ERROR:vcontact2: Unable to identify file format for viral_genomes_g2g.

Issue #66 resolved
Former user created an issue

Hi, I am trying to run vContact but it generates this error:

INFO:vcontact2: Loading proteins...
INFO:vcontact2: Merging ProkaryoticViralRefSeq94-Merged to user gene-to-genome mapping...
ERROR:vcontact2: Unable to identify file format for viral_genomes_g2g.
Traceback (most recent call last):
  File "/mnt/projects/miniconda2/envs/vContact2/bin/vcontact2", line 757, in <module>
    main(options)
  File "/mnt/projects/miniconda2/envs/vContact2/bin/vcontact2", line 427, in main
    gene2genome_df = pd.concat([usr_gene2genome_df, ref_proteins_df])
  File "/mnt/projects/miniconda2/envs/vContact2/lib/python3.7/site-packages/pandas/core/reshape/concat.py", line 255, in concat
    sort=sort,
  File "/mnt/projects/miniconda2/envs/vContact2/lib/python3.7/site-packages/pandas/core/reshape/concat.py", line 332, in __init__
    raise TypeError(msg)
TypeError: cannot concatenate object of type '<class 'bool'>'; only Series and DataFrame objs are valid

The code I used to generate the g2g.csv file is:

vcontact2_gene2genome -p proteins.faa -o viral_genomes_g2g.csv -s 'Prodigal-FAA'

The code I ran is:

vcontact2 --raw-proteins proteins.faa --proteins-fp viral_genomes_g2g --rel-mode 'Diamond' --db 'ProkaryoticViralRefSeq94-Merged' --pcs-mode MCL --vcs-mode ClusterONE --c1-bin /mnt/projects/miniconda2/envs/vContact2/bin/cluster --output-dir .

Do you know what might be causing it?

Thank you for your time. Best regards, Michele

Comments (2)

  1. Michele Zuppi

    I just found out that it was a spelling mistake. I wrote viral_genome_g2g instead of viral_genome_g2g.csv.

    My bad.

    Michele

  2. Log in to comment