Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

MAGs fails with larger sample file #217

Open
mflynn-lanl opened this issue Jul 1, 2024 · 0 comments
Open

MAGs fails with larger sample file #217

mflynn-lanl opened this issue Jul 1, 2024 · 0 comments
Assignees

Comments

@mflynn-lanl
Copy link
Collaborator

Ran metaG pipeline with sample SRR7877884-int-0.1.fastq.gz (385MB) failed in MAGs. Smaller sample, Ecoli_10x-int.fastq.gz (43MB) ran successfully

Traceback (most recent call last):
  File "/opt/conda/bin/mbin.py", line 276, in <module>
    run(args.fna, args.aln, args.map, args.gff, args.lin, args.lintsv, args.threads, args.pthreads, args.combined, args.sortfna, args.sortaln, args.checkpoint, args.eukccdb)
  File "/opt/conda/bin/mbin.py", line 212, in run
    mbin_lineage.gtdbtk(hqmq_bins_dir, gtdbtk_dir, sdb_name, numcores, pplacer_cores, log)
  File "/opt/conda/bin/mbin_lineage.py", line 16, in gtdbtk
    rcode = subprocess.check_call(["gtdbtk", "classify_wf", "--pplacer_cpus", str(pplacer_threads), "--cpus", str(numcores), "--genome_dir", bins_dir, "--out_dir", godir, "--extension", "fa"])
  File "/opt/conda/lib/python3.9/subprocess.py", line 373, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['gtdbtk', 'classify_wf', '--pplacer_cpus', '1', '--cpus', '64', '--genome_dir', 'hqmq-metabat-bins', '--out_dir', 'gtdbtk-output', '--extension', 'fa']' returned non-zero exit status 1.
@mflynn-lanl mflynn-lanl self-assigned this Jul 1, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
Status: In Progress
Development

No branches or pull requests

1 participant