Threads exit when given VCF about neat-genreads HOT 2 OPEN

I've run this a few times, and the only way to guarantee no threads exit seems to be with MAX_JOB=8 _when running with an input VCF. I'm 90% certain it's a memory issue as the threads start to drop when the memory maxes out, but for some reason, each job quits quietly (vs. running w/o a VCF and too many jobs, which quits with MemoryError).

However, splitting the job into more parts and only running 8 at a time still works, but you only get the regions for those 8 jobs. I'm assuming the region split is constant (otherwise it wouldn't work in the first place), so you could potentially split as much as you like and just run 8 at a time; unfortunately, this negates any benefits from running regions in parallel.

I don't know if this was an issue before, and I just missed it, or if this is something new.

from neat-genreads.

I had the same problem, when trying to call gen-reads.py in parallel. It looks like everything is working and then the jobs abort themselves without a message part way through. It is easy to miss becasue you think everything ran to completeion without error.

COMMAND:

find L*.vcf | sed 's/.vcf$//' | parallel 'python3.6 neat-genreads/gen_reads.py -M 0 -R 150 -o {} -v {}.vcf -c 1 --vcf -r ref.fa'

from neat-genreads.