samstat not Running on Long File Names
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I tried running samstat on a bam file, and it terminated immediately without producing any results. The file had a very long name, so I re-named it to have a shorter name. After re-naming the file, samstat started running. Is samstat unable to handle very long file names?
Thanks.
Hi, long names should not be a problem for samstat - I suspect something else is causing the problem. Could you send me a few of the lines causing the problem?
Running the following command did not work:
samstat /pylon5/mc5fq4p/ikaplow/AnimalAtac/BrainRep2SubsampleMulti2/cromwell-executions/atac/d27cd995-cca7-4c06-b7ac-e3df10850d11/call-filter/shard-0/execution/Animal1_Brain_2_PFE116A15_S14_R1_001.merged_sample60M.nodup.bam
Running the following command did work:
samstat /pylon5/mc5fq4p/ikaplow/AnimalAtac/BrainRep2SubsampleMulti2/cromwell-executions/atac/d27cd995-cca7-4c06-b7ac-e3df10850d11/call-filter/shard-0/execution/test.bam
test.bam was created by running:
cp /pylon5/mc5fq4p/ikaplow/AnimalAtac/BrainRep2SubsampleMulti2/cromwell-executions/atac/d27cd995-cca7-4c06-b7ac-e3df10850d11/call-filter/shard-0/execution/Animal1_Brain_2_PFE116A15_S14_R1_001.merged_sample60M.nodup.bam /pylon5/mc5fq4p/ikaplow/AnimalAtac/BrainRep2SubsampleMulti2/cromwell-executions/atac/d27cd995-cca7-4c06-b7ac-e3df10850d11/call-filter/shard-0/execution/test.bam
Hi - I meant some of the bam / sam lines so I can run these locally and diagnose the problem.
The two bam files (the one that worked and the one that did not work) were identical; the only difference was the file names.