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tfwillems / HipSTR

Genotype and phase short tandem repeats using Illumina whole-genome sequencing data
GNU General Public License v2.0
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Unknown source of error #81

Open gabrielle-altman opened 3 years ago

gabrielle-altman commented 3 years ago

Hi, I have been using hipSTR recently on cram files. I initially did it on a small set of files to get familiar with the tool and how it works. Everything worked well. After this, I wanted to scale up to running hipSTR on 99 files at a time. In this run, after a long time of running, I got the following error message: ERROR: Failed to extract passes filters tag from BAM alignment I am having a hard time figuring out what is causing this error. I don't know if it is a problem with just one file or multiple. Is there anything in my cram files I should check or change to avoid this issue? Any insights would be helpful! Thanks!

aubreybailey commented 2 years ago

I suspect that you ran out of memory or hit an open-files ulimit. perhaps this will fix:

ulimit -n 10000