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TypeError: stat: path should be string, bytes, os.PathLike or integer, not NoneType
Dear Developer,
Thank you for vcontact2. I tried to resume vContact2 after the diamond step using following command:
vcontact2 --pcs vcontact_diamond/vConTACT_pcs.csv --contigs vcontact_diamond/vConTACT_contigs.csv --pc-profiles vcontact_diamond/vConTACT_profiles.csv --db 'ProkaryoticViralRefSeq211-Merged' --output-dir vcontact_diamond --c1-bin /dss/dsshome1/0F/ra78zut/Alex/test/cluster_one-1.0.jar
But I got the following error:
----------------------------------Pre-Analysis----------------------------------
INFO:vcontact2: Found Diamond: /dss/dsshome1/0F/ra78zut/miniconda3/envs/vContact2/bin/diamond
INFO:vcontact2: Found MCL: /dss/dsshome1/0F/ra78zut/miniconda3/envs/vContact2/bin/mcxload
INFO:vcontact2: Identified 28 CPUs
INFO:vcontact2: Using reference database: ProkaryoticViralRefSeq211-Merged
INFO:vcontact2: Using existing directory vcontact_diamond.
------------------------------Reference databases-------------------------------
Traceback (most recent call last):
File "/dss/dsshome1/0F/ra78zut/miniconda3/envs/vContact2/bin/vcontact2", line 834, in <module>
main(options)
File "/dss/dsshome1/0F/ra78zut/miniconda3/envs/vContact2/bin/vcontact2", line 356, in main
if os.path.exists(gene2genome_fp):
File "/dss/dsshome1/0F/ra78zut/miniconda3/envs/vContact2/lib/python3.10/genericpath.py", line 19, in exists
os.stat(path)
TypeError: stat: path should be string, bytes, os.PathLike or integer, not NoneType
Really sorry for the silly question. I am not sure how to solve this. Any help would be appreciated.
Thank you in advance
Regards
Monica
Comments (1)
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I just included --proteins-fp viral_genomes_g2g.csv in the command line