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microbiomedata / nmdc-edge

Web-based interface to the NMDC EDGE platform
https://nmdc-edge.org
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MAGs fails with larger sample file #217

Open mflynn-lanl opened 4 days ago

mflynn-lanl commented 4 days ago

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.