Open mlewinsohn opened 2 years ago
Hi @mlewinsohn - thanks for posting the issue, and sorry for the trouble. If this is happening in the count_alleles
step it is likely a bug introduced in v1.0.2
that didn't get resolved in v1.1
as we would have hoped. Fortunately this behavior is somewhat easily reproducible on our end, and thus very fixable. Let me take a deep dive into HATCHet v1.1
and get back to you.
Hi @vineetbansal, thanks for the prompt reply and for looking into this!
I am running HATCHet v1.1 (recently upgraded from v1.0) in bioconda. I am having trouble with
count-alleles
generating incomplete output files. I am working within thehatchet run
pipeline, but have also tried calling thecount-alleles
step directly.Where my complete dataset has 48 samples with 1 matched normal, and all autosomal chromosomes are included.
I am noticing that when I set
-j
to 1, only variants from chromosome 22 are written to normal.1bed and tumor.1bed. The number of chromosomes written seems to match the number of processes. So, for example, if I set-j 8
then chromosomes 15-22 are included in the output file. If I set--processes=22
(the number of chromosomes), then all chromosomes are written in normal.1bed, but only one sample is written in tumor.1bed.I think this was noted in a previous issue, but might be a separate problem.
Thank you!