should I worry if the tmp folder not empty after completing GenotypeGVCFs

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Jue Jiang

• August 11, 2022 12:08

I'm not sure if I should re-run the genotyping if there are files left in the tmp folder. The left files have names end with ".so" and are cleaned if I re-run the genotyping. I'm not sure if I need to re-run all the intervals with non-empty tmp folder just in case, though the generated VCF files of one interval are the same between the one with empty tmp folder and the one with non-empty tmp folder.

 

REQUIRED for all errors and issues:
a) GATK version used: gatk/4.2.5.0
b) Exact command used:

gatk --java-options "-Xmx28g -Xms28g" \ GenotypeGVCFs \ -R ${ref} \ -V gendb://${gendbdir}/${index} \ --tmp-dir ${tmp} \ -O ${out} >>${log} 2>&1  

 
c) Entire program log:

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  Genevieve Brandt (she/her)

  • August 12, 2022 19:33

  Hi Jue Jiang,

  Could you post the program log from your two genotyping runs? Looking at the program log is the most helpful for troubleshooting.

  Best,

  Genevieve

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