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Segmentation fault on multiple bam files #57
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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 |
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 Then it prints the script and finished the log file. Thank you for your help Best wishes, Hannah
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Hi Hannah, Could you try the run again with verbosity set to 5 and post the new log? Thanks |
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 Thanks very much. Best wishes, Hannah
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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.
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