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RasmussenLab / phamb

Downstream processing of VAMB binning for Viral Elucidation
MIT License
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Empty or outcommented file #37

Closed susheelbhanu closed 2 years ago

susheelbhanu commented 2 years ago

Hi,

I'm trying to run PHAMB with the following:

python /work/projects/nomis/assemblies/viromes/submodules/phamb/workflows/mag_annotation/scripts/run_RF.py /work/projects/nomis/assemblies/virome_results/annotations/goodQual_final.fna.gz /work/projects/nomis/assemblies/virome_results/vamb_output/clusters.tsv /work/projects/nomis/assemblies/virome_results/dbs/phamb /work/projects/nomis/assemblies/virome_results/phamb_output

I have the below error, so could you please let me know how to fix it?

Traceback (most recent call last):
  File "/work/projects/nomis/assemblies/viromes/submodules/phamb/workflows/mag_annotation/scripts/run_RF.py", line 217, in <module>
    fastadict = _vambtools.loadfasta(infile,compress=False)
  File "/mnt/irisgpfs/projects/nomis/assemblies/viromes/submodules/phamb/workflows/mag_annotation/scripts/vambtools.py", line 383, in loadfasta
    for entry in byte_iterfasta(byte_iterator, comment=comment):
  File "/mnt/irisgpfs/projects/nomis/assemblies/viromes/submodules/phamb/workflows/mag_annotation/scripts/vambtools.py", line 264, in byte_iterfasta
    raise ValueError('Empty or outcommented file')
ValueError: Empty or outcommented file

Thank you, Susheel

susheelbhanu commented 2 years ago

Turns out I had an incomplete FASTA file. Sorry for the confusion!