221140208inputs+43144outputs (37major+169349minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_60.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_ASCAT_allele_count_61 Job ID: 379374475 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_61.o379374475 Updated: Tue Sep 20 14:58:41 UTC 2016 Contents Excerpt: Errors from command: /opt/wtsi-cgp/bin/alleleCounter -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam -o /var/spool/cwl/0/ascat/tmpAscat/allele_count/8c0354eb-6a3e-4a98-b41c-f8add599884c.allct -l /var/spool/cwl/reference_files/ascat/SnpLocus.tsv -m 20 3864.82user 67.24system 1:09:07elapsed 94%CPU (0avgtext+0avgdata 2350544maxresident)k 157460240inputs+43120outputs (57major+167795minor)pagefaults 0swaps 11476.37user 140.61system 6:48:23elapsed 47%CPU (0avgtext+0avgdata 3035728maxresident)k 7380072inputs+56816outputs (0major+196640minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_39.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_41 Job ID: 335639489 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_41.o335639489 Updated: Tue Sep 20 07:35:04 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr15.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.15.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 9429.90user 117.09system 5:54:22elapsed 44%CPU (0avgtext+0avgdata 2739152maxresident)k 5273744inputs+51000outputs (0major+177355minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_41.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_45 Job ID: 335639845 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_45.o335639845 Updated: Tue Sep 20 07:29:41 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr17.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.17.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 9231.30user 116.04system 5:49:00elapsed 44%CPU (0avgtext+0avgdata 2540400maxresident)k 5255296inputs+46736outputs (0major+165277minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_45.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_43 Job ID: 335639853 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_43.o335639853 Updated: Tue Sep 20 08:28:45 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr16.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.16.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 11465.31user 146.48system 6:48:03elapsed 47%CPU (0avgtext+0avgdata 2945712maxresident)k 6906080inputs+54432outputs (0major+190932minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_43.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_renameSampleFile_208 Job ID: 373317274 ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_33 Job ID: 335639420 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_33.o335639420 Updated: Tue Sep 20 10:42:41 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr11.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.11.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 18904.62user 233.41system 9:02:00elapsed 58%CPU (0avgtext+0avgdata 4537600maxresident)k 15888800inputs+86400outputs (0major+292553minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_33.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_35 Job ID: 335639430 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_35.o335639430 Updated: Tue Sep 20 10:03:48 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr12.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.12.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 16584.76user 210.26system 8:23:07elapsed 55%CPU (0avgtext+0avgdata 4373600maxresident)k 12917040inputs+82896outputs (0major+281480minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_35.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_37 Job ID: 335639431 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_37.o335639431 Updated: Tue Sep 20 08:26:17 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr13.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.13.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 11361.18user 138.30system 6:45:36elapsed 47%CPU (0avgtext+0avgdata 3301008maxresident)k 7418080inputs+62192outputs (0major+212951minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_37.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_39 Job ID: 335639452 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_39.o335639452 Updated: Tue Sep 20 08:29:04 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr14.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.14.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam Updated: Tue Sep 20 11:02:29 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr7.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.7.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 20088.69user 242.69system 9:21:48elapsed 60%CPU (0avgtext+0avgdata 5281504maxresident)k 18604808inputs+96776outputs (0major+339332minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_25.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_27 Job ID: 335639400 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_27.o335639400 Updated: Tue Sep 20 11:02:53 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr8.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.8.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 20108.48user 243.42system 9:22:11elapsed 60%CPU (0avgtext+0avgdata 5228912maxresident)k 17295080inputs+95440outputs (0major+335764minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_27.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_29 Job ID: 335639401 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_29.o335639401 Updated: Tue Sep 20 09:18:32 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr9.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.9.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 13962.23user 175.03system 7:37:51elapsed 51%CPU (0avgtext+0avgdata 3971872maxresident)k 12246072inputs+72144outputs (0major+255173minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_29.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_31 Job ID: 335639417 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_31.o335639417 Updated: Tue Sep 20 10:11:08 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr10.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.10.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 17052.42user 207.86system 8:30:26elapsed 56%CPU (0avgtext+0avgdata 4504144maxresident)k 13931760inputs+85488outputs (0major+289717minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_31.stdout ----------------------------------------------------------------------- 23593416inputs+121608outputs (0major+421477minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_17.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_15 Job ID: 335639180 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_15.o335639180 Updated: Tue Sep 20 12:08:37 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr2.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.2.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 24021.20user 275.32system 10:27:56elapsed 64%CPU (0avgtext+0avgdata 7851136maxresident)k 24358016inputs+146264outputs (0major+499924minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_15.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_19 Job ID: 335639200 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_19.o335639200 Updated: Tue Sep 20 11:57:43 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr4.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.4.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 23336.68user 273.00system 10:17:02elapsed 63%CPU (0avgtext+0avgdata 6501344maxresident)k 22397816inputs+120192outputs (0major+416448minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_19.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_23 Job ID: 335639375 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_23.o335639375 Updated: Tue Sep 20 11:14:37 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr6.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.6.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 20846.11user 251.83system 9:33:55elapsed 61%CPU (0avgtext+0avgdata 5765024maxresident)k 19462064inputs+106080outputs (0major+369701minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_23.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_25 Job ID: 335639387 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_25.o335639387 ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_56 Job ID: 335639173 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_56.o335639173 Updated: Tue Sep 20 03:39:33 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr22.txt -o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.22.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam 2810.79user 34.33system 1:58:52elapsed 39%CPU (0avgtext+0avgdata 1250144maxresident)k 1243552inputs+22208outputs (0major+82726minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_56.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_54 Job ID: 335639174 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_54.o335639174 Updated: Tue Sep 20 03:55:15 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr21.txt -o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.21.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam 3187.08user 39.68system 2:14:34elapsed 39%CPU (0avgtext+0avgdata 1302656maxresident)k 1689216inputs+23256outputs (0major+86038minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_54.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_58 Job ID: 335639178 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_58.o335639178 Updated: Tue Sep 20 04:41:10 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr23.txt -o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.23.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam 4375.73user 53.14system 3:00:29elapsed 40%CPU (0avgtext+0avgdata 3123136maxresident)k 4325272inputs+56240outputs (0major+199643minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_58.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_17 Job ID: 335639179 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_17.o335639179 Updated: Tue Sep 20 12:05:07 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr3.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.3.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 23819.53user 283.10system 10:24:27elapsed 64%CPU (0avgtext+0avgdata 6576048maxresident)k Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr17.txt -o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.17.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam 5945.65user 71.96system 4:00:01elapsed 41%CPU (0avgtext+0avgdata 2544496maxresident)k 5572568inputs+46720outputs (0major+163875minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_46.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_48 Job ID: 335639020 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_48.o335639020 Updated: Tue Sep 20 05:54:57 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr18.txt -o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.18.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam 6337.11user 77.66system 4:14:16elapsed 42%CPU (0avgtext+0avgdata 2647504maxresident)k 5337616inputs+48704outputs (0major+170347minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_48.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_50 Job ID: 335639025 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_50.o335639025 Updated: Tue Sep 20 04:48:39 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr19.txt -o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.19.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam 4542.91user 55.47system 3:07:58elapsed 40%CPU (0avgtext+0avgdata 1995904maxresident)k 3514080inputs+36192outputs (0major+129470minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_50.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_52 Job ID: 335639111 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_52.o335639111 Updated: Tue Sep 20 05:05:25 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr20.txt -o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.20.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam 4979.15user 61.39system 3:24:44elapsed 41%CPU (0avgtext+0avgdata 2102832maxresident)k 3653168inputs+38272outputs (0major+136206minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_52.stdout ----------------------------------------------------------------------- -6a3e-4a98-b41c-f8add599884c.11.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam 11287.76user 142.04system 6:43:55elapsed 47%CPU (0avgtext+0avgdata 4543376maxresident)k 9747344inputs+86048outputs (0major+289230minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_34.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_38 Job ID: 335638783 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_38.o335638783 Updated: Tue Sep 20 06:49:18 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr13.txt -o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.13.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam 7981.44user 98.27system 5:08:39elapsed 43%CPU (0avgtext+0avgdata 3310512maxresident)k 6948640inputs+62176outputs (7major+211942minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_38.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_42 Job ID: 335638805 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_42.o335638805 Updated: Tue Sep 20 06:07:49 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr15.txt -o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.15.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam 6705.59user 83.09system 4:27:09elapsed 42%CPU (0avgtext+0avgdata 2746816maxresident)k 6146600inputs+50992outputs (0major+176574minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_42.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_46 Job ID: 379374477 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_cgpPindel_input_70.e379374477 Updated: Tue Sep 20 13:50:00 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_cgpPindel_input_70.sh Output from command: /usr/bin/perl /opt/wtsi-cgp/bin/pindel_input_gen.pl -b /var/lib/cwl/stg33415604-d4eb-49aa-8f81-345b6fb2a6f3/fdcb1bd7cffca69d15383ca9566c58e0.bam -o /var/spool/cwl/0/pindel/tmpPindel/8c0354eb-6a3e-4a98-b41c-f8add599884c -t 4 -e /var/spool/cwl/reference_files/brass/ucscHiDepth_0.01_mrg1000_no_exon_coreChrs.bed.gz [SeqWare Pipeline] ERROR [2016/09/20 13:50:00] | The exit value was 25 Command exit code: 1 Output from command: /usr/bin/perl /opt/wtsi-cgp/bin/pindel_input_gen.pl -b /var/lib/cwl/stg33415604-d4eb-49aa-8f81-345b6fb2a6f3/fdcb1bd7cffca69d15383ca9566c58e0.bam -o /var/spool/cwl/0/pindel/tmpPindel/8c0354eb-6a3e-4a98-b41c-f8add599884c -t 4 -e /var/spool/cwl/reference_files/brass/ucscHiDepth_0.01_mrg1000_no_exon_coreChrs.bed.gz Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_cgpPindel_input_70.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_merge_59 Job ID: 379374478 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.e379374478 Updated: Tue Sep 20 13:51:15 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.stderr ----------------------------------------------------------------------- The method 'do_run' exited abnormally so the Runner will terminate here! Return value was: 15 [WARNING] command: seqware bundle launch --dir /home/seqware/CGP-Somatic-Docker/target/Workflow_Bundle_CgpSomaticCore_0.0.0_SeqWare_1.1.1/ --engine whitestar-parallel --ini /var/spool/cwl/workflow.ini --no-metadata exited with code: 15 Error while running job: Error collecting output for parameter 'somatic_cnv_tar_gz': Did not find output file with glob pattern: '['*.somatic.cnv.tar.gz']' [job temp319312608049643386.cwl] completed permanentFail Final process status is permanentFail Workflow error, try again with --debug for more information: Process status is ['permanentFail'] stdout : java.lang.RuntimeException: problems running command: cwltool --enable-dev --non-strict --enable-net --outdir /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/outputs/ --tmpdir-prefix /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/working/ /tmp/1474331255066-0/temp319312608049643386.cwl /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/workflow_params.json ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ f f: command not found ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ df Filesystem 1K-blocks Used Available Use% Mounted on udev 62947280 12 62947268 1% /dev tmpfs 12590448 364 12590084 1% /run /dev/xvda1 8115168 6093092 1586800 80% / none 4 0 4 0% /sys/fs/cgroup none 5120 0 5120 0% /run/lock none 62952228 0 62952228 0% /run/shm none 102400 0 102400 0% /run/user /dev/xvdb 1031992064 303267080 676279800 31% /mnt/1TB ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ df -h Filesystem Size Used Avail Use% Mounted on udev 61G 12K 61G 1% /dev tmpfs 13G 364K 13G 1% /run /dev/xvda1 7.8G 5.9G 1.6G 80% / none 4.0K 0 4.0K 0% /sys/fs/cgroup none 5.0M 0 5.0M 0% /run/lock none 61G 0 61G 0% /run/shm none 100M 0 100M 0% /run/user /dev/xvdb 985G 290G 645G 31% /mnt/1TB ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ vi Dockstore.json { "bbFrom": { "bbFrom": { "path": "https://s3-eu-west-1.amazonaws.com/wtsi-pancancer/reference/GRCh37d5_battenberg.tar.gz", "class": "File" }, "refFrom": { "path": "https://s3-eu-west-1.amazonaws.com/wtsi-pancancer/reference/GRCh37d5_CGP_refBundle.tar.gz", "class": "File" }, "tumor": { "path": "/home/ubuntu/DockerTest-Miguel/data/7875b5196f6b8b52847f99bf370aada0.bam", "class": "File" }, "normal": { "path": "/home/ubuntu/DockerTest-Miguel/data/fdcb1bd7cffca69d15383ca9566c58e0.bam", "class": "File" }, "somatic_sv_tar_gz": { "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.sv.tar.gz", "class": "File" }, "somatic_snv_mnv_tar_gz": { "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.snv.mnv.tar.gz", "class": "File" }, "somatic_verifyBamId_tar_gz": { "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.verifyBamId.tar.gz", "class": "File" }, "somatic_cnv_tar_gz": { "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.cnv.tar.gz", "class": "File" }, "somatic_imputeCounts_tar_gz": { "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.imputeCounts.tar.gz", "class": "File" }, "somatic_genotype_tar_gz": { "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.genotype.tar.gz", "class": "File" }, "somatic_indel_tar_gz": { "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.indel.tar.gz", "class": "File" } } ~ ~ ~ ~ ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ l results/ ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ vi Dockstore.json ^C Updated: Tue Sep 20 13:51:15 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.stderr ----------------------------------------------------------------------- The method 'do_run' exited abnormally so the Runner will terminate here! Return value was: 15 [WARNING] command: seqware bundle launch --dir /home/seqware/CGP-Somatic-Docker/target/Workflow_Bundle_CgpSomaticCore_0.0.0_SeqWare_1.1.1/ --engine whitestar-parallel --ini /var/spool/cwl/workflow.ini --no-metadata exited with code: 15 Error while running job: Error collecting output for parameter 'somatic_cnv_tar_gz': Did not find output file with glob pattern: '['*.somatic.cnv.tar.gz']' [job temp319312608049643386.cwl] completed permanentFail Final process status is permanentFail Workflow error, try again with --debug for more information: Process status is ['permanentFail'] stdout : java.lang.RuntimeException: problems running command: cwltool --enable-dev --non-strict --enable-net --outdir /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/outputs/ --tmpdir-prefix /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/working/ /tmp/1474331255066-0/temp319312608049643386.cwl /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/workflow_params.json ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ f f: command not found ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ df Filesystem 1K-blocks Used Available Use% Mounted on udev 62947280 12 62947268 1% /dev tmpfs 12590448 364 12590084 1% /run /dev/xvda1 8115168 6093092 1586800 80% / none 4 0 4 0% /sys/fs/cgroup none 5120 0 5120 0% /run/lock none 62952228 0 62952228 0% /run/shm none 102400 0 102400 0% /run/user /dev/xvdb 1031992064 303267080 676279800 31% /mnt/1TB ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ df -h Filesystem Size Used Avail Use% Mounted on udev 61G 12K 61G 1% /dev tmpfs 13G 364K 13G 1% /run /dev/xvda1 7.8G 5.9G 1.6G 80% / none 4.0K 0 4.0K 0% /sys/fs/cgroup none 5.0M 0 5.0M 0% /run/lock none 61G 0 61G 0% /run/shm none 100M 0 100M 0% /run/user /dev/xvdb 985G 290G 645G 31% /mnt/1TB ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ vi Dockstore.json { Output from command: /opt/wtsi-cgp/bin/alleleCounter -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam -o /var/spool/cwl/0/ascat/tmpAscat/allele_count/b02b4bba-6e66-44fb-a48f-38c309aaaac5.allct -l /var/spool/cwl/reference_files/ascat/SnpLocus.tsv -m 20 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_60.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_ASCAT_allele_count_61 Job ID: 379374475 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_61.e379374475 Updated: Tue Sep 20 14:58:41 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_61.sh Command exit code: 0 Output from command: /opt/wtsi-cgp/bin/alleleCounter -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam -o /var/spool/cwl/0/ascat/tmpAscat/allele_count/8c0354eb-6a3e-4a98-b41c-f8add599884c.allct -l /var/spool/cwl/reference_files/ascat/SnpLocus.tsv -m 20 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_61.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_cgpPindel_input_70 Job ID: 379374477 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_cgpPindel_input_70.e379374477 Updated: Tue Sep 20 13:50:00 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_cgpPindel_input_70.sh Output from command: /usr/bin/perl /opt/wtsi-cgp/bin/pindel_input_gen.pl -b /var/lib/cwl/stg33415604-d4eb-49aa-8f81-345b6fb2a6f3/fdcb1bd7cffca69d15383ca9566c58e0.bam -o /var/spool/cwl/0/pindel/tmpPindel/8c0354eb-6a3e-4a98-b41c-f8add599884c -t 4 -e /var/spool/cwl/reference_files/brass/ucscHiDepth_0.01_mrg1000_no_exon_coreChrs.bed.gz [SeqWare Pipeline] ERROR [2016/09/20 13:50:00] | The exit value was 25 Command exit code: 1 Output from command: /usr/bin/perl /opt/wtsi-cgp/bin/pindel_input_gen.pl -b /var/lib/cwl/stg33415604-d4eb-49aa-8f81-345b6fb2a6f3/fdcb1bd7cffca69d15383ca9566c58e0.bam -o /var/spool/cwl/0/pindel/tmpPindel/8c0354eb-6a3e-4a98-b41c-f8add599884c -t 4 -e /var/spool/cwl/reference_files/brass/ucscHiDepth_0.01_mrg1000_no_exon_coreChrs.bed.gz Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_cgpPindel_input_70.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_merge_59 Job ID: 379374478 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.e379374478 Updated: Tue Sep 20 13:51:15 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.stderr ----------------------------------------------------------------------- The method 'do_run' exited abnormally so the Runner will terminate here! Return value was: 15 [WARNING] command: seqware bundle launch --dir /home/seqware/CGP-Somatic-Docker/target/Workflow_Bundle_CgpSomaticCore_0.0.0_SeqWare_1.1.1/ --engine whitestar-parallel --ini /var/spool/cwl/workflow.ini --no-metadata exited with code: 15 Error while running job: Error collecting output for parameter 'somatic_cnv_tar_gz': Did not find output file with glob pattern: '['*.somatic.cnv.tar.gz']' [job temp319312608049643386.cwl] completed permanentFail Final process status is permanentFail Workflow error, try again with --debug for more information: Process status is ['permanentFail'] stdout : java.lang.RuntimeException: problems running command: cwltool --enable-dev --non-strict --enable-net --outdir /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/outputs/ --tmpdir-prefix /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/working/ /tmp/1474331255066-0/temp319312608049643386.cwl /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/workflow_params.json -------------- next part -------------- An HTML attachment was scrubbed... URL: From Denis.Yuen at oicr.on.ca Wed Sep 21 10:15:00 2016 From: Denis.Yuen at oicr.on.ca (Denis Yuen) Date: Wed, 21 Sep 2016 14:15:00 +0000 Subject: [DOCKTESTERS] Amazon account In-Reply-To: <2C84FF4CF2F0A04EB7691F988A717B47CB660030@exmb2.ad.oicr.on.ca> References: <27512884B2D81B41AAB7BB266248F240C099E23C@exmb2.ad.oicr.on.ca> <2C84FF4CF2F0A04EB7691F988A717B47CB65E809@exmb2.ad.oicr.on.ca> <27512884B2D81B41AAB7BB266248F240C099E2A3@exmb2.ad.oicr.on.ca> <27512884B2D81B41AAB7BB266248F240C099E397@exmb2.ad.oicr.on.ca>, , <27512884B2D81B41AAB7BB266248F240C099E3B6@exmb2.ad.oicr.on.ca>, <2C84FF4CF2F0A04EB7691F988A717B47CB660030@exmb2.ad.oicr.on.ca> Message-ID: <27512884B2D81B41AAB7BB266248F240C099E3F9@exmb2.ad.oicr.on.ca> Hi, One additional thought. Before investigating error code 25, try running the test data https://github.com/ICGC-TCGA-PanCancer/CGP-Somatic-Docker/blob/develop/test1.json This can help us narrow down whether there is an issue with the environment or whether there is an issue with the data. The test data can be downloaded from the link documented at https://github.com/ICGC-TCGA-PanCancer/CGP-Somatic-Docker#running-with-the-dockstore-command-line Also a reminder to send the output starting with "docker run -i", this will let me see if there's anything obviously strange with the call to Docker. Denis Yuen Bioinformatics Software Developer Ontario Institute for Cancer Research MaRS Centre 661 University Avenue Suite 510 Toronto, Ontario, Canada M5G 0A3 Toll-free: 1-866-678-6427 Twitter: @OICR_news www.oicr.on.ca This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization. ________________________________ From: Junjun Zhang Sent: September 20, 2016 4:09 PM To: Denis Yuen; Miguel Vazquez Cc: docktesters at lists.icgc.org; Brian O'Connor Subject: RE: [DOCKTESTERS] Amazon account My run failed with same error message. ________________________________ From: Denis Yuen Sent: Tuesday, September 20, 2016 3:20 PM To: Miguel Vazquez Cc: docktesters at lists.icgc.org; Brian O'Connor; Junjun Zhang Subject: RE: [DOCKTESTERS] Amazon account I think there are a few pieces of information that could be useful. Look in this ticket https://github.com/ICGC-TCGA-PanCancer/CGP-Somatic-Docker/issues/5 there's a section that starts with "docker run -i", this will let me see if there's anything obviously strange with the call to Docker. Failing that, I think we'll have to see what exit code 25 denotes for Pindel. ________________________________ From: Miguel Vazquez [mikisvaz at gmail.com] Sent: September 20, 2016 3:15 PM To: Denis Yuen Cc: docktesters at lists.icgc.org; Brian O'Connor; Junjun Zhang Subject: RE: [DOCKTESTERS] Amazon account Well, that's a bummer. Any ideas? On Sep 20, 2016 9:11 PM, "Denis Yuen" > wrote: Hi, That's really just saying that cwltool was unable to find the output. Changing the entry will just save the output somewhere else. The real problem is probably in the section: ---- bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_cgpPindel_input_70.sh Output from command: /usr/bin/perl /opt/wtsi-cgp/bin/pindel_input_gen.pl -b /var/lib/cwl/stg33415604-d4eb-49aa-8f81-345b6fb2a6f3/fdcb1bd7cffca69d15383ca9566c58e0.bam -o /var/spool/cwl/0/pindel/tmpPindel/8c0354eb-6a3e-4a98-b41c-f8add599884c -t 4 -e /var/spool/cwl/reference_files/brass/ucscHiDepth_0.01_mrg1000_no_exon_coreChrs.bed.gz [SeqWare Pipeline] ERROR [2016/09/20 13:50:00] | The exit value was 25 Command exit code: 1 Output from command: /usr/bin/perl /opt/wtsi-cgp/bin/pindel_input_gen.pl -b /var/lib/cwl/stg33415604-d4eb-49aa-8f81-345b6fb2a6f3/fdcb1bd7cffca69d15383ca9566c58e0.bam -o /var/spool/cwl/0/pindel/tmpPindel/8c0354eb-6a3e-4a98-b41c-f8add599884c -t 4 -e /var/spool/cwl/reference_files/brass/ucscHiDepth_0.01_mrg1000_no_exon_coreChrs.bed.gz ---- That says that pindel failed, but there doesn't appear to be any more explanation as to why. Denis Yuen Bioinformatics Software Developer Ontario Institute for Cancer Research MaRS Centre 661 University Avenue Suite 510 Toronto, Ontario, Canada M5G 0A3 Toll-free: 1-866-678-6427 Twitter: @OICR_news www.oicr.on.ca This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization. ________________________________ From: Miguel Vazquez [mikisvaz at gmail.com] Sent: September 20, 2016 2:55 PM To: Junjun Zhang Cc: Denis Yuen; Brian O'Connor; docktesters at lists.icgc.org Subject: Re: [DOCKTESTERS] Amazon account Just a heads up, the process failed. The complete log is bellow, but I think this is the culprit: Error while running job: Error collecting output for parameter 'somatic_cnv_tar_gz': Did not find output file with glob pattern: '['*.somatic.cnv.tar.gz']' I wrote something like this in Dockerstore.json "somatic_cnv_tar_gz": { "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.cnv.tar.gz", "class": "File" } I've replace those entries with this "somatic_cnv_tar_gz": { "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/DONOR.somatic.cnv.tar.gz", "class": "File" } so that the glob work. I'm trying again. I'll update the documentation Best Miguel ------------------ Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_25.stderr ----------------------------------------------------------------------- Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_56.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_54 Job ID: 335639174 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_54.e335639174 Updated: Tue Sep 20 03:55:15 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_54.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_54.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_13 Job ID: 335639178 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_13.e335639178 Updated: Tue Sep 20 12:07:55 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_13.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_13.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_17 Job ID: 335639179 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_17.e335639179 Updated: Tue Sep 20 12:05:07 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_17.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_17.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_15 Job ID: 335639180 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_15.e335639180 ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_48 Job ID: 335639020 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_48.e335639020 Updated: Tue Sep 20 05:54:57 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_48.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_48.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_50 Job ID: 335639025 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_50.e335639025 Updated: Tue Sep 20 04:48:39 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_50.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_50.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_52 Job ID: 335639111 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_52.e335639111 Updated: Tue Sep 20 05:05:25 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_52.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_52.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_56 Job ID: 335639173 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_56.e335639173 Updated: Tue Sep 20 03:39:33 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_56.sh Command exit code: 0 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_34.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_34.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_38 Job ID: 335638783 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_38.e335638783 Updated: Tue Sep 20 06:49:18 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_38.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_38.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_42 Job ID: 335638805 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_42.e335638805 Updated: Tue Sep 20 06:07:49 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_42.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_42.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_46 Job ID: 335638826 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_46.e335638826 Updated: Tue Sep 20 05:40:42 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_46.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_46.stderr ----------------------------------------------------------------------- Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_unpackRef_NA_10.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_22 Job ID: 335638775 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_22.e335638775 Updated: Tue Sep 20 09:32:19 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_22.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_22.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_28 Job ID: 335638776 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_28.e335638776 Updated: Tue Sep 20 08:57:31 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_28.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_28.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_32 Job ID: 335638777 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_32.e335638777 Updated: Tue Sep 20 08:12:44 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_32.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_32.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_34 Job ID: 335638778 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_34.e335638778 Updated: Tue Sep 20 08:24:35 UTC 2016 Job Name: s58_unpackRef_NA_9 Job ID: 331891142 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_unpackRef_NA_9.e331891142 Updated: Tue Sep 20 00:39:16 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_unpackRef_NA_9.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_unpackRef_NA_9.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_verifyBamHomChk_control_6 Job ID: 331891143 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_verifyBamHomChk_control_6.e331891143 Updated: Tue Sep 20 00:44:52 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_verifyBamHomChk_control_6.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_verifyBamHomChk_control_6.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_basFileGenerate_control_11 Job ID: 332292910 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_basFileGenerate_control_11.e332292910 Updated: Tue Sep 20 01:20:39 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_basFileGenerate_control_11.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_basFileGenerate_control_11.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_unpackRef_NA_10 Job ID: 332292911 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_unpackRef_NA_10.e332292911 Updated: Tue Sep 20 00:44:57 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_unpackRef_NA_10.sh Command exit code: 0 Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_start_0.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_start_0.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_mark_start_1 Job ID: 331890603 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_mark_start_1.e331890603 Updated: Tue Sep 20 00:38:10 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_mark_start_1.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_mark_start_1.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_prepBam_control_3 Job ID: 331890831 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_prepBam_control_3.e331890831 Updated: Tue Sep 20 00:38:11 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_prepBam_control_3.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_prepBam_control_3.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_prepBam_tumour_2 Job ID: 331890832 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_prepBam_tumour_2.e331890832 Updated: Tue Sep 20 00:38:11 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_prepBam_tumour_2.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_prepBam_tumour_2.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_61.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_BRASS_input_99 Job ID: 379374477 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_BRASS_input_99.o379374477 Updated: Tue Sep 20 16:49:15 UTC 2016 Contents Excerpt: [V] 18 0.49745MB/s 1781.56 [V] 19 0.525041MB/s 1879.07 [V] 20 0.552722MB/s 1976.44 [V] 21 0.579942MB/s 2072.21 [V] 22 0.607543MB/s 2169.2 [V] 23 0.635118MB/s 2266.04 [V] 24264262 [V] MemUsage(size=71.1484,rss=10.9336,peak=291.977) wall clock time 02:57:24:31175299 11827.06user 310.09system 2:59:40elapsed 112%CPU (0avgtext+0avgdata 4265632maxresident)k 117507424inputs+14421104outputs (84major+234838minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_BRASS_input_99.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_merge_59 Job ID: 379374478 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.o379374478 Updated: Tue Sep 20 13:51:15 UTC 2016 Contents Excerpt: 87.14user 5.10system 1:41.25elapsed 91%CPU (0avgtext+0avgdata 66448maxresident)k 2720952inputs+4360560outputs (5major+7600minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.stdout ----------------------------------------------------------------------- % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 54.9M 100 54.9M 0 0 1016k 0 0:00:55 0:00:55 --:--:-- 1047k % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 174k 100 174k 0 0 174k 0 0:00:01 0:00:01 --:--:-- 567k [2016/09/20 16:49:15] | Output for stderr due to workflow run failure: ----------------------------------------------------------------------- Job Name: s58_start_0 Job ID: 331890362 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_start_0.e331890362 Updated: Tue Sep 20 00:38:10 UTC 2016 Contents Excerpt: File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_renameSampleFile_208.o373317274 Updated: Tue Sep 20 12:08:37 UTC 2016 Contents Excerpt: Modified command: cp /var/spool/cwl/b02b4bba-6e66-44fb-a48f-38c309aaaac5.genotype.tar.gz /var/spool/cwl/b02b4bba-6e66-44fb-a48f-38c309aaaac5.csc_0-0-0.20160920.somatic.genotype.tar.gz Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_renameSampleFile_208.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_57 Job ID: 373317275 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_57.o373317275 Updated: Tue Sep 20 13:29:27 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr23.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.23.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 4798.51user 50.73system 1:20:50elapsed 99%CPU (0avgtext+0avgdata 3115856maxresident)k 9833328inputs+56328outputs (0major+199552minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_57.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_ASCAT_allele_count_60 Job ID: 379374473 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_60.o379374473 Updated: Tue Sep 20 15:34:45 UTC 2016 Contents Excerpt: Errors from command: /opt/wtsi-cgp/bin/alleleCounter -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam -o /var/spool/cwl/0/ascat/tmpAscat/allele_count/b02b4bba-6e66-44fb-a48f-38c309aaaac5.allct -l /var/spool/cwl/reference_files/ascat/SnpLocus.tsv -m 20 5928.09user 101.55system 1:45:10elapsed 95%CPU (0avgtext+0avgdata 2345888maxresident)k 221140208inputs+43144outputs (37major+169349minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_60.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_ASCAT_allele_count_61 Job ID: 379374475 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_61.o379374475 Updated: Tue Sep 20 14:58:41 UTC 2016 Contents Excerpt: Errors from command: /opt/wtsi-cgp/bin/alleleCounter -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam -o /var/spool/cwl/0/ascat/tmpAscat/allele_count/8c0354eb-6a3e-4a98-b41c-f8add599884c.allct -l /var/spool/cwl/reference_files/ascat/SnpLocus.tsv -m 20 3864.82user 67.24system 1:09:07elapsed 94%CPU (0avgtext+0avgdata 2350544maxresident)k 157460240inputs+43120outputs (57major+167795minor)pagefaults 0swaps 11476.37user 140.61system 6:48:23elapsed 47%CPU (0avgtext+0avgdata 3035728maxresident)k 7380072inputs+56816outputs (0major+196640minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_39.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_41 Job ID: 335639489 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_41.o335639489 Updated: Tue Sep 20 07:35:04 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr15.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.15.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 9429.90user 117.09system 5:54:22elapsed 44%CPU (0avgtext+0avgdata 2739152maxresident)k 5273744inputs+51000outputs (0major+177355minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_41.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_45 Job ID: 335639845 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_45.o335639845 Updated: Tue Sep 20 07:29:41 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr17.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.17.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 9231.30user 116.04system 5:49:00elapsed 44%CPU (0avgtext+0avgdata 2540400maxresident)k 5255296inputs+46736outputs (0major+165277minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_45.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_43 Job ID: 335639853 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_43.o335639853 Updated: Tue Sep 20 08:28:45 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr16.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.16.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 11465.31user 146.48system 6:48:03elapsed 47%CPU (0avgtext+0avgdata 2945712maxresident)k 6906080inputs+54432outputs (0major+190932minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_43.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_renameSampleFile_208 Job ID: 373317274 ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_33 Job ID: 335639420 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_33.o335639420 Updated: Tue Sep 20 10:42:41 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr11.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.11.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 18904.62user 233.41system 9:02:00elapsed 58%CPU (0avgtext+0avgdata 4537600maxresident)k 15888800inputs+86400outputs (0major+292553minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_33.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_35 Job ID: 335639430 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_35.o335639430 Updated: Tue Sep 20 10:03:48 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr12.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.12.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 16584.76user 210.26system 8:23:07elapsed 55%CPU (0avgtext+0avgdata 4373600maxresident)k 12917040inputs+82896outputs (0major+281480minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_35.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_37 Job ID: 335639431 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_37.o335639431 Updated: Tue Sep 20 08:26:17 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr13.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.13.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 11361.18user 138.30system 6:45:36elapsed 47%CPU (0avgtext+0avgdata 3301008maxresident)k 7418080inputs+62192outputs (0major+212951minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_37.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_39 Job ID: 335639452 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_39.o335639452 Updated: Tue Sep 20 08:29:04 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr14.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.14.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam Updated: Tue Sep 20 11:02:29 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr7.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.7.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 20088.69user 242.69system 9:21:48elapsed 60%CPU (0avgtext+0avgdata 5281504maxresident)k 18604808inputs+96776outputs (0major+339332minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_25.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_27 Job ID: 335639400 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_27.o335639400 Updated: Tue Sep 20 11:02:53 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr8.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.8.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 20108.48user 243.42system 9:22:11elapsed 60%CPU (0avgtext+0avgdata 5228912maxresident)k 17295080inputs+95440outputs (0major+335764minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_27.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_29 Job ID: 335639401 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_29.o335639401 Updated: Tue Sep 20 09:18:32 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr9.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.9.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 13962.23user 175.03system 7:37:51elapsed 51%CPU (0avgtext+0avgdata 3971872maxresident)k 12246072inputs+72144outputs (0major+255173minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_29.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_31 Job ID: 335639417 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_31.o335639417 Updated: Tue Sep 20 10:11:08 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr10.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.10.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 17052.42user 207.86system 8:30:26elapsed 56%CPU (0avgtext+0avgdata 4504144maxresident)k 13931760inputs+85488outputs (0major+289717minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_31.stdout ----------------------------------------------------------------------- 23593416inputs+121608outputs (0major+421477minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_17.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_15 Job ID: 335639180 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_15.o335639180 Updated: Tue Sep 20 12:08:37 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr2.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.2.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 24021.20user 275.32system 10:27:56elapsed 64%CPU (0avgtext+0avgdata 7851136maxresident)k 24358016inputs+146264outputs (0major+499924minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_15.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_19 Job ID: 335639200 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_19.o335639200 Updated: Tue Sep 20 11:57:43 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr4.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.4.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 23336.68user 273.00system 10:17:02elapsed 63%CPU (0avgtext+0avgdata 6501344maxresident)k 22397816inputs+120192outputs (0major+416448minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_19.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_23 Job ID: 335639375 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_23.o335639375 Updated: Tue Sep 20 11:14:37 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr6.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.6.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 20846.11user 251.83system 9:33:55elapsed 61%CPU (0avgtext+0avgdata 5765024maxresident)k 19462064inputs+106080outputs (0major+369701minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_23.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_25 Job ID: 335639387 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_25.o335639387 ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_56 Job ID: 335639173 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_56.o335639173 Updated: Tue Sep 20 03:39:33 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr22.txt -o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.22.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam 2810.79user 34.33system 1:58:52elapsed 39%CPU (0avgtext+0avgdata 1250144maxresident)k 1243552inputs+22208outputs (0major+82726minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_56.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_54 Job ID: 335639174 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_54.o335639174 Updated: Tue Sep 20 03:55:15 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr21.txt -o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.21.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam 3187.08user 39.68system 2:14:34elapsed 39%CPU (0avgtext+0avgdata 1302656maxresident)k 1689216inputs+23256outputs (0major+86038minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_54.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_58 Job ID: 335639178 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_58.o335639178 Updated: Tue Sep 20 04:41:10 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr23.txt -o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.23.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam 4375.73user 53.14system 3:00:29elapsed 40%CPU (0avgtext+0avgdata 3123136maxresident)k 4325272inputs+56240outputs (0major+199643minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_58.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_tumour_17 Job ID: 335639179 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_17.o335639179 Updated: Tue Sep 20 12:05:07 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr3.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.3.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam 23819.53user 283.10system 10:24:27elapsed 64%CPU (0avgtext+0avgdata 6576048maxresident)k Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr17.txt -o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.17.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam 5945.65user 71.96system 4:00:01elapsed 41%CPU (0avgtext+0avgdata 2544496maxresident)k 5572568inputs+46720outputs (0major+163875minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_46.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_48 Job ID: 335639020 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_48.o335639020 Updated: Tue Sep 20 05:54:57 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr18.txt -o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.18.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam 6337.11user 77.66system 4:14:16elapsed 42%CPU (0avgtext+0avgdata 2647504maxresident)k 5337616inputs+48704outputs (0major+170347minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_48.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_50 Job ID: 335639025 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_50.o335639025 Updated: Tue Sep 20 04:48:39 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr19.txt -o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.19.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam 4542.91user 55.47system 3:07:58elapsed 40%CPU (0avgtext+0avgdata 1995904maxresident)k 3514080inputs+36192outputs (0major+129470minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_50.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_52 Job ID: 335639111 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_52.o335639111 Updated: Tue Sep 20 05:05:25 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr20.txt -o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.20.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam 4979.15user 61.39system 3:24:44elapsed 41%CPU (0avgtext+0avgdata 2102832maxresident)k 3653168inputs+38272outputs (0major+136206minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_52.stdout ----------------------------------------------------------------------- -6a3e-4a98-b41c-f8add599884c.11.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam 11287.76user 142.04system 6:43:55elapsed 47%CPU (0avgtext+0avgdata 4543376maxresident)k 9747344inputs+86048outputs (0major+289230minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_34.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_38 Job ID: 335638783 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_38.o335638783 Updated: Tue Sep 20 06:49:18 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr13.txt -o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.13.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam 7981.44user 98.27system 5:08:39elapsed 43%CPU (0avgtext+0avgdata 3310512maxresident)k 6948640inputs+62176outputs (7major+211942minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_38.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_42 Job ID: 335638805 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_42.o335638805 Updated: Tue Sep 20 06:07:49 UTC 2016 Contents Excerpt: Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr15.txt -o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.15.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam 6705.59user 83.09system 4:27:09elapsed 42%CPU (0avgtext+0avgdata 2746816maxresident)k 6146600inputs+50992outputs (0major+176574minor)pagefaults 0swaps Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_42.stdout ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_control_46 Job ID: 379374477 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_cgpPindel_input_70.e379374477 Updated: Tue Sep 20 13:50:00 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_cgpPindel_input_70.sh Output from command: /usr/bin/perl /opt/wtsi-cgp/bin/pindel_input_gen.pl -b /var/lib/cwl/stg33415604-d4eb-49aa-8f81-345b6fb2a6f3/fdcb1bd7cffca69d15383ca9566c58e0.bam -o /var/spool/cwl/0/pindel/tmpPindel/8c0354eb-6a3e-4a98-b41c-f8add599884c -t 4 -e /var/spool/cwl/reference_files/brass/ucscHiDepth_0.01_mrg1000_no_exon_coreChrs.bed.gz [SeqWare Pipeline] ERROR [2016/09/20 13:50:00] | The exit value was 25 Command exit code: 1 Output from command: /usr/bin/perl /opt/wtsi-cgp/bin/pindel_input_gen.pl -b /var/lib/cwl/stg33415604-d4eb-49aa-8f81-345b6fb2a6f3/fdcb1bd7cffca69d15383ca9566c58e0.bam -o /var/spool/cwl/0/pindel/tmpPindel/8c0354eb-6a3e-4a98-b41c-f8add599884c -t 4 -e /var/spool/cwl/reference_files/brass/ucscHiDepth_0.01_mrg1000_no_exon_coreChrs.bed.gz Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_cgpPindel_input_70.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_merge_59 Job ID: 379374478 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.e379374478 Updated: Tue Sep 20 13:51:15 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.stderr ----------------------------------------------------------------------- The method 'do_run' exited abnormally so the Runner will terminate here! Return value was: 15 [WARNING] command: seqware bundle launch --dir /home/seqware/CGP-Somatic-Docker/target/Workflow_Bundle_CgpSomaticCore_0.0.0_SeqWare_1.1.1/ --engine whitestar-parallel --ini /var/spool/cwl/workflow.ini --no-metadata exited with code: 15 Error while running job: Error collecting output for parameter 'somatic_cnv_tar_gz': Did not find output file with glob pattern: '['*.somatic.cnv.tar.gz']' [job temp319312608049643386.cwl] completed permanentFail Final process status is permanentFail Workflow error, try again with --debug for more information: Process status is ['permanentFail'] stdout : java.lang.RuntimeException: problems running command: cwltool --enable-dev --non-strict --enable-net --outdir /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/outputs/ --tmpdir-prefix /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/working/ /tmp/1474331255066-0/temp319312608049643386.cwl /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/workflow_params.json ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ f f: command not found ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ df Filesystem 1K-blocks Used Available Use% Mounted on udev 62947280 12 62947268 1% /dev tmpfs 12590448 364 12590084 1% /run /dev/xvda1 8115168 6093092 1586800 80% / none 4 0 4 0% /sys/fs/cgroup none 5120 0 5120 0% /run/lock none 62952228 0 62952228 0% /run/shm none 102400 0 102400 0% /run/user /dev/xvdb 1031992064 303267080 676279800 31% /mnt/1TB ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ df -h Filesystem Size Used Avail Use% Mounted on udev 61G 12K 61G 1% /dev tmpfs 13G 364K 13G 1% /run /dev/xvda1 7.8G 5.9G 1.6G 80% / none 4.0K 0 4.0K 0% /sys/fs/cgroup none 5.0M 0 5.0M 0% /run/lock none 61G 0 61G 0% /run/shm none 100M 0 100M 0% /run/user /dev/xvdb 985G 290G 645G 31% /mnt/1TB ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ vi Dockstore.json { "bbFrom": { "bbFrom": { "path": "https://s3-eu-west-1.amazonaws.com/wtsi-pancancer/reference/GRCh37d5_battenberg.tar.gz", "class": "File" }, "refFrom": { "path": "https://s3-eu-west-1.amazonaws.com/wtsi-pancancer/reference/GRCh37d5_CGP_refBundle.tar.gz", "class": "File" }, "tumor": { "path": "/home/ubuntu/DockerTest-Miguel/data/7875b5196f6b8b52847f99bf370aada0.bam", "class": "File" }, "normal": { "path": "/home/ubuntu/DockerTest-Miguel/data/fdcb1bd7cffca69d15383ca9566c58e0.bam", "class": "File" }, "somatic_sv_tar_gz": { "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.sv.tar.gz", "class": "File" }, "somatic_snv_mnv_tar_gz": { "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.snv.mnv.tar.gz", "class": "File" }, "somatic_verifyBamId_tar_gz": { "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.verifyBamId.tar.gz", "class": "File" }, "somatic_cnv_tar_gz": { "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.cnv.tar.gz", "class": "File" }, "somatic_imputeCounts_tar_gz": { "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.imputeCounts.tar.gz", "class": "File" }, "somatic_genotype_tar_gz": { "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.genotype.tar.gz", "class": "File" }, "somatic_indel_tar_gz": { "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.indel.tar.gz", "class": "File" } } ~ ~ ~ ~ ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ l results/ ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ vi Dockstore.json ^C Updated: Tue Sep 20 13:51:15 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.stderr ----------------------------------------------------------------------- The method 'do_run' exited abnormally so the Runner will terminate here! Return value was: 15 [WARNING] command: seqware bundle launch --dir /home/seqware/CGP-Somatic-Docker/target/Workflow_Bundle_CgpSomaticCore_0.0.0_SeqWare_1.1.1/ --engine whitestar-parallel --ini /var/spool/cwl/workflow.ini --no-metadata exited with code: 15 Error while running job: Error collecting output for parameter 'somatic_cnv_tar_gz': Did not find output file with glob pattern: '['*.somatic.cnv.tar.gz']' [job temp319312608049643386.cwl] completed permanentFail Final process status is permanentFail Workflow error, try again with --debug for more information: Process status is ['permanentFail'] stdout : java.lang.RuntimeException: problems running command: cwltool --enable-dev --non-strict --enable-net --outdir /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/outputs/ --tmpdir-prefix /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/working/ /tmp/1474331255066-0/temp319312608049643386.cwl /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/workflow_params.json ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ f f: command not found ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ df Filesystem 1K-blocks Used Available Use% Mounted on udev 62947280 12 62947268 1% /dev tmpfs 12590448 364 12590084 1% /run /dev/xvda1 8115168 6093092 1586800 80% / none 4 0 4 0% /sys/fs/cgroup none 5120 0 5120 0% /run/lock none 62952228 0 62952228 0% /run/shm none 102400 0 102400 0% /run/user /dev/xvdb 1031992064 303267080 676279800 31% /mnt/1TB ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ df -h Filesystem Size Used Avail Use% Mounted on udev 61G 12K 61G 1% /dev tmpfs 13G 364K 13G 1% /run /dev/xvda1 7.8G 5.9G 1.6G 80% / none 4.0K 0 4.0K 0% /sys/fs/cgroup none 5.0M 0 5.0M 0% /run/lock none 61G 0 61G 0% /run/shm none 100M 0 100M 0% /run/user /dev/xvdb 985G 290G 645G 31% /mnt/1TB ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ vi Dockstore.json { Output from command: /opt/wtsi-cgp/bin/alleleCounter -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam -o /var/spool/cwl/0/ascat/tmpAscat/allele_count/b02b4bba-6e66-44fb-a48f-38c309aaaac5.allct -l /var/spool/cwl/reference_files/ascat/SnpLocus.tsv -m 20 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_60.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_ASCAT_allele_count_61 Job ID: 379374475 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_61.e379374475 Updated: Tue Sep 20 14:58:41 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_61.sh Command exit code: 0 Output from command: /opt/wtsi-cgp/bin/alleleCounter -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam -o /var/spool/cwl/0/ascat/tmpAscat/allele_count/8c0354eb-6a3e-4a98-b41c-f8add599884c.allct -l /var/spool/cwl/reference_files/ascat/SnpLocus.tsv -m 20 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_61.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_cgpPindel_input_70 Job ID: 379374477 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_cgpPindel_input_70.e379374477 Updated: Tue Sep 20 13:50:00 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_cgpPindel_input_70.sh Output from command: /usr/bin/perl /opt/wtsi-cgp/bin/pindel_input_gen.pl -b /var/lib/cwl/stg33415604-d4eb-49aa-8f81-345b6fb2a6f3/fdcb1bd7cffca69d15383ca9566c58e0.bam -o /var/spool/cwl/0/pindel/tmpPindel/8c0354eb-6a3e-4a98-b41c-f8add599884c -t 4 -e /var/spool/cwl/reference_files/brass/ucscHiDepth_0.01_mrg1000_no_exon_coreChrs.bed.gz [SeqWare Pipeline] ERROR [2016/09/20 13:50:00] | The exit value was 25 Command exit code: 1 Output from command: /usr/bin/perl /opt/wtsi-cgp/bin/pindel_input_gen.pl -b /var/lib/cwl/stg33415604-d4eb-49aa-8f81-345b6fb2a6f3/fdcb1bd7cffca69d15383ca9566c58e0.bam -o /var/spool/cwl/0/pindel/tmpPindel/8c0354eb-6a3e-4a98-b41c-f8add599884c -t 4 -e /var/spool/cwl/reference_files/brass/ucscHiDepth_0.01_mrg1000_no_exon_coreChrs.bed.gz Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_cgpPindel_input_70.stderr ----------------------------------------------------------------------- ----------------------------------------------------------------------- Job Name: s58_bbAllele_merge_59 Job ID: 379374478 File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.e379374478 Updated: Tue Sep 20 13:51:15 UTC 2016 Contents Excerpt: Command run: bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.sh Command exit code: 0 Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.stderr ----------------------------------------------------------------------- The method 'do_run' exited abnormally so the Runner will terminate here! Return value was: 15 [WARNING] command: seqware bundle launch --dir /home/seqware/CGP-Somatic-Docker/target/Workflow_Bundle_CgpSomaticCore_0.0.0_SeqWare_1.1.1/ --engine whitestar-parallel --ini /var/spool/cwl/workflow.ini --no-metadata exited with code: 15 Error while running job: Error collecting output for parameter 'somatic_cnv_tar_gz': Did not find output file with glob pattern: '['*.somatic.cnv.tar.gz']' [job temp319312608049643386.cwl] completed permanentFail Final process status is permanentFail Workflow error, try again with --debug for more information: Process status is ['permanentFail'] stdout : java.lang.RuntimeException: problems running command: cwltool --enable-dev --non-strict --enable-net --outdir /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/outputs/ --tmpdir-prefix /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/working/ /tmp/1474331255066-0/temp319312608049643386.cwl /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/workflow_params.json -------------- next part -------------- An HTML attachment was scrubbed... URL: From miguel.vazquez at cnio.es Wed Sep 21 11:13:03 2016 From: miguel.vazquez at cnio.es (Miguel Vazquez) Date: Wed, 21 Sep 2016 17:13:03 +0200 Subject: [DOCKTESTERS] Amazon account In-Reply-To: <27512884B2D81B41AAB7BB266248F240C099E3F9@exmb2.ad.oicr.on.ca> References: <27512884B2D81B41AAB7BB266248F240C099E23C@exmb2.ad.oicr.on.ca> <2C84FF4CF2F0A04EB7691F988A717B47CB65E809@exmb2.ad.oicr.on.ca> <27512884B2D81B41AAB7BB266248F240C099E2A3@exmb2.ad.oicr.on.ca> <27512884B2D81B41AAB7BB266248F240C099E397@exmb2.ad.oicr.on.ca> <27512884B2D81B41AAB7BB266248F240C099E3B6@exmb2.ad.oicr.on.ca> <2C84FF4CF2F0A04EB7691F988A717B47CB660030@exmb2.ad.oicr.on.ca> <27512884B2D81B41AAB7BB266248F240C099E3F9@exmb2.ad.oicr.on.ca> Message-ID: Thanks Denis, I will try it as soon as I have a change and get back to you On Wed, Sep 21, 2016 at 4:15 PM, Denis Yuen wrote: > Hi, > One additional thought. Before investigating error code 25, try running > the test data https://github.com/ICGC-TCGA-PanCancer/CGP-Somatic-Docker/ > blob/develop/test1.json > This can help us narrow down whether there is an issue with the > environment or whether there is an issue with the data. > The test data can be downloaded from the link documented at > https://github.com/ICGC-TCGA-PanCancer/CGP-Somatic-Docker# > running-with-the-dockstore-command-line > > Also a reminder to send the output starting with "docker run -i", this > will let me see if there's anything obviously strange with the call to > Docker. > > *Denis Yuen* > Bioinformatics Software Developer > > > *Ontario* *Institute* *for* *Cancer* *Research* > MaRS Centre > 661 University Avenue > Suite 510 > Toronto, Ontario, Canada M5G 0A3 > > Toll-free: 1-866-678-6427 > Twitter: @OICR_news > *www.oicr.on.ca * > > This message and any attachments may contain confidential and/or > privileged information for the sole use of the intended recipient. Any > review or distribution by anyone other than the person for whom it was > originally intended is strictly prohibited. If you have received this > message in error, please contact the sender and delete all copies. > Opinions, conclusions or other information contained in this message may > not be that of the organization. > ------------------------------ > *From:* Junjun Zhang > *Sent:* September 20, 2016 4:09 PM > *To:* Denis Yuen; Miguel Vazquez > *Cc:* docktesters at lists.icgc.org; Brian O'Connor > *Subject:* RE: [DOCKTESTERS] Amazon account > > My run failed with same error message. > > > ------------------------------ > *From:* Denis Yuen > *Sent:* Tuesday, September 20, 2016 3:20 PM > *To:* Miguel Vazquez > *Cc:* docktesters at lists.icgc.org; Brian O'Connor; Junjun Zhang > *Subject:* RE: [DOCKTESTERS] Amazon account > > I think there are a few pieces of information that could be useful. > > Look in this ticket https://github.com/ICGC-TCGA- > PanCancer/CGP-Somatic-Docker/issues/5 > there's a section that starts with "docker run -i", this will let me see if > there's anything obviously strange with the call to Docker. > > Failing that, I think we'll have to see what exit code 25 denotes for > Pindel. > > > ------------------------------ > *From:* Miguel Vazquez [mikisvaz at gmail.com] > *Sent:* September 20, 2016 3:15 PM > *To:* Denis Yuen > *Cc:* docktesters at lists.icgc.org; Brian O'Connor; Junjun Zhang > *Subject:* RE: [DOCKTESTERS] Amazon account > > Well, that's a bummer. Any ideas? > > On Sep 20, 2016 9:11 PM, "Denis Yuen" > wrote: > >> Hi, >> That's really just saying that cwltool was unable to find the output. >> Changing the entry will just save the output somewhere else. >> >> The real problem is probably in the section: >> ---- >> bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_cgpPindel_input_70.sh >> >> Output from command: /usr/bin/perl /opt/wtsi-cgp/bin/pindel_input_gen.pl >> -b /var/lib/cwl/stg33415604-d4eb- >> 49aa-8f81-345b6fb2a6f3/fdcb1bd7cffca69d15383ca9566c58e0.bam -o >> /var/spool/cwl/0/pindel/tmpPindel/8c0354eb-6a3e-4a98-b41c-f8add599884c >> -t 4 -e /var/spool/cwl/reference_files/brass/ucscHiDepth_0.01_mrg100 >> 0_no_exon_coreChrs.bed.gz >> >> [SeqWare Pipeline] ERROR [2016/09/20 13:50:00] | The exit value was 25 >> Command exit code: 1 >> >> Output from command: /usr/bin/perl /opt/wtsi-cgp/bin/pindel_input_gen.pl >> -b /var/lib/cwl/stg33415604-d4eb- >> 49aa-8f81-345b6fb2a6f3/fdcb1bd7cffca69d15383ca9566c58e0.bam -o >> /var/spool/cwl/0/pindel/tmpPindel/8c0354eb-6a3e-4a98-b41c-f8add599884c >> -t 4 -e /var/spool/cwl/reference_files/brass/ucscHiDepth_0.01_mrg100 >> 0_no_exon_coreChrs.bed.gz >> ---- >> >> That says that pindel failed, but there doesn't appear to be any more >> explanation as to why. >> >> >> *Denis Yuen* >> Bioinformatics Software Developer >> >> >> *Ontario* *Institute* *for* *Cancer* *Research* >> MaRS Centre >> 661 University Avenue >> Suite 510 >> Toronto, Ontario, Canada M5G 0A3 >> >> Toll-free: 1-866-678-6427 >> Twitter: @OICR_news >> *www.oicr.on.ca * >> >> This message and any attachments may contain confidential and/or >> privileged information for the sole use of the intended recipient. Any >> review or distribution by anyone other than the person for whom it was >> originally intended is strictly prohibited. If you have received this >> message in error, please contact the sender and delete all copies. >> Opinions, conclusions or other information contained in this message may >> not be that of the organization. >> ------------------------------ >> *From:* Miguel Vazquez [mikisvaz at gmail.com ] >> *Sent:* September 20, 2016 2:55 PM >> *To:* Junjun Zhang >> *Cc:* Denis Yuen; Brian O'Connor; docktesters at lists.icgc.org >> >> *Subject:* Re: [DOCKTESTERS] Amazon account >> >> Just a heads up, the process failed. >> >> The complete log is bellow, but I think this is the culprit: >> >> Error while running job: Error collecting output for parameter >> 'somatic_cnv_tar_gz': Did not find output file with glob pattern: >> '['*.somatic.cnv.tar.gz']' >> >> I wrote something like this in Dockerstore.json >> >> "somatic_cnv_tar_gz": { >> "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.cnv. >> tar.gz", >> "class": "File" >> } >> >> I've replace those entries with this >> >> "somatic_cnv_tar_gz": { >> "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/DONOR.somatic >> .cnv.tar.gz", >> "class": "File" >> } >> >> so that the glob work. I'm trying again. I'll update the documentation >> >> Best >> >> Miguel >> >> >> >> >> >> ------------------ >> >> >> >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_tumour_25.stderr >> ----------------------------------------------------------------------- >> >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_control_56.stderr >> ----------------------------------------------------------------------- >> >> ----------------------------------------------------------------------- >> Job Name: s58_bbAllele_control_54 >> Job ID: 335639174 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_control_54.e335639174 >> Updated: Tue Sep 20 03:55:15 UTC 2016 >> Contents Excerpt: >> Command run: >> bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_control_54.sh >> Command exit code: 0 >> >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_control_54.stderr >> ----------------------------------------------------------------------- >> >> ----------------------------------------------------------------------- >> Job Name: s58_bbAllele_tumour_13 >> Job ID: 335639178 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_tumour_13.e335639178 >> Updated: Tue Sep 20 12:07:55 UTC 2016 >> Contents Excerpt: >> Command run: >> bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_tumour_13.sh >> Command exit code: 0 >> >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_tumour_13.stderr >> ----------------------------------------------------------------------- >> >> ----------------------------------------------------------------------- >> Job Name: s58_bbAllele_tumour_17 >> Job ID: 335639179 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_tumour_17.e335639179 >> Updated: Tue Sep 20 12:05:07 UTC 2016 >> Contents Excerpt: >> Command run: >> bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_tumour_17.sh >> Command exit code: 0 >> >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_tumour_17.stderr >> ----------------------------------------------------------------------- >> >> ----------------------------------------------------------------------- >> Job Name: s58_bbAllele_tumour_15 >> Job ID: 335639180 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_tumour_15.e335639180 >> ----------------------------------------------------------------------- >> Job Name: s58_bbAllele_control_48 >> Job ID: 335639020 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_control_48.e335639020 >> Updated: Tue Sep 20 05:54:57 UTC 2016 >> Contents Excerpt: >> Command run: >> bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_control_48.sh >> Command exit code: 0 >> >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_control_48.stderr >> ----------------------------------------------------------------------- >> >> ----------------------------------------------------------------------- >> Job Name: s58_bbAllele_control_50 >> Job ID: 335639025 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_control_50.e335639025 >> Updated: Tue Sep 20 04:48:39 UTC 2016 >> Contents Excerpt: >> Command run: >> bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_control_50.sh >> Command exit code: 0 >> >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_control_50.stderr >> ----------------------------------------------------------------------- >> >> ----------------------------------------------------------------------- >> Job Name: s58_bbAllele_control_52 >> Job ID: 335639111 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_control_52.e335639111 >> Updated: Tue Sep 20 05:05:25 UTC 2016 >> Contents Excerpt: >> Command run: >> bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_control_52.sh >> Command exit code: 0 >> >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_control_52.stderr >> ----------------------------------------------------------------------- >> >> ----------------------------------------------------------------------- >> Job Name: s58_bbAllele_control_56 >> Job ID: 335639173 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_control_56.e335639173 >> Updated: Tue Sep 20 03:39:33 UTC 2016 >> Contents Excerpt: >> Command run: >> bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_control_56.sh >> Command exit code: 0 >> Contents Excerpt: >> Command run: >> bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_control_34.sh >> Command exit code: 0 >> >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_control_34.stderr >> ----------------------------------------------------------------------- >> >> ----------------------------------------------------------------------- >> Job Name: s58_bbAllele_control_38 >> Job ID: 335638783 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_control_38.e335638783 >> Updated: Tue Sep 20 06:49:18 UTC 2016 >> Contents Excerpt: >> Command run: >> bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_control_38.sh >> Command exit code: 0 >> >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_control_38.stderr >> ----------------------------------------------------------------------- >> >> ----------------------------------------------------------------------- >> Job Name: s58_bbAllele_control_42 >> Job ID: 335638805 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_control_42.e335638805 >> Updated: Tue Sep 20 06:07:49 UTC 2016 >> Contents Excerpt: >> Command run: >> bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_control_42.sh >> Command exit code: 0 >> >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_control_42.stderr >> ----------------------------------------------------------------------- >> >> ----------------------------------------------------------------------- >> Job Name: s58_bbAllele_control_46 >> Job ID: 335638826 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_control_46.e335638826 >> Updated: Tue Sep 20 05:40:42 UTC 2016 >> Contents Excerpt: >> Command run: >> bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_control_46.sh >> Command exit code: 0 >> >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_control_46.stderr >> ----------------------------------------------------------------------- >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_unpackRef_NA_10.stderr >> ----------------------------------------------------------------------- >> >> ----------------------------------------------------------------------- >> Job Name: s58_bbAllele_control_22 >> Job ID: 335638775 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_control_22.e335638775 >> Updated: Tue Sep 20 09:32:19 UTC 2016 >> Contents Excerpt: >> Command run: >> bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_control_22.sh >> Command exit code: 0 >> >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_control_22.stderr >> ----------------------------------------------------------------------- >> >> ----------------------------------------------------------------------- >> Job Name: s58_bbAllele_control_28 >> Job ID: 335638776 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_control_28.e335638776 >> Updated: Tue Sep 20 08:57:31 UTC 2016 >> Contents Excerpt: >> Command run: >> bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_control_28.sh >> Command exit code: 0 >> >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_control_28.stderr >> ----------------------------------------------------------------------- >> >> ----------------------------------------------------------------------- >> Job Name: s58_bbAllele_control_32 >> Job ID: 335638777 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_control_32.e335638777 >> Updated: Tue Sep 20 08:12:44 UTC 2016 >> Contents Excerpt: >> Command run: >> bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_control_32.sh >> Command exit code: 0 >> >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_control_32.stderr >> ----------------------------------------------------------------------- >> >> ----------------------------------------------------------------------- >> Job Name: s58_bbAllele_control_34 >> Job ID: 335638778 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_control_34.e335638778 >> Updated: Tue Sep 20 08:24:35 UTC 2016 >> Job Name: s58_unpackRef_NA_9 >> Job ID: 331891142 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_unpackRef_NA_9.e331891142 >> Updated: Tue Sep 20 00:39:16 UTC 2016 >> Contents Excerpt: >> Command run: >> bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_unpackRef_NA_9.sh >> Command exit code: 0 >> >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_unpackRef_NA_9.stderr >> ----------------------------------------------------------------------- >> >> ----------------------------------------------------------------------- >> Job Name: s58_verifyBamHomChk_control_6 >> Job ID: 331891143 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_verifyBamHomChk_control_6.e331891143 >> Updated: Tue Sep 20 00:44:52 UTC 2016 >> Contents Excerpt: >> Command run: >> bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_verifyBamHomChk_control_6.sh >> Command exit code: 0 >> >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_verifyBamHomChk_control_6.stderr >> ----------------------------------------------------------------------- >> >> ----------------------------------------------------------------------- >> Job Name: s58_basFileGenerate_control_11 >> Job ID: 332292910 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_basFileGenerate_control_11.e332292910 >> Updated: Tue Sep 20 01:20:39 UTC 2016 >> Contents Excerpt: >> Command run: >> bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_basFileGenerate_control_11.sh >> Command exit code: 0 >> >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_basFileGenerate_control_11.stderr >> ----------------------------------------------------------------------- >> >> ----------------------------------------------------------------------- >> Job Name: s58_unpackRef_NA_10 >> Job ID: 332292911 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_unpackRef_NA_10.e332292911 >> Updated: Tue Sep 20 00:44:57 UTC 2016 >> Contents Excerpt: >> Command run: >> bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_unpackRef_NA_10.sh >> Command exit code: 0 >> Command run: >> bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_start_0.sh >> Command exit code: 0 >> >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_start_0.stderr >> ----------------------------------------------------------------------- >> >> ----------------------------------------------------------------------- >> Job Name: s58_mark_start_1 >> Job ID: 331890603 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_mark_start_1.e331890603 >> Updated: Tue Sep 20 00:38:10 UTC 2016 >> Contents Excerpt: >> Command run: >> bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_mark_start_1.sh >> Command exit code: 0 >> >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_mark_start_1.stderr >> ----------------------------------------------------------------------- >> >> ----------------------------------------------------------------------- >> Job Name: s58_prepBam_control_3 >> Job ID: 331890831 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_prepBam_control_3.e331890831 >> Updated: Tue Sep 20 00:38:11 UTC 2016 >> Contents Excerpt: >> Command run: >> bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_prepBam_control_3.sh >> Command exit code: 0 >> >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_prepBam_control_3.stderr >> ----------------------------------------------------------------------- >> >> ----------------------------------------------------------------------- >> Job Name: s58_prepBam_tumour_2 >> Job ID: 331890832 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_prepBam_tumour_2.e331890832 >> Updated: Tue Sep 20 00:38:11 UTC 2016 >> Contents Excerpt: >> Command run: >> bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_prepBam_tumour_2.sh >> Command exit code: 0 >> >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_prepBam_tumour_2.stderr >> ----------------------------------------------------------------------- >> >> ----------------------------------------------------------------------- >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_ASCAT_allele_count_61.stdout >> ----------------------------------------------------------------------- >> >> ----------------------------------------------------------------------- >> Job Name: s58_BRASS_input_99 >> Job ID: 379374477 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_BRASS_input_99.o379374477 >> Updated: Tue Sep 20 16:49:15 UTC 2016 >> Contents Excerpt: >> [V] 18 0.49745MB/s 1781.56 >> [V] 19 0.525041MB/s 1879.07 >> [V] 20 0.552722MB/s 1976.44 >> [V] 21 0.579942MB/s 2072.21 >> [V] 22 0.607543MB/s 2169.2 >> [V] 23 0.635118MB/s 2266.04 >> [V] 24264262 >> [V] MemUsage(size=71.1484,rss=10.9336,peak=291.977) wall clock time >> 02:57:24:31175299 >> 11827.06user 310.09system 2:59:40elapsed 112%CPU (0avgtext+0avgdata >> 4265632maxresident)k >> 117507424inputs+14421104outputs (84major+234838minor)pagefaults 0swaps >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_BRASS_input_99.stdout >> ----------------------------------------------------------------------- >> >> ----------------------------------------------------------------------- >> Job Name: s58_bbAllele_merge_59 >> Job ID: 379374478 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_merge_59.o379374478 >> Updated: Tue Sep 20 13:51:15 UTC 2016 >> Contents Excerpt: >> 87.14user 5.10system 1:41.25elapsed 91%CPU (0avgtext+0avgdata >> 66448maxresident)k >> 2720952inputs+4360560outputs (5major+7600minor)pagefaults 0swaps >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_merge_59.stdout >> ----------------------------------------------------------------------- >> >> >> % Total % Received % Xferd Average Speed Time Time Time >> Current >> Dload Upload Total Spent Left >> Speed >> 0 0 0 0 0 0 0 0 --:--:-- --:--:-- >> --:--:-- 0 >> 100 54.9M 100 54.9M 0 0 1016k 0 0:00:55 0:00:55 --:--:-- >> 1047k >> % Total % Received % Xferd Average Speed Time Time Time >> Current >> Dload Upload Total Spent Left >> Speed >> 0 0 0 0 0 0 0 0 --:--:-- --:--:-- >> --:--:-- 0 >> 100 174k 100 174k 0 0 174k 0 0:00:01 0:00:01 --:--:-- >> 567k >> [2016/09/20 16:49:15] | Output for stderr due to workflow run failure: >> ----------------------------------------------------------------------- >> Job Name: s58_start_0 >> Job ID: 331890362 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_start_0.e331890362 >> Updated: Tue Sep 20 00:38:10 UTC 2016 >> Contents Excerpt: >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_renameSampleFile_208.o373317274 >> Updated: Tue Sep 20 12:08:37 UTC 2016 >> Contents Excerpt: >> Modified command: cp /var/spool/cwl/b02b4bba-6e66-4 >> 4fb-a48f-38c309aaaac5.genotype.tar.gz /var/spool/cwl/b02b4bba-6e66-4 >> 4fb-a48f-38c309aaaac5.csc_0-0-0.20160920.somatic.genotype.tar.gz >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_renameSampleFile_208.stdout >> ----------------------------------------------------------------------- >> >> ----------------------------------------------------------------------- >> Job Name: s58_bbAllele_tumour_57 >> Job ID: 373317275 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_tumour_57.o373317275 >> Updated: Tue Sep 20 13:29:27 UTC 2016 >> Contents Excerpt: >> Modified command: alleleCounter -l /var/spool/cwl/reference_files >> /battenberg/1000genomesloci/1000genomesloci2012_chr23.txt -o >> /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.23.tsv -b >> /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam >> 4798.51user 50.73system 1:20:50elapsed 99%CPU (0avgtext+0avgdata >> 3115856maxresident)k >> 9833328inputs+56328outputs (0major+199552minor)pagefaults 0swaps >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_tumour_57.stdout >> ----------------------------------------------------------------------- >> >> ----------------------------------------------------------------------- >> Job Name: s58_ASCAT_allele_count_60 >> Job ID: 379374473 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_ASCAT_allele_count_60.o379374473 >> Updated: Tue Sep 20 15:34:45 UTC 2016 >> Contents Excerpt: >> >> Errors from command: /opt/wtsi-cgp/bin/alleleCounter -b >> /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam -o >> /var/spool/cwl/0/ascat/tmpAscat/allele_count/b02b4bba-6e66-44fb-a48f-38c309aaaac5.allct >> -l /var/spool/cwl/reference_files/ascat/SnpLocus.tsv -m 20 >> >> 5928.09user 101.55system 1:45:10elapsed 95%CPU (0avgtext+0avgdata >> 2345888maxresident)k >> 221140208inputs+43144outputs (37major+169349minor)pagefaults 0swaps >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_ASCAT_allele_count_60.stdout >> ----------------------------------------------------------------------- >> >> ----------------------------------------------------------------------- >> Job Name: s58_ASCAT_allele_count_61 >> Job ID: 379374475 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_ASCAT_allele_count_61.o379374475 >> Updated: Tue Sep 20 14:58:41 UTC 2016 >> Contents Excerpt: >> >> Errors from command: /opt/wtsi-cgp/bin/alleleCounter -b >> /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam -o >> /var/spool/cwl/0/ascat/tmpAscat/allele_count/8c0354eb-6a3e-4a98-b41c-f8add599884c.allct >> -l /var/spool/cwl/reference_files/ascat/SnpLocus.tsv -m 20 >> >> 3864.82user 67.24system 1:09:07elapsed 94%CPU (0avgtext+0avgdata >> 2350544maxresident)k >> 157460240inputs+43120outputs (57major+167795minor)pagefaults 0swaps >> 11476.37user 140.61system 6:48:23elapsed 47%CPU (0avgtext+0avgdata >> 3035728maxresident)k >> 7380072inputs+56816outputs (0major+196640minor)pagefaults 0swaps >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_tumour_39.stdout >> ----------------------------------------------------------------------- >> >> ----------------------------------------------------------------------- >> Job Name: s58_bbAllele_tumour_41 >> Job ID: 335639489 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_tumour_41.o335639489 >> Updated: Tue Sep 20 07:35:04 UTC 2016 >> Contents Excerpt: >> Modified command: alleleCounter -l /var/spool/cwl/reference_files >> /battenberg/1000genomesloci/1000genomesloci2012_chr15.txt -o >> /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.15.tsv -b >> /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam >> 9429.90user 117.09system 5:54:22elapsed 44%CPU (0avgtext+0avgdata >> 2739152maxresident)k >> 5273744inputs+51000outputs (0major+177355minor)pagefaults 0swaps >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_tumour_41.stdout >> ----------------------------------------------------------------------- >> >> ----------------------------------------------------------------------- >> Job Name: s58_bbAllele_tumour_45 >> Job ID: 335639845 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_tumour_45.o335639845 >> Updated: Tue Sep 20 07:29:41 UTC 2016 >> Contents Excerpt: >> Modified command: alleleCounter -l /var/spool/cwl/reference_files >> /battenberg/1000genomesloci/1000genomesloci2012_chr17.txt -o >> /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.17.tsv -b >> /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam >> 9231.30user 116.04system 5:49:00elapsed 44%CPU (0avgtext+0avgdata >> 2540400maxresident)k >> 5255296inputs+46736outputs (0major+165277minor)pagefaults 0swaps >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_tumour_45.stdout >> ----------------------------------------------------------------------- >> >> ----------------------------------------------------------------------- >> Job Name: s58_bbAllele_tumour_43 >> Job ID: 335639853 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_tumour_43.o335639853 >> Updated: Tue Sep 20 08:28:45 UTC 2016 >> Contents Excerpt: >> Modified command: alleleCounter -l /var/spool/cwl/reference_files >> /battenberg/1000genomesloci/1000genomesloci2012_chr16.txt -o >> /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.16.tsv -b >> /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam >> 11465.31user 146.48system 6:48:03elapsed 47%CPU (0avgtext+0avgdata >> 2945712maxresident)k >> 6906080inputs+54432outputs (0major+190932minor)pagefaults 0swaps >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_tumour_43.stdout >> ----------------------------------------------------------------------- >> >> ----------------------------------------------------------------------- >> Job Name: s58_renameSampleFile_208 >> Job ID: 373317274 >> >> ----------------------------------------------------------------------- >> Job Name: s58_bbAllele_tumour_33 >> Job ID: 335639420 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_tumour_33.o335639420 >> Updated: Tue Sep 20 10:42:41 UTC 2016 >> Contents Excerpt: >> Modified command: alleleCounter -l /var/spool/cwl/reference_files >> /battenberg/1000genomesloci/1000genomesloci2012_chr11.txt -o >> /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.11.tsv -b >> /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam >> 18904.62user 233.41system 9:02:00elapsed 58%CPU (0avgtext+0avgdata >> 4537600maxresident)k >> 15888800inputs+86400outputs (0major+292553minor)pagefaults 0swaps >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_tumour_33.stdout >> ----------------------------------------------------------------------- >> >> ----------------------------------------------------------------------- >> Job Name: s58_bbAllele_tumour_35 >> Job ID: 335639430 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_tumour_35.o335639430 >> Updated: Tue Sep 20 10:03:48 UTC 2016 >> Contents Excerpt: >> Modified command: alleleCounter -l /var/spool/cwl/reference_files >> /battenberg/1000genomesloci/1000genomesloci2012_chr12.txt -o >> /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.12.tsv -b >> /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam >> 16584.76user 210.26system 8:23:07elapsed 55%CPU (0avgtext+0avgdata >> 4373600maxresident)k >> 12917040inputs+82896outputs (0major+281480minor)pagefaults 0swaps >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_tumour_35.stdout >> ----------------------------------------------------------------------- >> >> ----------------------------------------------------------------------- >> Job Name: s58_bbAllele_tumour_37 >> Job ID: 335639431 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_tumour_37.o335639431 >> Updated: Tue Sep 20 08:26:17 UTC 2016 >> Contents Excerpt: >> Modified command: alleleCounter -l /var/spool/cwl/reference_files >> /battenberg/1000genomesloci/1000genomesloci2012_chr13.txt -o >> /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.13.tsv -b >> /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam >> 11361.18user 138.30system 6:45:36elapsed 47%CPU (0avgtext+0avgdata >> 3301008maxresident)k >> 7418080inputs+62192outputs (0major+212951minor)pagefaults 0swaps >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_tumour_37.stdout >> ----------------------------------------------------------------------- >> >> ----------------------------------------------------------------------- >> Job Name: s58_bbAllele_tumour_39 >> Job ID: 335639452 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_tumour_39.o335639452 >> Updated: Tue Sep 20 08:29:04 UTC 2016 >> Contents Excerpt: >> Modified command: alleleCounter -l /var/spool/cwl/reference_files >> /battenberg/1000genomesloci/1000genomesloci2012_chr14.txt -o >> /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.14.tsv -b >> /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam >> Updated: Tue Sep 20 11:02:29 UTC 2016 >> Contents Excerpt: >> Modified command: alleleCounter -l /var/spool/cwl/reference_files >> /battenberg/1000genomesloci/1000genomesloci2012_chr7.txt -o >> /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.7.tsv -b >> /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam >> 20088.69user 242.69system 9:21:48elapsed 60%CPU (0avgtext+0avgdata >> 5281504maxresident)k >> 18604808inputs+96776outputs (0major+339332minor)pagefaults 0swaps >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_tumour_25.stdout >> ----------------------------------------------------------------------- >> >> ----------------------------------------------------------------------- >> Job Name: s58_bbAllele_tumour_27 >> Job ID: 335639400 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_tumour_27.o335639400 >> Updated: Tue Sep 20 11:02:53 UTC 2016 >> Contents Excerpt: >> Modified command: alleleCounter -l /var/spool/cwl/reference_files >> /battenberg/1000genomesloci/1000genomesloci2012_chr8.txt -o >> /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.8.tsv -b >> /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam >> 20108.48user 243.42system 9:22:11elapsed 60%CPU (0avgtext+0avgdata >> 5228912maxresident)k >> 17295080inputs+95440outputs (0major+335764minor)pagefaults 0swaps >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_tumour_27.stdout >> ----------------------------------------------------------------------- >> >> ----------------------------------------------------------------------- >> Job Name: s58_bbAllele_tumour_29 >> Job ID: 335639401 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_tumour_29.o335639401 >> Updated: Tue Sep 20 09:18:32 UTC 2016 >> Contents Excerpt: >> Modified command: alleleCounter -l /var/spool/cwl/reference_files >> /battenberg/1000genomesloci/1000genomesloci2012_chr9.txt -o >> /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.9.tsv -b >> /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam >> 13962.23user 175.03system 7:37:51elapsed 51%CPU (0avgtext+0avgdata >> 3971872maxresident)k >> 12246072inputs+72144outputs (0major+255173minor)pagefaults 0swaps >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_tumour_29.stdout >> ----------------------------------------------------------------------- >> >> ----------------------------------------------------------------------- >> Job Name: s58_bbAllele_tumour_31 >> Job ID: 335639417 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_tumour_31.o335639417 >> Updated: Tue Sep 20 10:11:08 UTC 2016 >> Contents Excerpt: >> Modified command: alleleCounter -l /var/spool/cwl/reference_files >> /battenberg/1000genomesloci/1000genomesloci2012_chr10.txt -o >> /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.10.tsv -b >> /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam >> 17052.42user 207.86system 8:30:26elapsed 56%CPU (0avgtext+0avgdata >> 4504144maxresident)k >> 13931760inputs+85488outputs (0major+289717minor)pagefaults 0swaps >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_tumour_31.stdout >> ----------------------------------------------------------------------- >> 23593416inputs+121608outputs (0major+421477minor)pagefaults 0swaps >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_tumour_17.stdout >> ----------------------------------------------------------------------- >> >> ----------------------------------------------------------------------- >> Job Name: s58_bbAllele_tumour_15 >> Job ID: 335639180 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_tumour_15.o335639180 >> Updated: Tue Sep 20 12:08:37 UTC 2016 >> Contents Excerpt: >> Modified command: alleleCounter -l /var/spool/cwl/reference_files >> /battenberg/1000genomesloci/1000genomesloci2012_chr2.txt -o >> /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.2.tsv -b >> /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam >> 24021.20user 275.32system 10:27:56elapsed 64%CPU (0avgtext+0avgdata >> 7851136maxresident)k >> 24358016inputs+146264outputs (0major+499924minor)pagefaults 0swaps >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_tumour_15.stdout >> ----------------------------------------------------------------------- >> >> ----------------------------------------------------------------------- >> Job Name: s58_bbAllele_tumour_19 >> Job ID: 335639200 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_tumour_19.o335639200 >> Updated: Tue Sep 20 11:57:43 UTC 2016 >> Contents Excerpt: >> Modified command: alleleCounter -l /var/spool/cwl/reference_files >> /battenberg/1000genomesloci/1000genomesloci2012_chr4.txt -o >> /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.4.tsv -b >> /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam >> 23336.68user 273.00system 10:17:02elapsed 63%CPU (0avgtext+0avgdata >> 6501344maxresident)k >> 22397816inputs+120192outputs (0major+416448minor)pagefaults 0swaps >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_tumour_19.stdout >> ----------------------------------------------------------------------- >> >> ----------------------------------------------------------------------- >> Job Name: s58_bbAllele_tumour_23 >> Job ID: 335639375 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_tumour_23.o335639375 >> Updated: Tue Sep 20 11:14:37 UTC 2016 >> Contents Excerpt: >> Modified command: alleleCounter -l /var/spool/cwl/reference_files >> /battenberg/1000genomesloci/1000genomesloci2012_chr6.txt -o >> /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.6.tsv -b >> /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam >> 20846.11user 251.83system 9:33:55elapsed 61%CPU (0avgtext+0avgdata >> 5765024maxresident)k >> 19462064inputs+106080outputs (0major+369701minor)pagefaults 0swaps >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_tumour_23.stdout >> ----------------------------------------------------------------------- >> >> ----------------------------------------------------------------------- >> Job Name: s58_bbAllele_tumour_25 >> Job ID: 335639387 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_tumour_25.o335639387 >> ----------------------------------------------------------------------- >> Job Name: s58_bbAllele_control_56 >> Job ID: 335639173 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_control_56.o335639173 >> Updated: Tue Sep 20 03:39:33 UTC 2016 >> Contents Excerpt: >> Modified command: alleleCounter -l /var/spool/cwl/reference_files >> /battenberg/1000genomesloci/1000genomesloci2012_chr22.txt -o >> /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.22.tsv -b >> /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam >> 2810.79user 34.33system 1:58:52elapsed 39%CPU (0avgtext+0avgdata >> 1250144maxresident)k >> 1243552inputs+22208outputs (0major+82726minor)pagefaults 0swaps >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_control_56.stdout >> ----------------------------------------------------------------------- >> >> ----------------------------------------------------------------------- >> Job Name: s58_bbAllele_control_54 >> Job ID: 335639174 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_control_54.o335639174 >> Updated: Tue Sep 20 03:55:15 UTC 2016 >> Contents Excerpt: >> Modified command: alleleCounter -l /var/spool/cwl/reference_files >> /battenberg/1000genomesloci/1000genomesloci2012_chr21.txt -o >> /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.21.tsv -b >> /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam >> 3187.08user 39.68system 2:14:34elapsed 39%CPU (0avgtext+0avgdata >> 1302656maxresident)k >> 1689216inputs+23256outputs (0major+86038minor)pagefaults 0swaps >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_control_54.stdout >> ----------------------------------------------------------------------- >> >> ----------------------------------------------------------------------- >> Job Name: s58_bbAllele_control_58 >> Job ID: 335639178 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_control_58.o335639178 >> Updated: Tue Sep 20 04:41:10 UTC 2016 >> Contents Excerpt: >> Modified command: alleleCounter -l /var/spool/cwl/reference_files >> /battenberg/1000genomesloci/1000genomesloci2012_chr23.txt -o >> /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.23.tsv -b >> /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam >> 4375.73user 53.14system 3:00:29elapsed 40%CPU (0avgtext+0avgdata >> 3123136maxresident)k >> 4325272inputs+56240outputs (0major+199643minor)pagefaults 0swaps >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_control_58.stdout >> ----------------------------------------------------------------------- >> >> ----------------------------------------------------------------------- >> Job Name: s58_bbAllele_tumour_17 >> Job ID: 335639179 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_tumour_17.o335639179 >> Updated: Tue Sep 20 12:05:07 UTC 2016 >> Contents Excerpt: >> Modified command: alleleCounter -l /var/spool/cwl/reference_files >> /battenberg/1000genomesloci/1000genomesloci2012_chr3.txt -o >> /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.3.tsv -b >> /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam >> 23819.53user 283.10system 10:24:27elapsed 64%CPU (0avgtext+0avgdata >> 6576048maxresident)k >> Contents Excerpt: >> Modified command: alleleCounter -l /var/spool/cwl/reference_files >> /battenberg/1000genomesloci/1000genomesloci2012_chr17.txt -o >> /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.17.tsv -b >> /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam >> 5945.65user 71.96system 4:00:01elapsed 41%CPU (0avgtext+0avgdata >> 2544496maxresident)k >> 5572568inputs+46720outputs (0major+163875minor)pagefaults 0swaps >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_control_46.stdout >> ----------------------------------------------------------------------- >> >> ----------------------------------------------------------------------- >> Job Name: s58_bbAllele_control_48 >> Job ID: 335639020 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_control_48.o335639020 >> Updated: Tue Sep 20 05:54:57 UTC 2016 >> Contents Excerpt: >> Modified command: alleleCounter -l /var/spool/cwl/reference_files >> /battenberg/1000genomesloci/1000genomesloci2012_chr18.txt -o >> /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.18.tsv -b >> /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam >> 6337.11user 77.66system 4:14:16elapsed 42%CPU (0avgtext+0avgdata >> 2647504maxresident)k >> 5337616inputs+48704outputs (0major+170347minor)pagefaults 0swaps >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_control_48.stdout >> ----------------------------------------------------------------------- >> >> ----------------------------------------------------------------------- >> Job Name: s58_bbAllele_control_50 >> Job ID: 335639025 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_control_50.o335639025 >> Updated: Tue Sep 20 04:48:39 UTC 2016 >> Contents Excerpt: >> Modified command: alleleCounter -l /var/spool/cwl/reference_files >> /battenberg/1000genomesloci/1000genomesloci2012_chr19.txt -o >> /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.19.tsv -b >> /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam >> 4542.91user 55.47system 3:07:58elapsed 40%CPU (0avgtext+0avgdata >> 1995904maxresident)k >> 3514080inputs+36192outputs (0major+129470minor)pagefaults 0swaps >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_control_50.stdout >> ----------------------------------------------------------------------- >> >> ----------------------------------------------------------------------- >> Job Name: s58_bbAllele_control_52 >> Job ID: 335639111 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_control_52.o335639111 >> Updated: Tue Sep 20 05:05:25 UTC 2016 >> Contents Excerpt: >> Modified command: alleleCounter -l /var/spool/cwl/reference_files >> /battenberg/1000genomesloci/1000genomesloci2012_chr20.txt -o >> /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.20.tsv -b >> /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam >> 4979.15user 61.39system 3:24:44elapsed 41%CPU (0avgtext+0avgdata >> 2102832maxresident)k >> 3653168inputs+38272outputs (0major+136206minor)pagefaults 0swaps >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_control_52.stdout >> ----------------------------------------------------------------------- >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> -6a3e-4a98-b41c-f8add599884c.11.tsv -b /var/spool/cwl/fdcb1bd7cffca69 >> d15383ca9566c58e0.bam >> 11287.76user 142.04system 6:43:55elapsed 47%CPU (0avgtext+0avgdata >> 4543376maxresident)k >> 9747344inputs+86048outputs (0major+289230minor)pagefaults 0swaps >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_control_34.stdout >> ----------------------------------------------------------------------- >> >> ----------------------------------------------------------------------- >> Job Name: s58_bbAllele_control_38 >> Job ID: 335638783 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_control_38.o335638783 >> Updated: Tue Sep 20 06:49:18 UTC 2016 >> Contents Excerpt: >> Modified command: alleleCounter -l /var/spool/cwl/reference_files >> /battenberg/1000genomesloci/1000genomesloci2012_chr13.txt -o >> /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.13.tsv -b >> /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam >> 7981.44user 98.27system 5:08:39elapsed 43%CPU (0avgtext+0avgdata >> 3310512maxresident)k >> 6948640inputs+62176outputs (7major+211942minor)pagefaults 0swaps >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_control_38.stdout >> ----------------------------------------------------------------------- >> >> ----------------------------------------------------------------------- >> Job Name: s58_bbAllele_control_42 >> Job ID: 335638805 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_control_42.o335638805 >> Updated: Tue Sep 20 06:07:49 UTC 2016 >> Contents Excerpt: >> Modified command: alleleCounter -l /var/spool/cwl/reference_files >> /battenberg/1000genomesloci/1000genomesloci2012_chr15.txt -o >> /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.15.tsv -b >> /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam >> 6705.59user 83.09system 4:27:09elapsed 42%CPU (0avgtext+0avgdata >> 2746816maxresident)k >> 6146600inputs+50992outputs (0major+176574minor)pagefaults 0swaps >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_control_42.stdout >> ----------------------------------------------------------------------- >> >> ----------------------------------------------------------------------- >> Job Name: s58_bbAllele_control_46 >> Job ID: 379374477 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_cgpPindel_input_70.e379374477 >> Updated: Tue Sep 20 13:50:00 UTC 2016 >> Contents Excerpt: >> Command run: >> bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_cgpPindel_input_70.sh >> >> Output from command: /usr/bin/perl /opt/wtsi-cgp/bin/pindel_input_gen.pl >> -b /var/lib/cwl/stg33415604-d4eb- >> 49aa-8f81-345b6fb2a6f3/fdcb1bd7cffca69d15383ca9566c58e0.bam -o >> /var/spool/cwl/0/pindel/tmpPindel/8c0354eb-6a3e-4a98-b41c-f8add599884c >> -t 4 -e /var/spool/cwl/reference_files/brass/ucscHiDepth_0.01_mrg100 >> 0_no_exon_coreChrs.bed.gz >> >> [SeqWare Pipeline] ERROR [2016/09/20 13:50:00] | The exit value was 25 >> Command exit code: 1 >> >> Output from command: /usr/bin/perl /opt/wtsi-cgp/bin/pindel_input_gen.pl >> -b /var/lib/cwl/stg33415604-d4eb- >> 49aa-8f81-345b6fb2a6f3/fdcb1bd7cffca69d15383ca9566c58e0.bam -o >> /var/spool/cwl/0/pindel/tmpPindel/8c0354eb-6a3e-4a98-b41c-f8add599884c >> -t 4 -e /var/spool/cwl/reference_files/brass/ucscHiDepth_0.01_mrg100 >> 0_no_exon_coreChrs.bed.gz >> >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_cgpPindel_input_70.stderr >> ----------------------------------------------------------------------- >> >> ----------------------------------------------------------------------- >> Job Name: s58_bbAllele_merge_59 >> Job ID: 379374478 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_merge_59.e379374478 >> Updated: Tue Sep 20 13:51:15 UTC 2016 >> Contents Excerpt: >> Command run: >> bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_merge_59.sh >> Command exit code: 0 >> >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_merge_59.stderr >> ----------------------------------------------------------------------- >> >> >> The method 'do_run' exited abnormally so the Runner will terminate here! >> Return value was: 15 >> >> [WARNING] command: seqware bundle launch --dir >> /home/seqware/CGP-Somatic-Docker/target/Workflow_Bundle_CgpS >> omaticCore_0.0.0_SeqWare_1.1.1/ --engine whitestar-parallel --ini >> /var/spool/cwl/workflow.ini --no-metadata exited with code: 15 >> Error while running job: Error collecting output for parameter >> 'somatic_cnv_tar_gz': Did not find output file with glob pattern: >> '['*.somatic.cnv.tar.gz']' >> [job temp319312608049643386.cwl] completed permanentFail >> Final process status is permanentFail >> Workflow error, try again with --debug for more information: >> Process status is ['permanentFail'] >> >> stdout : >> java.lang.RuntimeException: problems running command: cwltool >> --enable-dev --non-strict --enable-net --outdir >> /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher- >> 780ac637-b999-4a70-8ab7-79b51c64f428/outputs/ --tmpdir-prefix >> /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher- >> 780ac637-b999-4a70-8ab7-79b51c64f428/working/ >> /tmp/1474331255066-0/temp319312608049643386.cwl >> /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher- >> 780ac637-b999-4a70-8ab7-79b51c64f428/workflow_params.json >> ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ f >> f: command not found >> ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ df >> Filesystem 1K-blocks Used Available Use% Mounted on >> udev 62947280 12 62947268 1% /dev >> tmpfs 12590448 364 12590084 1% /run >> /dev/xvda1 8115168 6093092 1586800 80% / >> none 4 0 4 0% /sys/fs/cgroup >> none 5120 0 5120 0% /run/lock >> none 62952228 0 62952228 0% /run/shm >> none 102400 0 102400 0% /run/user >> /dev/xvdb 1031992064 303267080 676279800 31% /mnt/1TB >> ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ df -h >> Filesystem Size Used Avail Use% Mounted on >> udev 61G 12K 61G 1% /dev >> tmpfs 13G 364K 13G 1% /run >> /dev/xvda1 7.8G 5.9G 1.6G 80% / >> none 4.0K 0 4.0K 0% /sys/fs/cgroup >> none 5.0M 0 5.0M 0% /run/lock >> none 61G 0 61G 0% /run/shm >> none 100M 0 100M 0% /run/user >> /dev/xvdb 985G 290G 645G 31% /mnt/1TB >> ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ vi Dockstore.json >> { >> "bbFrom": { >> "bbFrom": { >> "path": "https://s3-eu-west-1.amazonaws.com/wtsi-pancancer/reference >> /GRCh37d5_battenberg.tar.gz ", >> "class": "File" >> }, >> "refFrom": { >> "path": "https://s3-eu-west-1.amazonaws.com/wtsi-pancancer/reference >> /GRCh37d5_CGP_refBundle.tar.gz ", >> "class": "File" >> }, >> "tumor": { >> "path": "/home/ubuntu/DockerTest-Miguel/data/7875b5196f6b8b52847f99b >> f370aada0.bam", >> "class": "File" >> }, >> "normal": { >> "path": "/home/ubuntu/DockerTest-Miguel/data/fdcb1bd7cffca69d15383ca >> 9566c58e0.bam", >> "class": "File" >> }, >> "somatic_sv_tar_gz": { >> "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.sv. >> tar.gz", >> "class": "File" >> }, >> "somatic_snv_mnv_tar_gz": { >> "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.snv. >> mnv.tar.gz", >> "class": "File" >> }, >> "somatic_verifyBamId_tar_gz": { >> "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.verif >> yBamId.tar.gz", >> "class": "File" >> }, >> "somatic_cnv_tar_gz": { >> "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.cnv. >> tar.gz", >> "class": "File" >> }, >> "somatic_imputeCounts_tar_gz": { >> "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.imput >> eCounts.tar.gz", >> "class": "File" >> }, >> "somatic_genotype_tar_gz": { >> "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.genot >> ype.tar.gz", >> "class": "File" >> }, >> "somatic_indel_tar_gz": { >> "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.indel >> .tar.gz", >> "class": "File" >> } >> } >> ~ >> ~ >> ~ >> ~ >> ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ l results/ >> ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ vi Dockstore.json ^C >> Updated: Tue Sep 20 13:51:15 UTC 2016 >> Contents Excerpt: >> Command run: >> bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_merge_59.sh >> Command exit code: 0 >> >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_merge_59.stderr >> ----------------------------------------------------------------------- >> >> >> The method 'do_run' exited abnormally so the Runner will terminate here! >> Return value was: 15 >> >> [WARNING] command: seqware bundle launch --dir >> /home/seqware/CGP-Somatic-Docker/target/Workflow_Bundle_CgpS >> omaticCore_0.0.0_SeqWare_1.1.1/ --engine whitestar-parallel --ini >> /var/spool/cwl/workflow.ini --no-metadata exited with code: 15 >> Error while running job: Error collecting output for parameter >> 'somatic_cnv_tar_gz': Did not find output file with glob pattern: >> '['*.somatic.cnv.tar.gz']' >> [job temp319312608049643386.cwl] completed permanentFail >> Final process status is permanentFail >> Workflow error, try again with --debug for more information: >> Process status is ['permanentFail'] >> >> stdout : >> java.lang.RuntimeException: problems running command: cwltool >> --enable-dev --non-strict --enable-net --outdir >> /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher- >> 780ac637-b999-4a70-8ab7-79b51c64f428/outputs/ --tmpdir-prefix >> /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher- >> 780ac637-b999-4a70-8ab7-79b51c64f428/working/ >> /tmp/1474331255066-0/temp319312608049643386.cwl >> /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher- >> 780ac637-b999-4a70-8ab7-79b51c64f428/workflow_params.json >> ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ f >> f: command not found >> ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ df >> Filesystem 1K-blocks Used Available Use% Mounted on >> udev 62947280 12 62947268 1% /dev >> tmpfs 12590448 364 12590084 1% /run >> /dev/xvda1 8115168 6093092 1586800 80% / >> none 4 0 4 0% /sys/fs/cgroup >> none 5120 0 5120 0% /run/lock >> none 62952228 0 62952228 0% /run/shm >> none 102400 0 102400 0% /run/user >> /dev/xvdb 1031992064 303267080 676279800 31% /mnt/1TB >> ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ df -h >> Filesystem Size Used Avail Use% Mounted on >> udev 61G 12K 61G 1% /dev >> tmpfs 13G 364K 13G 1% /run >> /dev/xvda1 7.8G 5.9G 1.6G 80% / >> none 4.0K 0 4.0K 0% /sys/fs/cgroup >> none 5.0M 0 5.0M 0% /run/lock >> none 61G 0 61G 0% /run/shm >> none 100M 0 100M 0% /run/user >> /dev/xvdb 985G 290G 645G 31% /mnt/1TB >> ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ vi Dockstore.json >> >> { >> >> Output from command: /opt/wtsi-cgp/bin/alleleCounter -b >> /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam -o >> /var/spool/cwl/0/ascat/tmpAscat/allele_count/b02b4bba-6e66-44fb-a48f-38c309aaaac5.allct >> -l /var/spool/cwl/reference_files/ascat/SnpLocus.tsv -m 20 >> >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_ASCAT_allele_count_60.stderr >> ----------------------------------------------------------------------- >> >> ----------------------------------------------------------------------- >> Job Name: s58_ASCAT_allele_count_61 >> Job ID: 379374475 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_ASCAT_allele_count_61.e379374475 >> Updated: Tue Sep 20 14:58:41 UTC 2016 >> Contents Excerpt: >> Command run: >> bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_ASCAT_allele_count_61.sh >> Command exit code: 0 >> >> Output from command: /opt/wtsi-cgp/bin/alleleCounter -b >> /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam -o >> /var/spool/cwl/0/ascat/tmpAscat/allele_count/8c0354eb-6a3e-4a98-b41c-f8add599884c.allct >> -l /var/spool/cwl/reference_files/ascat/SnpLocus.tsv -m 20 >> >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_ASCAT_allele_count_61.stderr >> ----------------------------------------------------------------------- >> >> ----------------------------------------------------------------------- >> Job Name: s58_cgpPindel_input_70 >> Job ID: 379374477 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_cgpPindel_input_70.e379374477 >> Updated: Tue Sep 20 13:50:00 UTC 2016 >> Contents Excerpt: >> Command run: >> bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_cgpPindel_input_70.sh >> >> Output from command: /usr/bin/perl /opt/wtsi-cgp/bin/pindel_input_gen.pl >> -b /var/lib/cwl/stg33415604-d4eb- >> 49aa-8f81-345b6fb2a6f3/fdcb1bd7cffca69d15383ca9566c58e0.bam -o >> /var/spool/cwl/0/pindel/tmpPindel/8c0354eb-6a3e-4a98-b41c-f8add599884c >> -t 4 -e /var/spool/cwl/reference_files/brass/ucscHiDepth_0.01_mrg100 >> 0_no_exon_coreChrs.bed.gz >> >> [SeqWare Pipeline] ERROR [2016/09/20 13:50:00] | The exit value was 25 >> Command exit code: 1 >> >> Output from command: /usr/bin/perl /opt/wtsi-cgp/bin/pindel_input_gen.pl >> -b /var/lib/cwl/stg33415604-d4eb- >> 49aa-8f81-345b6fb2a6f3/fdcb1bd7cffca69d15383ca9566c58e0.bam -o >> /var/spool/cwl/0/pindel/tmpPindel/8c0354eb-6a3e-4a98-b41c-f8add599884c >> -t 4 -e /var/spool/cwl/reference_files/brass/ucscHiDepth_0.01_mrg100 >> 0_no_exon_coreChrs.bed.gz >> >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_cgpPindel_input_70.stderr >> ----------------------------------------------------------------------- >> >> ----------------------------------------------------------------------- >> Job Name: s58_bbAllele_merge_59 >> Job ID: 379374478 >> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_merge_59.e379374478 >> Updated: Tue Sep 20 13:51:15 UTC 2016 >> Contents Excerpt: >> Command run: >> bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_merge_59.sh >> Command exit code: 0 >> >> >> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera >> ted-scripts/s58_bbAllele_merge_59.stderr >> ----------------------------------------------------------------------- >> >> >> The method 'do_run' exited abnormally so the Runner will terminate here! >> Return value was: 15 >> >> [WARNING] command: seqware bundle launch --dir >> /home/seqware/CGP-Somatic-Docker/target/Workflow_Bundle_CgpS >> omaticCore_0.0.0_SeqWare_1.1.1/ --engine whitestar-parallel --ini >> /var/spool/cwl/workflow.ini --no-metadata exited with code: 15 >> Error while running job: Error collecting output for parameter >> 'somatic_cnv_tar_gz': Did not find output file with glob pattern: >> '['*.somatic.cnv.tar.gz']' >> [job temp319312608049643386.cwl] completed permanentFail >> Final process status is permanentFail >> Workflow error, try again with --debug for more information: >> Process status is ['permanentFail'] >> >> stdout : >> java.lang.RuntimeException: problems running command: cwltool >> --enable-dev --non-strict --enable-net --outdir >> /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher- >> 780ac637-b999-4a70-8ab7-79b51c64f428/outputs/ --tmpdir-prefix >> /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher- >> 780ac637-b999-4a70-8ab7-79b51c64f428/working/ >> /tmp/1474331255066-0/temp319312608049643386.cwl >> /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher- >> 780ac637-b999-4a70-8ab7-79b51c64f428/workflow_params.json >> >> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: From francis at oicr.on.ca Fri Sep 23 13:02:32 2016 From: francis at oicr.on.ca (Francis Ouellette) Date: Fri, 23 Sep 2016 17:02:32 +0000 Subject: [DOCKTESTERS] updates Message-ID: Hello All, It was great for Junjun and I to see Miguel, Brian and Oliver in Boston. Junjun and Miguel (with some starting help from Brian) had a good first stab at testing a Sanger-SNV workflow with ICGC data ? It didn?t quite work, but with the help of Dennis, we have some good next-step ideas on what to try next. If either of you try something before Monday?s PCAWG-tech call please let me know, and I will add that to my docktester update. Other update, Gordon (from the Broad) is now part of this list. I add below the full list membership. The home page on the wiki is here: https://wiki.oicr.on.ca/display/PANCANCER/PCAWG+Docker+%28Dockstore%29+Testing+Working+Group So, we now have a growing google doc with the steps we have taken to get things going, and it will be good for others to use this for their testing, and to add their own ?if-then? statements, and to make this a richer document which we will use for all testing. https://docs.google.com/document/d/1EPo2Wgh-WJz75GdykgTI1fpm89yIdoGGHAyVlJ9PbcA/edit (there is also a link to this page on the wiki: https://wiki.oicr.on.ca/display/PANCANCER/Workflow+Testing+SOP ) If you are doing a test, please consult with me and note it on this page: https://wiki.oicr.on.ca/display/PANCANCER/Workflow+Testing+Data Let me know if you have questions. Right now we are trying to get simplest workflow (sanger ;) to work on ICGC data ? We will test on TCGA data later, and other dockers as well. Cheers to all, and again, thank you Miguel and Junjun for getting us started! @bffo brian.oconnor at oicr.on.ca broconno at ucsc.edu christina.Yung at oicr.on.ca denis.Yuen at oicr.on.ca ellrott at ohsu.edu francis at oicr.on.ca gsaksena at broadinstitute.org junjun.zhang at oicr.on.ca miguel.vazquez at cnio.es ohofmann72 at gmail.com solomon.shorser at oicr.on.ca strucka at ohsu.edu zhibin.Lu at oicr.on.ca From francis at oicr.on.ca Fri Sep 30 09:52:20 2016 From: francis at oicr.on.ca (Francis Ouellette) Date: Fri, 30 Sep 2016 13:52:20 +0000 Subject: [DOCKTESTERS] Fwd: [PAWG-TECH] Draft agenda for PCAWG-TECH teleconference References: <0F84ED6166CE664E8563B61CB2ECB98CCBA7F1FA@exmb2.ad.oicr.on.ca> Message-ID: <16D5F0B4-2278-4A78-A038-02A3C61737CF@oicr.on.ca> Dear Miguel and Junjun, Any more attempts on testing the PCAWG sanger docker container? If you reproduce the same error, we will need to involve Bryan and Keiran Raine > (author of the container). Let?s get this one figured out. I am going to assume that the making of the docker container is what needs resolving. Brian: We may need your input here. Details of our current experiment should continue to be posted here: https://goo.gl/XX5BG9 Thank you all, francis PS would be good for others on list to follow directions on above google doc and also see if they can succeed on this workflow. Junjun and Miguel have tried different clouds, but used the sanger workflow, on the same data set. Thank you for trying to do this. Would be good if I heard back from anybody before Monday AM (tech call). @bffo PS I CCed Keiran, but waiting to hear back from Brian before we need to involve him some more. PPS Junjun/Miguel: maybe you can try the DKFZ docker as well? (on the same data set). -- B.F. Francis Ouellette http://oicr.on.ca/person/francis-ouellette Begin forwarded message: From: Christina Yung > Subject: [PAWG-TECH] Draft agenda for PCAWG-TECH teleconference Date: September 30, 2016 at 9:19:39 AM EDT To: "pawg-tech (pawg-tech at lists.icgc.org)" > Hi Everyone, Below is a draft agenda for Monday?s tech call. Please let me know if you have any agenda items for discussion. https://wiki.oicr.on.ca/display/PANCANCER/2016-10-03+PCAWG-TECH+Teleconference Have a great weekend! Christina Call Info Usual Time 9 AM Eastern Time, Mondays UK 0208 322 2500 Canada 1-866-220-6419 United States 1-877-420-0272 All Others Please see attached PDF file with a list of numbers for other countries. Participant Code 5910819# Agenda Time Item Who Attachments/Links 5min Welcome. Wait for group members to log on Christina Yung, OICR 10min Overall status Christina Yung, OICR ? Linkouts to Most Current PCAWG Data ? Report data issues to pcawg-data at icgc.org, GNOS issue to: Help at annaisystems.com ? From Boston F2F: PCAWG datasets & dependencies Action Items 1. [Joachim] Consensus SV - final? 2. [Jakob] Consensus SNVs - changes to "SNV near indels" annotation? 3. [Junjun] Specimen ID mapping for miRNA and methylation 4. [Jonathan & Joachim] Consensus calls for cell lines, followed by filtering 5. [Matthias & Gordon] Docker containers for filtering methods 6. [Christina] Run alignment & variant workflows on medulloblastoma sample (tumor 40x, normal 30x) from ICGC benchmark to estimate false negative rate 7. [Christina] Follow up with institutes interested in hosting PCAWG data long-term 8. [All] As per Jennifer's email on Sept 16, please provide authorship information again or for the first time using PCAWG Author Form (http://goo.gl/forms/5Wq5x5X1DK). Save the link "Edit your response" so you can go back later to provide updates, for example about your evolving role in writing specific papers. 9. [All] Contribute to the manuscripts on a. infrastructure: https://docs.google.com/document/d/10alAxrWLdLSyhci-rfNuVH13rFXCJkaY_rzf1KJn7nc/edit b. variants: Paper ( https://goo.gl/g9CLsu ), Supplement ( https://goo.gl/EWYh7e ) c. Rogue's Gallery of Cancer Genome Sequencing Artifacts ( outline ) 10. [Junjun] Discuss PCAWG vs DCC glossary terms at next PCAWG-10/13 conference 10min Status of dockerizing workflows Brian O'Connor, UCSC Gordon Saksena, Broad Francis Ouellette, OICR Status of PCAWG Workflow ports to Dockstore: Denis has been porting the Dockstore entries to CWL version 1.0 which is part of our effort to publish Dockstore (this doesn't affect the content of the pipelines, simply their "descriptors" which allow them to be runnable via Dockstore). Denis has also worked on testing BWA-Mem, Sanger, EMBL (which all work with CWL 1.0 and Kerian's test dataset) and has fixed issues with DKFZ and is testing the latter with a real sample shortly. 1. BWA-Mem - Ready for testing by Francis' team 2. Sanger - Ready for testing by Francis' team. 3. EMBL - Ready for testing by Francis' team. 4. DKFZ - Ready for testing by Francis' team. I've exchanged emails with Manuel Ballesteros who has been testing this pipeline. 5. Broad - Variant calling (MuTect, dRanger, snowman), need some work, Gordan sent details previously 6. OxoG - Waiting for Dimitri to provide OxoG docker 7. Variantbam 8. Consensus algorithm PCAWG Docker (Dockstore) Testing Working Group 5min Other business? Group Christina K. Yung, PhD Project Manager, Cancer Genome Collaboratory Ontario Institute for Cancer Research MaRS Centre 661 University Avenue, Suite 510 Toronto, Ontario, Canada M5G 0A3 Tel: 416-673-8578 www.oicr.on.ca This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization. _______________________________________________ PAWG-TECH mailing list PAWG-TECH at lists.icgc.org https://lists.icgc.org/mailman/listinfo/pawg-tech -------------- next part -------------- An HTML attachment was scrubbed... URL: From Denis.Yuen at oicr.on.ca Fri Sep 30 10:10:53 2016 From: Denis.Yuen at oicr.on.ca (Denis Yuen) Date: Fri, 30 Sep 2016 14:10:53 +0000 Subject: [DOCKTESTERS] Fwd: [PAWG-TECH] Draft agenda for PCAWG-TECH teleconference In-Reply-To: <16D5F0B4-2278-4A78-A038-02A3C61737CF@oicr.on.ca> References: <0F84ED6166CE664E8563B61CB2ECB98CCBA7F1FA@exmb2.ad.oicr.on.ca>, <16D5F0B4-2278-4A78-A038-02A3C61737CF@oicr.on.ca> Message-ID: <27512884B2D81B41AAB7BB266248F240C09A0330@exmb2.ad.oicr.on.ca> Hi, I'd like to add a reminder to test your environment by running through test data (that we've run successfully through on the Dockstore side) before trying real data. That will hopefully allow us to distinguish between environmental/setup issues and issues with the actual pipeline. For Sanger, that would be: https://github.com/ICGC-TCGA-PanCancer/CGP-Somatic-Docker/blob/develop/test1.json For DKFZ, that would be: https://github.com/ICGC-TCGA-PanCancer/dkfz_dockered_workflows/blob/develop/Dockstore-BTCA-SG.json Denis Yuen Bioinformatics Software Developer Ontario Institute for Cancer Research MaRS Centre 661 University Avenue Suite 510 Toronto, Ontario, Canada M5G 0A3 Toll-free: 1-866-678-6427 Twitter: @OICR_news www.oicr.on.ca This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization. ________________________________ From: docktesters-bounces+denis.yuen=oicr.on.ca at lists.icgc.org [docktesters-bounces+denis.yuen=oicr.on.ca at lists.icgc.org] on behalf of Francis Ouellette [francis at oicr.on.ca] Sent: September 30, 2016 9:52 AM To: docktesters at lists.icgc.org Cc: kr2 at sanger.ac.uk Subject: [DOCKTESTERS] Fwd: [PAWG-TECH] Draft agenda for PCAWG-TECH teleconference Dear Miguel and Junjun, Any more attempts on testing the PCAWG sanger docker container? If you reproduce the same error, we will need to involve Bryan and Keiran Raine > (author of the container). Let?s get this one figured out. I am going to assume that the making of the docker container is what needs resolving. Brian: We may need your input here. Details of our current experiment should continue to be posted here: https://goo.gl/XX5BG9 Thank you all, francis PS would be good for others on list to follow directions on above google doc and also see if they can succeed on this workflow. Junjun and Miguel have tried different clouds, but used the sanger workflow, on the same data set. Thank you for trying to do this. Would be good if I heard back from anybody before Monday AM (tech call). @bffo PS I CCed Keiran, but waiting to hear back from Brian before we need to involve him some more. PPS Junjun/Miguel: maybe you can try the DKFZ docker as well? (on the same data set). -- B.F. Francis Ouellette http://oicr.on.ca/person/francis-ouellette Begin forwarded message: From: Christina Yung > Subject: [PAWG-TECH] Draft agenda for PCAWG-TECH teleconference Date: September 30, 2016 at 9:19:39 AM EDT To: "pawg-tech (pawg-tech at lists.icgc.org)" > Hi Everyone, Below is a draft agenda for Monday?s tech call. Please let me know if you have any agenda items for discussion. https://wiki.oicr.on.ca/display/PANCANCER/2016-10-03+PCAWG-TECH+Teleconference Have a great weekend! Christina Call Info Usual Time 9 AM Eastern Time, Mondays UK 0208 322 2500 Canada 1-866-220-6419 United States 1-877-420-0272 All Others Please see attached PDF file with a list of numbers for other countries. Participant Code 5910819# Agenda Time Item Who Attachments/Links 5min Welcome. Wait for group members to log on Christina Yung, OICR 10min Overall status Christina Yung, OICR ? Linkouts to Most Current PCAWG Data ? Report data issues to pcawg-data at icgc.org, GNOS issue to: Help at annaisystems.com ? From Boston F2F: PCAWG datasets & dependencies Action Items 1. [Joachim] Consensus SV - final? 2. [Jakob] Consensus SNVs - changes to "SNV near indels" annotation? 3. [Junjun] Specimen ID mapping for miRNA and methylation 4. [Jonathan & Joachim] Consensus calls for cell lines, followed by filtering 5. [Matthias & Gordon] Docker containers for filtering methods 6. [Christina] Run alignment & variant workflows on medulloblastoma sample (tumor 40x, normal 30x) from ICGC benchmark to estimate false negative rate 7. [Christina] Follow up with institutes interested in hosting PCAWG data long-term 8. [All] As per Jennifer's email on Sept 16, please provide authorship information again or for the first time using PCAWG Author Form (http://goo.gl/forms/5Wq5x5X1DK). Save the link "Edit your response" so you can go back later to provide updates, for example about your evolving role in writing specific papers. 9. [All] Contribute to the manuscripts on a. infrastructure: https://docs.google.com/document/d/10alAxrWLdLSyhci-rfNuVH13rFXCJkaY_rzf1KJn7nc/edit b. variants: Paper ( https://goo.gl/g9CLsu ), Supplement ( https://goo.gl/EWYh7e ) c. Rogue's Gallery of Cancer Genome Sequencing Artifacts ( outline ) 10. [Junjun] Discuss PCAWG vs DCC glossary terms at next PCAWG-10/13 conference 10min Status of dockerizing workflows Brian O'Connor, UCSC Gordon Saksena, Broad Francis Ouellette, OICR Status of PCAWG Workflow ports to Dockstore: Denis has been porting the Dockstore entries to CWL version 1.0 which is part of our effort to publish Dockstore (this doesn't affect the content of the pipelines, simply their "descriptors" which allow them to be runnable via Dockstore). Denis has also worked on testing BWA-Mem, Sanger, EMBL (which all work with CWL 1.0 and Kerian's test dataset) and has fixed issues with DKFZ and is testing the latter with a real sample shortly. 1. BWA-Mem - Ready for testing by Francis' team 2. Sanger - Ready for testing by Francis' team. 3. EMBL - Ready for testing by Francis' team. 4. DKFZ - Ready for testing by Francis' team. I've exchanged emails with Manuel Ballesteros who has been testing this pipeline. 5. Broad - Variant calling (MuTect, dRanger, snowman), need some work, Gordan sent details previously 6. OxoG - Waiting for Dimitri to provide OxoG docker 7. Variantbam 8. Consensus algorithm PCAWG Docker (Dockstore) Testing Working Group 5min Other business? Group Christina K. Yung, PhD Project Manager, Cancer Genome Collaboratory Ontario Institute for Cancer Research MaRS Centre 661 University Avenue, Suite 510 Toronto, Ontario, Canada M5G 0A3 Tel: 416-673-8578 www.oicr.on.ca This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization. _______________________________________________ PAWG-TECH mailing list PAWG-TECH at lists.icgc.org https://lists.icgc.org/mailman/listinfo/pawg-tech -------------- next part -------------- An HTML attachment was scrubbed... URL: From francis at oicr.on.ca Fri Sep 30 10:28:48 2016 From: francis at oicr.on.ca (Francis Ouellette) Date: Fri, 30 Sep 2016 14:28:48 +0000 Subject: [DOCKTESTERS] [PAWG-TECH] Draft agenda for PCAWG-TECH teleconference In-Reply-To: <27512884B2D81B41AAB7BB266248F240C09A0330@exmb2.ad.oicr.on.ca> References: <0F84ED6166CE664E8563B61CB2ECB98CCBA7F1FA@exmb2.ad.oicr.on.ca> <16D5F0B4-2278-4A78-A038-02A3C61737CF@oicr.on.ca> <27512884B2D81B41AAB7BB266248F240C09A0330@exmb2.ad.oicr.on.ca> Message-ID: <77F97A09-FDEF-4C65-99AF-E9AD71A25BDB@oicr.on.ca> I added this information to the google doc. https://goo.gl/XX5BG9 @bffo -- B.F. Francis Ouellette http://oicr.on.ca/person/francis-ouellette On Sep 30, 2016, at 10:10 AM, Denis Yuen > wrote: Hi, I'd like to add a reminder to test your environment by running through test data (that we've run successfully through on the Dockstore side) before trying real data. That will hopefully allow us to distinguish between environmental/setup issues and issues with the actual pipeline. For Sanger, that would be: https://github.com/ICGC-TCGA-PanCancer/CGP-Somatic-Docker/blob/develop/test1.json For DKFZ, that would be: https://github.com/ICGC-TCGA-PanCancer/dkfz_dockered_workflows/blob/develop/Dockstore-BTCA-SG.json Denis Yuen Bioinformatics Software Developer Ontario Institute for Cancer Research MaRS Centre 661 University Avenue Suite 510 Toronto, Ontario, Canada M5G 0A3 Toll-free: 1-866-678-6427 Twitter: @OICR_news www.oicr.on.ca This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization. ________________________________ From: docktesters-bounces+denis.yuen=oicr.on.ca at lists.icgc.org [docktesters-bounces+denis.yuen=oicr.on.ca at lists.icgc.org] on behalf of Francis Ouellette [francis at oicr.on.ca] Sent: September 30, 2016 9:52 AM To: docktesters at lists.icgc.org Cc: kr2 at sanger.ac.uk Subject: [DOCKTESTERS] Fwd: [PAWG-TECH] Draft agenda for PCAWG-TECH teleconference Dear Miguel and Junjun, Any more attempts on testing the PCAWG sanger docker container? If you reproduce the same error, we will need to involve Bryan and Keiran Raine > (author of the container). Let?s get this one figured out. I am going to assume that the making of the docker container is what needs resolving. Brian: We may need your input here. Details of our current experiment should continue to be posted here: https://goo.gl/XX5BG9 Thank you all, francis PS would be good for others on list to follow directions on above google doc and also see if they can succeed on this workflow. Junjun and Miguel have tried different clouds, but used the sanger workflow, on the same data set. Thank you for trying to do this. Would be good if I heard back from anybody before Monday AM (tech call). @bffo PS I CCed Keiran, but waiting to hear back from Brian before we need to involve him some more. PPS Junjun/Miguel: maybe you can try the DKFZ docker as well? (on the same data set). -- B.F. Francis Ouellette http://oicr.on.ca/person/francis-ouellette Begin forwarded message: From: Christina Yung > Subject: [PAWG-TECH] Draft agenda for PCAWG-TECH teleconference Date: September 30, 2016 at 9:19:39 AM EDT To: "pawg-tech (pawg-tech at lists.icgc.org)" > Hi Everyone, Below is a draft agenda for Monday?s tech call. Please let me know if you have any agenda items for discussion. https://wiki.oicr.on.ca/display/PANCANCER/2016-10-03+PCAWG-TECH+Teleconference Have a great weekend! Christina Call Info Usual Time 9 AM Eastern Time, Mondays UK 0208 322 2500 Canada 1-866-220-6419 United States 1-877-420-0272 All Others Please see attached PDF file with a list of numbers for other countries. Participant Code 5910819# Agenda Time Item Who Attachments/Links 5min Welcome. Wait for group members to log on Christina Yung, OICR 10min Overall status Christina Yung, OICR ? Linkouts to Most Current PCAWG Data ? Report data issues to pcawg-data at icgc.org, GNOS issue to: Help at annaisystems.com ? From Boston F2F: PCAWG datasets & dependencies Action Items 1. [Joachim] Consensus SV - final? 2. [Jakob] Consensus SNVs - changes to "SNV near indels" annotation? 3. [Junjun] Specimen ID mapping for miRNA and methylation 4. [Jonathan & Joachim] Consensus calls for cell lines, followed by filtering 5. [Matthias & Gordon] Docker containers for filtering methods 6. [Christina] Run alignment & variant workflows on medulloblastoma sample (tumor 40x, normal 30x) from ICGC benchmark to estimate false negative rate 7. [Christina] Follow up with institutes interested in hosting PCAWG data long-term 8. [All] As per Jennifer's email on Sept 16, please provide authorship information again or for the first time using PCAWG Author Form (http://goo.gl/forms/5Wq5x5X1DK). Save the link "Edit your response" so you can go back later to provide updates, for example about your evolving role in writing specific papers. 9. [All] Contribute to the manuscripts on a. infrastructure: https://docs.google.com/document/d/10alAxrWLdLSyhci-rfNuVH13rFXCJkaY_rzf1KJn7nc/edit b. variants: Paper ( https://goo.gl/g9CLsu ), Supplement ( https://goo.gl/EWYh7e ) c. Rogue's Gallery of Cancer Genome Sequencing Artifacts ( outline ) 10. [Junjun] Discuss PCAWG vs DCC glossary terms at next PCAWG-10/13 conference 10min Status of dockerizing workflows Brian O'Connor, UCSC Gordon Saksena, Broad Francis Ouellette, OICR Status of PCAWG Workflow ports to Dockstore: Denis has been porting the Dockstore entries to CWL version 1.0 which is part of our effort to publish Dockstore (this doesn't affect the content of the pipelines, simply their "descriptors" which allow them to be runnable via Dockstore). Denis has also worked on testing BWA-Mem, Sanger, EMBL (which all work with CWL 1.0 and Kerian's test dataset) and has fixed issues with DKFZ and is testing the latter with a real sample shortly. 1. BWA-Mem - Ready for testing by Francis' team 2. Sanger - Ready for testing by Francis' team. 3. EMBL - Ready for testing by Francis' team. 4. DKFZ - Ready for testing by Francis' team. I've exchanged emails with Manuel Ballesteros who has been testing this pipeline. 5. Broad - Variant calling (MuTect, dRanger, snowman), need some work, Gordan sent details previously 6. OxoG - Waiting for Dimitri to provide OxoG docker 7. Variantbam 8. Consensus algorithm PCAWG Docker (Dockstore) Testing Working Group 5min Other business? Group Christina K. Yung, PhD Project Manager, Cancer Genome Collaboratory Ontario Institute for Cancer Research MaRS Centre 661 University Avenue, Suite 510 Toronto, Ontario, Canada M5G 0A3 Tel: 416-673-8578 www.oicr.on.ca This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization. _______________________________________________ PAWG-TECH mailing list PAWG-TECH at lists.icgc.org https://lists.icgc.org/mailman/listinfo/pawg-tech -------------- next part -------------- An HTML attachment was scrubbed... URL: From miguel.vazquez at cnio.es Fri Sep 30 10:46:11 2016 From: miguel.vazquez at cnio.es (Miguel Vazquez) Date: Fri, 30 Sep 2016 16:46:11 +0200 Subject: [DOCKTESTERS] Fwd: [PAWG-TECH] Draft agenda for PCAWG-TECH teleconference In-Reply-To: <16D5F0B4-2278-4A78-A038-02A3C61737CF@oicr.on.ca> References: <0F84ED6166CE664E8563B61CB2ECB98CCBA7F1FA@exmb2.ad.oicr.on.ca> <16D5F0B4-2278-4A78-A038-02A3C61737CF@oicr.on.ca> Message-ID: Dear Francis, I haven't had a chance to go at it again since the meeting, I got a new position in Norway, but next week I will try to find some time. I think I might just try another pipeline, since it seems like the Sanger pipeline needs fixing. Although perhaps I will first try Denis test data again and see if I can reproduce the error, after which we probably should contact the person in charge. Best M On Fri, Sep 30, 2016 at 3:52 PM, Francis Ouellette wrote: > Dear Miguel and Junjun, > > Any more attempts on testing the PCAWG sanger docker container? > > If you reproduce the same error, we will need to involve Bryan and > Keiran Raine (author of the container). > > Let?s get this one figured out. > > I am going to assume that the making of the docker container is what > needs resolving. > > Brian: We may need your input here. > > Details of our current experiment should continue to be posted here: > > https://goo.gl/XX5BG9 > > Thank you all, > > francis > > PS would be good for others on list to follow directions on above google > doc and also see if they can succeed on this workflow. > > Junjun and Miguel have tried different clouds, but used the sanger > workflow, on the same data set. > > Thank you for trying to do this. > > Would be good if I heard back from anybody before Monday AM (tech call). > > @bffo > > PS I CCed Keiran, but waiting to hear back from Brian before we need to > involve him some more. > PPS Junjun/Miguel: maybe you can try the DKFZ docker as well? (on the same > data set). > > > -- > B.F. Francis Ouellette http://oicr.on.ca/person/francis-ouellette > > > > > Begin forwarded message: > > *From: *Christina Yung > *Subject: **[PAWG-TECH] Draft agenda for PCAWG-TECH teleconference* > *Date: *September 30, 2016 at 9:19:39 AM EDT > *To: *"pawg-tech (pawg-tech at lists.icgc.org)" > > Hi Everyone, > > > > Below is a draft agenda for Monday?s tech call. Please let me know if you > have any agenda items for discussion. > > https://wiki.oicr.on.ca/display/PANCANCER/2016-10-03+ > PCAWG-TECH+Teleconference > > > > Have a great weekend! > > Christina > > > Call Info > > *Usual Time 9 AM Eastern Time, Mondays* > > *UK 0208 322 2500* > > *Canada 1-866-220-6419* > > *United States **1-877-420-0272* > > *All Others Please see attached PDF file > with > a list of numbers for other countries.* > > *Participant Code 5910819#* > Agenda > > > > *Time* > > *Item* > > *Who* > > *Attachments/Links* > > 5min > > Welcome. Wait for group members to log on > > Christina Yung , OICR > > 10min > > Overall status > Christina Yung , OICR > > ? Linkouts to Most Current PCAWG Data > > > ? Report data issues to pcawg-data at icgc.org, GNOS issue to: > Help at annaisystems.com > > ? From Boston F2F: PCAWG datasets & dependencies > > > *Action Items* > > 1. [Joachim] Consensus SV - final? > > 2. [Jakob] Consensus SNVs - changes to "SNV near indels" annotation? > > 3. [Junjun] Specimen ID mapping for miRNA and methylation > > 4. [Jonathan & Joachim] Consensus calls for cell lines, followed by > filtering > > 5. [Matthias & Gordon] Docker containers for filtering methods > > 6. [Christina] Run alignment & variant workflows on medulloblastoma > sample (tumor 40x, normal 30x) from ICGC benchmark to estimate false > negative rate > > 7. [Christina] Follow up with institutes interested in hosting > PCAWG data long-term > > 8. [All] As per Jennifer's email on Sept 16, please provide > authorship information again or for the first time using PCAWG Author Form ( > http://goo.gl/forms/5Wq5x5X1DK). Save the link "Edit your response" so > you can go back later to provide updates, for example about your evolving > role in writing specific papers. > > 9. [All] Contribute to the manuscripts on > > a. infrastructure: https://docs.google.com/ > document/d/10alAxrWLdLSyhci-rfNuVH13rFXCJkaY_rzf1KJn7nc/edit > > b. variants: Paper ( https://goo.gl/g9CLsu ), Supplement ( > https://goo.gl/EWYh7e ) > > c. Rogue's Gallery of Cancer Genome Sequencing Artifacts ( outline > > ) > > 10. [Junjun] Discuss PCAWG vs DCC glossary terms at next PCAWG-10/13 > conference > > 10min > > Status of dockerizing workflows > Brian O'Connor , UCSC > > Gordon Saksena > , Broad > > Francis Ouellette , OICR > *Status of PCAWG Workflow ports to Dockstore*: > > Denis has been porting the Dockstore entries to CWL version 1.0 which is > part of our effort to publish Dockstore (this doesn't affect the content of > the pipelines, simply their "descriptors" which allow them to be runnable > via Dockstore). Denis has also worked on testing BWA-Mem, Sanger, EMBL > (which all work with CWL 1.0 and Kerian's test dataset) and has fixed > issues with DKFZ and is testing the latter with a real sample shortly. > > 1. BWA-Mem - Ready for testing by Francis' team > > 2. Sanger - Ready for testing by Francis' team. > > 3. EMBL - Ready for testing by Francis' team. > > 4. DKFZ - Ready for testing by Francis' team. I've exchanged emails > with Manuel Ballesteros who has been testing this pipeline. > > 5. Broad - Variant calling (MuTect, dRanger, snowman), need some > work, Gordan sent details previously > > 6. OxoG - Waiting for Dimitri to provide OxoG docker > > 7. Variantbam > > 8. Consensus algorithm > > PCAWG Docker (Dockstore) Testing Working Group > > > 5min > > Other business? > > Group > > > > > > > > *Christina K. Yung, PhD* > Project Manager, Cancer Genome Collaboratory > > *Ontario Institute for Cancer Research* > MaRS Centre > > 661 University Avenue, Suite 510 > Toronto, Ontario, Canada M5G 0A3 > Tel: 416-673-8578 > > www.oicr.on.ca > > > > This message and any attachments may contain confidential and/or > privileged information for the sole use of the intended recipient. Any > review or distribution by anyone other than the person for whom it was > originally intended is strictly prohibited. If you have received this > message in error, please contact the sender and delete all copies. > Opinions, conclusions or other information contained in this message may > not be that of the organization. > > > _______________________________________________ > PAWG-TECH mailing list > PAWG-TECH at lists.icgc.org > https://lists.icgc.org/mailman/listinfo/pawg-tech > > > > _______________________________________________ > docktesters mailing list > docktesters at lists.icgc.org > https://lists.icgc.org/mailman/listinfo/docktesters > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From francis at oicr.on.ca Fri Sep 30 10:52:25 2016 From: francis at oicr.on.ca (Francis Ouellette) Date: Fri, 30 Sep 2016 14:52:25 +0000 Subject: [DOCKTESTERS] [PAWG-TECH] Draft agenda for PCAWG-TECH teleconference In-Reply-To: References: <0F84ED6166CE664E8563B61CB2ECB98CCBA7F1FA@exmb2.ad.oicr.on.ca> <16D5F0B4-2278-4A78-A038-02A3C61737CF@oicr.on.ca> Message-ID: <6DDD0535-6E45-413E-8E93-60E22F6C3510@oicr.on.ca> yes, good plan. @bffo -- B.F. Francis Ouellette http://oicr.on.ca/person/francis-ouellette On Sep 30, 2016, at 10:46 AM, Miguel Vazquez > wrote: Dear Francis, I haven't had a chance to go at it again since the meeting, I got a new position in Norway, but next week I will try to find some time. I think I might just try another pipeline, since it seems like the Sanger pipeline needs fixing. Although perhaps I will first try Denis test data again and see if I can reproduce the error, after which we probably should contact the person in charge. Best M On Fri, Sep 30, 2016 at 3:52 PM, Francis Ouellette > wrote: Dear Miguel and Junjun, Any more attempts on testing the PCAWG sanger docker container? If you reproduce the same error, we will need to involve Bryan and Keiran Raine > (author of the container). Let?s get this one figured out. I am going to assume that the making of the docker container is what needs resolving. Brian: We may need your input here. Details of our current experiment should continue to be posted here: https://goo.gl/XX5BG9 Thank you all, francis PS would be good for others on list to follow directions on above google doc and also see if they can succeed on this workflow. Junjun and Miguel have tried different clouds, but used the sanger workflow, on the same data set. Thank you for trying to do this. Would be good if I heard back from anybody before Monday AM (tech call). @bffo PS I CCed Keiran, but waiting to hear back from Brian before we need to involve him some more. PPS Junjun/Miguel: maybe you can try the DKFZ docker as well? (on the same data set). -- B.F. Francis Ouellette http://oicr.on.ca/person/francis-ouellette Begin forwarded message: From: Christina Yung > Subject: [PAWG-TECH] Draft agenda for PCAWG-TECH teleconference Date: September 30, 2016 at 9:19:39 AM EDT To: "pawg-tech (pawg-tech at lists.icgc.org)" > Hi Everyone, Below is a draft agenda for Monday?s tech call. Please let me know if you have any agenda items for discussion. https://wiki.oicr.on.ca/display/PANCANCER/2016-10-03+PCAWG-TECH+Teleconference Have a great weekend! Christina Call Info Usual Time 9 AM Eastern Time, Mondays UK 0208 322 2500 Canada 1-866-220-6419 United States 1-877-420-0272 All Others Please see attached PDF file with a list of numbers for other countries. Participant Code 5910819# Agenda Time Item Who Attachments/Links 5min Welcome. Wait for group members to log on Christina Yung, OICR 10min Overall status Christina Yung, OICR ? Linkouts to Most Current PCAWG Data ? Report data issues to pcawg-data at icgc.org, GNOS issue to: Help at annaisystems.com ? From Boston F2F: PCAWG datasets & dependencies Action Items 1. [Joachim] Consensus SV - final? 2. [Jakob] Consensus SNVs - changes to "SNV near indels" annotation? 3. [Junjun] Specimen ID mapping for miRNA and methylation 4. [Jonathan & Joachim] Consensus calls for cell lines, followed by filtering 5. [Matthias & Gordon] Docker containers for filtering methods 6. [Christina] Run alignment & variant workflows on medulloblastoma sample (tumor 40x, normal 30x) from ICGC benchmark to estimate false negative rate 7. [Christina] Follow up with institutes interested in hosting PCAWG data long-term 8. [All] As per Jennifer's email on Sept 16, please provide authorship information again or for the first time using PCAWG Author Form (http://goo.gl/forms/5Wq5x5X1DK). Save the link "Edit your response" so you can go back later to provide updates, for example about your evolving role in writing specific papers. 9. [All] Contribute to the manuscripts on a. infrastructure: https://docs.google.com/document/d/10alAxrWLdLSyhci-rfNuVH13rFXCJkaY_rzf1KJn7nc/edit b. variants: Paper ( https://goo.gl/g9CLsu ), Supplement ( https://goo.gl/EWYh7e ) c. Rogue's Gallery of Cancer Genome Sequencing Artifacts ( outline ) 10. [Junjun] Discuss PCAWG vs DCC glossary terms at next PCAWG-10/13 conference 10min Status of dockerizing workflows Brian O'Connor, UCSC Gordon Saksena, Broad Francis Ouellette, OICR Status of PCAWG Workflow ports to Dockstore: Denis has been porting the Dockstore entries to CWL version 1.0 which is part of our effort to publish Dockstore (this doesn't affect the content of the pipelines, simply their "descriptors" which allow them to be runnable via Dockstore). Denis has also worked on testing BWA-Mem, Sanger, EMBL (which all work with CWL 1.0 and Kerian's test dataset) and has fixed issues with DKFZ and is testing the latter with a real sample shortly. 1. BWA-Mem - Ready for testing by Francis' team 2. Sanger - Ready for testing by Francis' team. 3. EMBL - Ready for testing by Francis' team. 4. DKFZ - Ready for testing by Francis' team. I've exchanged emails with Manuel Ballesteros who has been testing this pipeline. 5. Broad - Variant calling (MuTect, dRanger, snowman), need some work, Gordan sent details previously 6. OxoG - Waiting for Dimitri to provide OxoG docker 7. Variantbam 8. Consensus algorithm PCAWG Docker (Dockstore) Testing Working Group 5min Other business? Group Christina K. Yung, PhD Project Manager, Cancer Genome Collaboratory Ontario Institute for Cancer Research MaRS Centre 661 University Avenue, Suite 510 Toronto, Ontario, Canada M5G 0A3 Tel: 416-673-8578 www.oicr.on.ca This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization. _______________________________________________ PAWG-TECH mailing list PAWG-TECH at lists.icgc.org https://lists.icgc.org/mailman/listinfo/pawg-tech _______________________________________________ docktesters mailing list docktesters at lists.icgc.org https://lists.icgc.org/mailman/listinfo/docktesters -------------- next part -------------- An HTML attachment was scrubbed... URL: From strucka at ohsu.edu Fri Sep 30 12:02:53 2016 From: strucka at ohsu.edu (Adam Struck) Date: Fri, 30 Sep 2016 16:02:53 +0000 Subject: [DOCKTESTERS] [PAWG-TECH] Draft agenda for PCAWG-TECH teleconference In-Reply-To: <6DDD0535-6E45-413E-8E93-60E22F6C3510@oicr.on.ca> References: <0F84ED6166CE664E8563B61CB2ECB98CCBA7F1FA@exmb2.ad.oicr.on.ca> <16D5F0B4-2278-4A78-A038-02A3C61737CF@oicr.on.ca> , <6DDD0535-6E45-413E-8E93-60E22F6C3510@oicr.on.ca> Message-ID: <8231F9BE-D796-4F7C-9F61-8BAEA336F038@ohsu.edu> I thought I should add that I've run the Sanger pipeline on the test data in three separate environments using both CWL and WDL descriptors. Feel free to email me the errors you are seeing and I'll try and debug. Adam Struck Scientific Programmer Computational Biology Oregon Health and Science University On Sep 30, 2016, at 7:52 AM, Francis Ouellette > wrote: yes, good plan. @bffo -- B.F. Francis Ouellette http://oicr.on.ca/person/francis-ouellette On Sep 30, 2016, at 10:46 AM, Miguel Vazquez > wrote: Dear Francis, I haven't had a chance to go at it again since the meeting, I got a new position in Norway, but next week I will try to find some time. I think I might just try another pipeline, since it seems like the Sanger pipeline needs fixing. Although perhaps I will first try Denis test data again and see if I can reproduce the error, after which we probably should contact the person in charge. Best M On Fri, Sep 30, 2016 at 3:52 PM, Francis Ouellette > wrote: Dear Miguel and Junjun, Any more attempts on testing the PCAWG sanger docker container? If you reproduce the same error, we will need to involve Bryan and Keiran Raine > (author of the container). Let?s get this one figured out. I am going to assume that the making of the docker container is what needs resolving. Brian: We may need your input here. Details of our current experiment should continue to be posted here: https://goo.gl/XX5BG9 Thank you all, francis PS would be good for others on list to follow directions on above google doc and also see if they can succeed on this workflow. Junjun and Miguel have tried different clouds, but used the sanger workflow, on the same data set. Thank you for trying to do this. Would be good if I heard back from anybody before Monday AM (tech call). @bffo PS I CCed Keiran, but waiting to hear back from Brian before we need to involve him some more. PPS Junjun/Miguel: maybe you can try the DKFZ docker as well? (on the same data set). -- B.F. Francis Ouellette http://oicr.on.ca/person/francis-ouellette Begin forwarded message: From: Christina Yung > Subject: [PAWG-TECH] Draft agenda for PCAWG-TECH teleconference Date: September 30, 2016 at 9:19:39 AM EDT To: "pawg-tech (pawg-tech at lists.icgc.org)" > Hi Everyone, Below is a draft agenda for Monday?s tech call. Please let me know if you have any agenda items for discussion. https://wiki.oicr.on.ca/display/PANCANCER/2016-10-03+PCAWG-TECH+Teleconference Have a great weekend! Christina Call Info Usual Time 9 AM Eastern Time, Mondays UK 0208 322 2500 Canada 1-866-220-6419 United States 1-877-420-0272 All Others Please see attached PDF file with a list of numbers for other countries. Participant Code 5910819# Agenda Time Item Who Attachments/Links 5min Welcome. Wait for group members to log on Christina Yung, OICR 10min Overall status Christina Yung, OICR ? Linkouts to Most Current PCAWG Data ? Report data issues to pcawg-data at icgc.org, GNOS issue to: Help at annaisystems.com ? From Boston F2F: PCAWG datasets & dependencies Action Items 1. [Joachim] Consensus SV - final? 2. [Jakob] Consensus SNVs - changes to "SNV near indels" annotation? 3. [Junjun] Specimen ID mapping for miRNA and methylation 4. [Jonathan & Joachim] Consensus calls for cell lines, followed by filtering 5. [Matthias & Gordon] Docker containers for filtering methods 6. [Christina] Run alignment & variant workflows on medulloblastoma sample (tumor 40x, normal 30x) from ICGC benchmark to estimate false negative rate 7. [Christina] Follow up with institutes interested in hosting PCAWG data long-term 8. [All] As per Jennifer's email on Sept 16, please provide authorship information again or for the first time using PCAWG Author Form (http://goo.gl/forms/5Wq5x5X1DK). Save the link "Edit your response" so you can go back later to provide updates, for example about your evolving role in writing specific papers. 9. [All] Contribute to the manuscripts on a. infrastructure: https://docs.google.com/document/d/10alAxrWLdLSyhci-rfNuVH13rFXCJkaY_rzf1KJn7nc/edit b. variants: Paper ( https://goo.gl/g9CLsu ), Supplement ( https://goo.gl/EWYh7e ) c. Rogue's Gallery of Cancer Genome Sequencing Artifacts ( outline ) 10. [Junjun] Discuss PCAWG vs DCC glossary terms at next PCAWG-10/13 conference 10min Status of dockerizing workflows Brian O'Connor, UCSC Gordon Saksena, Broad Francis Ouellette, OICR Status of PCAWG Workflow ports to Dockstore: Denis has been porting the Dockstore entries to CWL version 1.0 which is part of our effort to publish Dockstore (this doesn't affect the content of the pipelines, simply their "descriptors" which allow them to be runnable via Dockstore). Denis has also worked on testing BWA-Mem, Sanger, EMBL (which all work with CWL 1.0 and Kerian's test dataset) and has fixed issues with DKFZ and is testing the latter with a real sample shortly. 1. BWA-Mem - Ready for testing by Francis' team 2. Sanger - Ready for testing by Francis' team. 3. EMBL - Ready for testing by Francis' team. 4. DKFZ - Ready for testing by Francis' team. I've exchanged emails with Manuel Ballesteros who has been testing this pipeline. 5. Broad - Variant calling (MuTect, dRanger, snowman), need some work, Gordan sent details previously 6. OxoG - Waiting for Dimitri to provide OxoG docker 7. Variantbam 8. Consensus algorithm PCAWG Docker (Dockstore) Testing Working Group 5min Other business? Group Christina K. Yung, PhD Project Manager, Cancer Genome Collaboratory Ontario Institute for Cancer Research MaRS Centre 661 University Avenue, Suite 510 Toronto, Ontario, Canada M5G 0A3 Tel: 416-673-8578 www.oicr.on.ca This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization. _______________________________________________ PAWG-TECH mailing list PAWG-TECH at lists.icgc.org https://lists.icgc.org/mailman/listinfo/pawg-tech _______________________________________________ docktesters mailing list docktesters at lists.icgc.org https://lists.icgc.org/mailman/listinfo/docktesters _______________________________________________ docktesters mailing list docktesters at lists.icgc.org https://lists.icgc.org/mailman/listinfo/docktesters -------------- next part -------------- An HTML attachment was scrubbed... URL: From francis at oicr.on.ca Fri Sep 30 12:08:02 2016 From: francis at oicr.on.ca (Francis Ouellette) Date: Fri, 30 Sep 2016 16:08:02 +0000 Subject: [DOCKTESTERS] [PAWG-TECH] Draft agenda for PCAWG-TECH teleconference In-Reply-To: <8231F9BE-D796-4F7C-9F61-8BAEA336F038@ohsu.edu> References: <0F84ED6166CE664E8563B61CB2ECB98CCBA7F1FA@exmb2.ad.oicr.on.ca> <16D5F0B4-2278-4A78-A038-02A3C61737CF@oicr.on.ca> <6DDD0535-6E45-413E-8E93-60E22F6C3510@oicr.on.ca> <8231F9BE-D796-4F7C-9F61-8BAEA336F038@ohsu.edu> Message-ID: Thank you Adam ? Junjun/Miguel: we should capture error messages on google doc as well. @bffo -- B.F. Francis Ouellette http://oicr.on.ca/person/francis-ouellette On Sep 30, 2016, at 12:02 PM, Adam Struck > wrote: I thought I should add that I've run the Sanger pipeline on the test data in three separate environments using both CWL and WDL descriptors. Feel free to email me the errors you are seeing and I'll try and debug. Adam Struck Scientific Programmer Computational Biology Oregon Health and Science University On Sep 30, 2016, at 7:52 AM, Francis Ouellette > wrote: yes, good plan. @bffo -- B.F. Francis Ouellette http://oicr.on.ca/person/francis-ouellette On Sep 30, 2016, at 10:46 AM, Miguel Vazquez > wrote: Dear Francis, I haven't had a chance to go at it again since the meeting, I got a new position in Norway, but next week I will try to find some time. I think I might just try another pipeline, since it seems like the Sanger pipeline needs fixing. Although perhaps I will first try Denis test data again and see if I can reproduce the error, after which we probably should contact the person in charge. Best M On Fri, Sep 30, 2016 at 3:52 PM, Francis Ouellette > wrote: Dear Miguel and Junjun, Any more attempts on testing the PCAWG sanger docker container? If you reproduce the same error, we will need to involve Bryan and Keiran Raine > (author of the container). Let?s get this one figured out. I am going to assume that the making of the docker container is what needs resolving. Brian: We may need your input here. Details of our current experiment should continue to be posted here: https://goo.gl/XX5BG9 Thank you all, francis PS would be good for others on list to follow directions on above google doc and also see if they can succeed on this workflow. Junjun and Miguel have tried different clouds, but used the sanger workflow, on the same data set. Thank you for trying to do this. Would be good if I heard back from anybody before Monday AM (tech call). @bffo PS I CCed Keiran, but waiting to hear back from Brian before we need to involve him some more. PPS Junjun/Miguel: maybe you can try the DKFZ docker as well? (on the same data set). -- B.F. Francis Ouellette http://oicr.on.ca/person/francis-ouellette Begin forwarded message: From: Christina Yung > Subject: [PAWG-TECH] Draft agenda for PCAWG-TECH teleconference Date: September 30, 2016 at 9:19:39 AM EDT To: "pawg-tech (pawg-tech at lists.icgc.org)" > Hi Everyone, Below is a draft agenda for Monday?s tech call. Please let me know if you have any agenda items for discussion. https://wiki.oicr.on.ca/display/PANCANCER/2016-10-03+PCAWG-TECH+Teleconference Have a great weekend! Christina Call Info Usual Time 9 AM Eastern Time, Mondays UK 0208 322 2500 Canada 1-866-220-6419 United States 1-877-420-0272 All Others Please see attached PDF file with a list of numbers for other countries. Participant Code 5910819# Agenda Time Item Who Attachments/Links 5min Welcome. Wait for group members to log on Christina Yung, OICR 10min Overall status Christina Yung, OICR ? Linkouts to Most Current PCAWG Data ? Report data issues to pcawg-data at icgc.org, GNOS issue to: Help at annaisystems.com ? From Boston F2F: PCAWG datasets & dependencies Action Items 1. [Joachim] Consensus SV - final? 2. [Jakob] Consensus SNVs - changes to "SNV near indels" annotation? 3. [Junjun] Specimen ID mapping for miRNA and methylation 4. [Jonathan & Joachim] Consensus calls for cell lines, followed by filtering 5. [Matthias & Gordon] Docker containers for filtering methods 6. [Christina] Run alignment & variant workflows on medulloblastoma sample (tumor 40x, normal 30x) from ICGC benchmark to estimate false negative rate 7. [Christina] Follow up with institutes interested in hosting PCAWG data long-term 8. [All] As per Jennifer's email on Sept 16, please provide authorship information again or for the first time using PCAWG Author Form (http://goo.gl/forms/5Wq5x5X1DK). Save the link "Edit your response" so you can go back later to provide updates, for example about your evolving role in writing specific papers. 9. [All] Contribute to the manuscripts on a. infrastructure: https://docs.google.com/document/d/10alAxrWLdLSyhci-rfNuVH13rFXCJkaY_rzf1KJn7nc/edit b. variants: Paper ( https://goo.gl/g9CLsu ), Supplement ( https://goo.gl/EWYh7e ) c. Rogue's Gallery of Cancer Genome Sequencing Artifacts ( outline ) 10. [Junjun] Discuss PCAWG vs DCC glossary terms at next PCAWG-10/13 conference 10min Status of dockerizing workflows Brian O'Connor, UCSC Gordon Saksena, Broad Francis Ouellette, OICR Status of PCAWG Workflow ports to Dockstore: Denis has been porting the Dockstore entries to CWL version 1.0 which is part of our effort to publish Dockstore (this doesn't affect the content of the pipelines, simply their "descriptors" which allow them to be runnable via Dockstore). Denis has also worked on testing BWA-Mem, Sanger, EMBL (which all work with CWL 1.0 and Kerian's test dataset) and has fixed issues with DKFZ and is testing the latter with a real sample shortly. 1. BWA-Mem - Ready for testing by Francis' team 2. Sanger - Ready for testing by Francis' team. 3. EMBL - Ready for testing by Francis' team. 4. DKFZ - Ready for testing by Francis' team. I've exchanged emails with Manuel Ballesteros who has been testing this pipeline. 5. Broad - Variant calling (MuTect, dRanger, snowman), need some work, Gordan sent details previously 6. OxoG - Waiting for Dimitri to provide OxoG docker 7. Variantbam 8. Consensus algorithm PCAWG Docker (Dockstore) Testing Working Group 5min Other business? Group Christina K. Yung, PhD Project Manager, Cancer Genome Collaboratory Ontario Institute for Cancer Research MaRS Centre 661 University Avenue, Suite 510 Toronto, Ontario, Canada M5G 0A3 Tel: 416-673-8578 www.oicr.on.ca This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization. _______________________________________________ PAWG-TECH mailing list PAWG-TECH at lists.icgc.org https://lists.icgc.org/mailman/listinfo/pawg-tech _______________________________________________ docktesters mailing list docktesters at lists.icgc.org https://lists.icgc.org/mailman/listinfo/docktesters _______________________________________________ docktesters mailing list docktesters at lists.icgc.org https://lists.icgc.org/mailman/listinfo/docktesters -------------- next part -------------- An HTML attachment was scrubbed... URL: From francis at oicr.on.ca Fri Sep 30 12:19:29 2016 From: francis at oicr.on.ca (Francis Ouellette) Date: Fri, 30 Sep 2016 16:19:29 +0000 Subject: [DOCKTESTERS] [PAWG-TECH] Draft agenda for PCAWG-TECH teleconference In-Reply-To: <8231F9BE-D796-4F7C-9F61-8BAEA336F038@ohsu.edu> References: <0F84ED6166CE664E8563B61CB2ECB98CCBA7F1FA@exmb2.ad.oicr.on.ca> <16D5F0B4-2278-4A78-A038-02A3C61737CF@oicr.on.ca> <6DDD0535-6E45-413E-8E93-60E22F6C3510@oicr.on.ca> <8231F9BE-D796-4F7C-9F61-8BAEA336F038@ohsu.edu> Message-ID: <8212A167-228D-4184-A707-F5DC39F8FA27@oicr.on.ca> Adam, Can you complete table on wiki: https://wiki.oicr.on.ca/pages/editpage.action?pageId=66309629 Actually: Miguel and Junjun, can you also somplete that table? Thank you. Adam: can you try and make workflow work on one platform with the same data that Miguel and Junjun tried? Thank you, @bffo -- B.F. Francis Ouellette http://oicr.on.ca/person/francis-ouellette On Sep 30, 2016, at 12:02 PM, Adam Struck > wrote: I thought I should add that I've run the Sanger pipeline on the test data in three separate environments using both CWL and WDL descriptors. Feel free to email me the errors you are seeing and I'll try and debug. Adam Struck Scientific Programmer Computational Biology Oregon Health and Science University On Sep 30, 2016, at 7:52 AM, Francis Ouellette > wrote: yes, good plan. @bffo -- B.F. Francis Ouellette http://oicr.on.ca/person/francis-ouellette On Sep 30, 2016, at 10:46 AM, Miguel Vazquez > wrote: Dear Francis, I haven't had a chance to go at it again since the meeting, I got a new position in Norway, but next week I will try to find some time. I think I might just try another pipeline, since it seems like the Sanger pipeline needs fixing. Although perhaps I will first try Denis test data again and see if I can reproduce the error, after which we probably should contact the person in charge. Best M On Fri, Sep 30, 2016 at 3:52 PM, Francis Ouellette > wrote: Dear Miguel and Junjun, Any more attempts on testing the PCAWG sanger docker container? If you reproduce the same error, we will need to involve Bryan and Keiran Raine > (author of the container). Let?s get this one figured out. I am going to assume that the making of the docker container is what needs resolving. Brian: We may need your input here. Details of our current experiment should continue to be posted here: https://goo.gl/XX5BG9 Thank you all, francis PS would be good for others on list to follow directions on above google doc and also see if they can succeed on this workflow. Junjun and Miguel have tried different clouds, but used the sanger workflow, on the same data set. Thank you for trying to do this. Would be good if I heard back from anybody before Monday AM (tech call). @bffo PS I CCed Keiran, but waiting to hear back from Brian before we need to involve him some more. PPS Junjun/Miguel: maybe you can try the DKFZ docker as well? (on the same data set). -- B.F. Francis Ouellette http://oicr.on.ca/person/francis-ouellette Begin forwarded message: From: Christina Yung > Subject: [PAWG-TECH] Draft agenda for PCAWG-TECH teleconference Date: September 30, 2016 at 9:19:39 AM EDT To: "pawg-tech (pawg-tech at lists.icgc.org)" > Hi Everyone, Below is a draft agenda for Monday?s tech call. Please let me know if you have any agenda items for discussion. https://wiki.oicr.on.ca/display/PANCANCER/2016-10-03+PCAWG-TECH+Teleconference Have a great weekend! Christina Call Info Usual Time 9 AM Eastern Time, Mondays UK 0208 322 2500 Canada 1-866-220-6419 United States 1-877-420-0272 All Others Please see attached PDF file with a list of numbers for other countries. Participant Code 5910819# Agenda Time Item Who Attachments/Links 5min Welcome. Wait for group members to log on Christina Yung, OICR 10min Overall status Christina Yung, OICR ? Linkouts to Most Current PCAWG Data ? Report data issues to pcawg-data at icgc.org, GNOS issue to: Help at annaisystems.com ? From Boston F2F: PCAWG datasets & dependencies Action Items 1. [Joachim] Consensus SV - final? 2. [Jakob] Consensus SNVs - changes to "SNV near indels" annotation? 3. [Junjun] Specimen ID mapping for miRNA and methylation 4. [Jonathan & Joachim] Consensus calls for cell lines, followed by filtering 5. [Matthias & Gordon] Docker containers for filtering methods 6. [Christina] Run alignment & variant workflows on medulloblastoma sample (tumor 40x, normal 30x) from ICGC benchmark to estimate false negative rate 7. [Christina] Follow up with institutes interested in hosting PCAWG data long-term 8. [All] As per Jennifer's email on Sept 16, please provide authorship information again or for the first time using PCAWG Author Form (http://goo.gl/forms/5Wq5x5X1DK). Save the link "Edit your response" so you can go back later to provide updates, for example about your evolving role in writing specific papers. 9. [All] Contribute to the manuscripts on a. infrastructure: https://docs.google.com/document/d/10alAxrWLdLSyhci-rfNuVH13rFXCJkaY_rzf1KJn7nc/edit b. variants: Paper ( https://goo.gl/g9CLsu ), Supplement ( https://goo.gl/EWYh7e ) c. Rogue's Gallery of Cancer Genome Sequencing Artifacts ( outline ) 10. [Junjun] Discuss PCAWG vs DCC glossary terms at next PCAWG-10/13 conference 10min Status of dockerizing workflows Brian O'Connor, UCSC Gordon Saksena, Broad Francis Ouellette, OICR Status of PCAWG Workflow ports to Dockstore: Denis has been porting the Dockstore entries to CWL version 1.0 which is part of our effort to publish Dockstore (this doesn't affect the content of the pipelines, simply their "descriptors" which allow them to be runnable via Dockstore). Denis has also worked on testing BWA-Mem, Sanger, EMBL (which all work with CWL 1.0 and Kerian's test dataset) and has fixed issues with DKFZ and is testing the latter with a real sample shortly. 1. BWA-Mem - Ready for testing by Francis' team 2. Sanger - Ready for testing by Francis' team. 3. EMBL - Ready for testing by Francis' team. 4. DKFZ - Ready for testing by Francis' team. I've exchanged emails with Manuel Ballesteros who has been testing this pipeline. 5. Broad - Variant calling (MuTect, dRanger, snowman), need some work, Gordan sent details previously 6. OxoG - Waiting for Dimitri to provide OxoG docker 7. Variantbam 8. Consensus algorithm PCAWG Docker (Dockstore) Testing Working Group 5min Other business? Group Christina K. Yung, PhD Project Manager, Cancer Genome Collaboratory Ontario Institute for Cancer Research MaRS Centre 661 University Avenue, Suite 510 Toronto, Ontario, Canada M5G 0A3 Tel: 416-673-8578 www.oicr.on.ca This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. 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