[DOCKTESTERS] Sanger pipeline taking a very long on DO50311 and issue with BWA-Mem

[Miguel Vazquez]

Thanks Denis.


On Tue, Nov 29, 2016 at 4:27 PM, Denis Yuen <Denis.Yuen at oicr.on.ca> wrote:

> Hi,
>
> re: bwa-mem on HCC1143
>
> I have not tried that. Unfortunately, according to the table (
> https://wiki.oicr.on.ca/display/PANCANCER/Workflow+Testing+Data ) I
> believe you're the first.
>
> re: Sanger on DO50311
> Yes, unfortunately it did take a bit over 8 days for me to run that donor
> on a pretty beefy machine (15 cpu, 125 GB ram).
>
>
>
> ------------------------------
> *From:* mikisvaz at gmail.com [mikisvaz at gmail.com] on behalf of Miguel
> Vazquez [miguel.vazquez at cnio.es]
> *Sent:* November 29, 2016 6:06 AM
> *To:* Denis Yuen
> *Cc:* Francis Ouellette; docktesters at lists.icgc.org
> *Subject:* [DOCKTESTERS] Sanger pipeline taking a very long on DO50311
> and issue with BWA-Mem
>
> Hi all,
>
> I just wanted to give a partial update on my side and ask about two
> issues.
>
> 1) I've ran BAW-Mem on the test data HCC1143 and the process has failed,
> should it work for that dataset or is there a reason it shouldn't. About
> unaligning the BAM files I've checked the instructions on
>
> https://wiki.oicr.on.ca/pages/viewpage.action?spaceKey=
> PANCANCER&title=Preparing+paired-end+data+for+upload
> <http://redir.aspx?REF=vzZnpHgQUQ-TmnK2WmjdtthDxHvxJtPVpEqrB_qN7UMgNBmdaxjUCAFodHRwczovL3dpa2kub2ljci5vbi5jYS9wYWdlcy92aWV3cGFnZS5hY3Rpb24_c3BhY2VLZXk9UEFOQ0FOQ0VSJnRpdGxlPVByZXBhcmluZytwYWlyZWQtZW5kK2RhdGErZm9yK3VwbG9hZA..>
>
>
> and I ended up just doing
>
> cat initial.bam | bamreset exclude=QCFAIL,SECONDARY,SUPPLEMENTARY  >
> cleaned.bam
>
> I skipped all the stuff about the SAM header, which I didn't fully
> understood but it seemed like housekeeping stuff that should affect the
> variant calling and didn't quite apply to this test data. Could that be
> the issue?
>
> I tried to run it on a normal donor but it turns out I had first to finish
> the test on Sanger. When I do I can save the container, thanks to Denis tip
> on a previous thread, and help debug it if need be. I'm sorry that I cannot
> give more details on the error but at the time I could not find the log
> files that where supposed to be there; when the next issue is resolved I'll
> come back to this.
>
> 2) I'm running Sanger on donor DO50311. I put the job on November 22,
> about a week ago, and it is still running. It seems to be doing caveman for
> the last few days. It going full throttle using 100% of the CPU and with
> running jobs not older than 15 hours, so I guess its not stuck or anything.
> But just in case, is taking this long normal?
>
> Best
>
> Miguel
>
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