Open xxYaaoo opened 10 months ago
Hi,
this error was induced by the samtools sort step which may be because of "out of memory" or "running time". it usually indicates the job was not finished yet. you will see an empty vcf file unless you already re-run it with the same sample names.
thanks, xun
ok, thank you for your answer! I will continue to adjust my parameters.~
Hello, Dr. Chen,
Recently, I met a problem that after completing the whole pipeline, sometimes there were still lots of "sort.bam.tmp.0000.bam" files left in the output folder, while sometimes they were removed, but I set the same CPU and Mem parameters for each running. I am not sure whether the output vcf file is complete if the bam files are not removed. What might cause this problem and how could I fix it?
Thank you!