ERROR:vcontact2: Unable to identify file format for viral_genomes_g2g.
Issue #66
resolved
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)
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- changed status to resolved
User was able to resolve! Hooray!
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I just found out that it was a spelling mistake. I wrote viral_genome_g2g instead of viral_genome_g2g.csv.
My bad.
Michele