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wheaton5 / souporcell

Clustering scRNAseq by genotypes
MIT License
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error debug help #124

Open maxozo opened 3 years ago

maxozo commented 3 years ago

Hi, running souporcell i get the following error:

Traceback (most recent call last):
  File "/opt/souporcell/souporcell_pipeline.py", line 596, in <module>
    doublets(args, ref_mtx, alt_mtx, cluster_file)
  File "/opt/souporcell/souporcell_pipeline.py", line 541, in doublets
    subprocess.check_call([directory+"/troublet/target/release/troublet", "--alts", alt_mtx, "--refs", ref_mtx, "--clusters", cluster_file], stdout = dub, stderr = err)
  File "/usr/local/envs/py36/lib/python3.6/subprocess.py", line 311, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/opt/souporcell/troublet/target/release/troublet', '--alts', '6123STDY10205670/alt.mtx', '--refs', '6123STDY10205670/ref.mtx', '--clusters', '6123STDY10205670/clusters_tmp.tsv']' returned non-zero exit status 101.

Any idea whats causing this?

GenOnyx commented 2 years ago

Hi, I am getting the same error. The input command I have used is: _python souporcell_pipeline.py -i A.merged.bam -b GSM2560245_barcodes.tsv -f genome.fa -t 32 -o CPT204c -k 6 --known_genotypes 2100204.vcf

Is there any specific input format required that I am missing? @maxozo were you able to fix the issue?

timslittle commented 10 months ago

This is quite old now but in case it is possibly helpful at all some solutions are suggested here: Issue#128. I also encountered this problem and the issue was that I was re-starting a failed pipeline and needed to delete the old .done files.