search

aryarm / varCA

Use an ensemble of variant callers to call variants from ATAC-seq data
MIT License
22 stars 7 forks source link

ChildIOException: File/directory is a child to another output: #23

Closed lindenb closed 3 years ago

lindenb commented 3 years ago

Hi, I'm trying to run the example dataset. (snakemake 5.19.2 ) My server crashed during the workflow and I tried to re-run it.

$ ./run.bash --sge-cluster && echo OK
$

this the the content of the log file:

Building DAG of jobs...
ChildIOException:
File/directory is a child to another output:
('/SCRATCH-BIRD/users/lindenbaum-p/work/20210312.varCA/merged_snp/jurkat_chr1/norm.tsv.gz', result)
('/SCRATCH-BIRD/users/lindenbaum-p/work/20210312.varCA/merged_snp/jurkat_chr1/norm.tsv.gz', norm_nums)

can you help me please ?

aryarm commented 3 years ago

Hi @lindenb, Thanks for trying out VarCA! Can you help me reproduce the issue? Do you know, by any chance, at which stage in the pipeline your server crashed? While the pipeline should theoretically work with Snakemake 5.19.2, it was officially built on 5.18.0, so I will try to reproduce the issue with the version of Snakemake that you're using.

aryarm commented 3 years ago

Just providing an update on this now that I've had some time to think on it and do some googling.

I now suspect that this was due to a bug in Snakemake, since I haven't seen this in v5.18.0. According to this GitHub issue, the problem arose somewhere around v5.18.1 and was patched in v5.32.0. I'm going to close this issue for now, but feel free to reopen if anyone runs into this problem with a version of Snakemake above v5.32.0. In any case, I soon plan to migrate VarCA to a version of Snakemake > v6.0.0, and this issue should be irrelevant at that point.