**Error in rule bgzip_vcf:**

[lauragails]

Hello all, I am running workflow/process_sample.local.sh and am getting the following error. Do you know what it may be? I still have 14TB in my drive so I don't think it's a space issue. Thank you!

Activating conda environment: /sc/arion/projects/buxbaj01a/sloofl01/pac_bio/results/pacbio_wgs/121422/.snakemake/conda/5ff67c95a92013e755a25aa039b66191
[Sun Jan  1 20:50:34 2023]
**Error in rule bgzip_vcf:**
    jobid: 40
    output: samples/sample_name/pbsv/sample_name.GRCh38.chrom_vcfs/sample_name.GRCh38.chr13.pbsv.vcf.gz
    log: samples/sample_name/logs/bgzip/pbsv/sample_name.GRCh38.chrom_vcfs/sample_name.GRCh38.chr13.pbsv.log (check log file(s) for error message)
    conda-env: /sc/arion/projects/buxbaj01a/sloofl01/pac_bio/results/pacbio_wgs/121422/.snakemake/conda/d50d78097d235df7b794ad93c4e7d7da
    shell:
        (bgzip --threads 2 samples/sample_name/pbsv/sample_name.GRCh38.chrom_vcfs/sample_name.GRCh38.chr13.pbsv.vcf) > samples/sample_name/logs/bgzip/pbsv/sample_name.GRCh38.chrom_vcfs/sample_name.GRCh38.chr13.pbsv.log 2>&1
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

[williamrowell]

Is there anything in samples/sample_name/logs/bgzip/pbsv/sample_name.GRCh38.chrom_vcfs/sample_name.GRCh38.chr13.pbsv.log?

[lauragails]

Yes

bgzip: invalid option -- '-'
bgzip: invalid option -- 't'

Usage:   bgzip [options] [file] ...

Options: -c      write on standard output, keep original files unchanged
         -d      decompress
         -f      overwrite files without asking
         -b INT  decompress at virtual file pointer INT
         -s INT  decompress INT bytes in the uncompressed file
         -h      give this help

[williamrowell]

I think it's running the wrong bgzip. Maybe there's another in your path that somehow has precedent?

Try:

which -a bgzip

[lauragails]

aaah I bet it's that same module issue that we had with python:

which -a bgzip /hpc/packages/minerva-common/tabix/0.2.6/tabix-0.2.6/bgzip /hpc/packages/minerva-centos7/htslib/1.9/bin/bgzip

The top one is the one that is chosen. Should one have been installed in the custom environment? I fixed the similar error with module unload python a while ago before loading the built environment.

[williamrowell]

Yeah, it should be using the bgzip in /sc/arion/projects/buxbaj01a/sloofl01/pac_bio/results/pacbio_wgs/121422/.snakemake/conda/5ff67c95a92013e755a25aa039b66191. Something in your environment is loading those hpc packages modules into your path after the conda environment has been activated.

[lauragails]

Got it - I sent an email to our hpc admins to see how to override this. Thank you again for your help, and happy new year!

[williamrowell]

No problem. Hope it's an easy fix. Happy new year!