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

[Miguel Vazquez]

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


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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.icgc.org/mailman/private/docktesters/attachments/20161129/1bedb6a9/attachment.html>