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freebayes joint calling memory exceeded #771
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Daryl;
Hope this helps. |
Okay, things ran for a bit with the bumped memory but seem to be stuck again i.e. no files being updated but jobs are still running. The controller job log doesn't end with an error. Still it's about 12g with a lot of lines like below:
There were a few earlier errors in the controller log:
Individual engine jobs have this as the last line:
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sacct seems to still indicate the calling script. Let's try 20g. |
Didn't run for too long before I got some GATK errors. The difference with this one was that the engine/controller jobs actually died. |
Reran and ended up with the same
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Daryl;
and see if anything looks truncated or obviously off. If so, removing it and re-running would probably fix it. If you can provide any more feedback about what is wrong I could try to improve recalling to avoid having the issue in the future. Hope this helps some. |
Should have thought of that. bcftools flags a file that ends in a truncated line. Might be worth adding a quick vcf validation step. Not sure how to quickly check the last line in a bgzip file without reading everything.
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Daryl; |
I thought I'd start a new issue regarding processes being killed and jobs going idle. The last run #741 ended up going to completion, thank you.
I'm trying to run the freebayes joint caller using bams and vcfs from #741. The previous run actually did pooled and not joint calling via
jointcaller: freebayes-joint
.The slurm scheduler killed some of the processes due to memory at what I think is the freebayes step. I previously increased the memory to 4g from 2g for freebayes. I'm now upping to 8g, does that seem rational?
However in the engine logs I do see some sambamba issues. I'm using the latest dev code with updated tools.
The submission script also shows a memory issue. It's using 8g and I'm now bumping to 12g.
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