search

andyrimmer / Platypus

Platypus Variant Caller
GNU General Public License v3.0
105 stars 38 forks source link

Segmentation fault on multiple bam files #57

Open HannahNieto opened 8 years ago

HannahNieto commented 8 years ago

We have some TCGA exome bam files, that have been realigned with Stampy (after adding read groups with piccard). The files were then sorted and indexed with samtools. Platypus is running on each individual file correctly but when there is more than one sample we get a segmentation fault error. I am wondering if this might be a sorting error? Thanks in advance.

dancooke commented 8 years ago

Hi Hannah,

How far into the run does the error occur? Could you post a snippet of the log file just before the fault occurs?

Thanks Dan

HannahNieto commented 8 years ago

Dear Dan,

Thank you for your email.

The error is early in the run, the following is the log file message, after the relevant programs have been called:

Thu Aug 25 10:41:07 BST 2016 2016-08-25 10:41:07,577 - INFO - Beginning variant calling 2016-08-25 10:41:07,579 - INFO - Output will go to /gpfs/bb/dixonh/nbu/TCGA/Platypus/combined3bamfiles.vcf 2016-08-25 10:41:07,945 - INFO - Processing region 1:0-100000. (Only printing this message every 10 regions of size 100000) /var/lib/adaptive/torque/mom_priv/jobs/1192937.bb2torque.bb2.cluster.SC: line 30: 16229 Segmentation fault

Then it prints the script and finished the log file.

Thank you for your help

Best wishes,

Hannah

On 26 Aug 2016, at 12:43, Daniel Cooke notifications@github.com wrote:

Hi Hannah,

How far into the run does the error occur? Could you post a snippet of the log file just before the fault occurs?

Thanks Dan

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/andyrimmer/Platypus/issues/57#issuecomment-242711930, or mute the thread https://github.com/notifications/unsubscribe-auth/AUQWtaI-bL9xuh1CtOAfboiPQHt-m5cZks5qjtFqgaJpZM4Js7fX.

dancooke commented 8 years ago

Hi Hannah,

Could you try the run again with verbosity set to 5 and post the new log?

Thanks Dan

HannahNieto commented 8 years ago

Dear Dan,

Thanks for your email - I’ve added verbosity set at 5 to the script and the log file now contains:

2016-08-30 13:59:27,653 - INFO - Beginning variant calling 2016-08-30 13:59:27,656 - INFO - Output will go to /gpfs/bb/dixonh/nbu/TCGA/Platypus/combined3bamfiles.vcf 2016-08-30 13:59:28,055 - INFO - Searching for variants in the following regions: [('1', 0, 100000), ('1', 100000, 200000), ('1', 200000, 300000), ('1', 300000, 400000), ('1', 400000, 500000), ('1', 500000, 600000), ('1', 600000, 700000), ('1', 700000, 800000), ('1', 800000, 900000), ('1', 900000, 1000000), ('1', 1000000, 1100000), ('1', 1100000, 1200000), ('1', 1200000, 1300000), ('1', 1300000, 1400000), ('1', 1400000, 1500000), ('1', 1500000, 1600000), #...etc etc - the log file prints this for every chromosome all the way to Y 2016-08-30 13:59:28,481 - INFO - Processing region 1:0-100000. (Only printing this message every 10 regions of size 100000) Segmentation fault

Thanks very much.

Best wishes,

Hannah

On 30 Aug 2016, at 10:14, Daniel Cooke notifications@github.com wrote:

Hi Hannah,

Could you try the run again with verbosity set to 5 and post the new log?

Thanks Dan

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/andyrimmer/Platypus/issues/57#issuecomment-243380571, or mute the thread https://github.com/notifications/unsubscribe-auth/AUQWtUKNm1MC31TRPdWfmgOpZ1nWm4GMks5qk_RugaJpZM4Js7fX.