TypeError: stat
Issue #39
new
Hi there,
Getting the following running vContact2 with standard settings:
$ vcontact2 --raw-proteins proteins.faa --rel-mode 'Diamond' --db 'ProkaryoticViralRefSeq97-Merged' --pcs-mode MCL --vcs-mode ClusterONE --c1-bin ../../vcontact2/bin/cluster_one-1.0.jar --output-dir vcontact2_out
============================This is vConTACT2 0.9.22============================
----------------------------------Pre-Analysis----------------------------------
INFO:vcontact2: Found Diamond: /Users/andre/miniconda3/bin/diamond
INFO:vcontact2: Found MCL: /Users/andre/miniconda3/bin/mcxload
INFO:vcontact2: Identified 8 CPUs
INFO:vcontact2: Using reference database: ProkaryoticViralRefSeq97-Merged
INFO:vcontact2: Using existing directory vcontact2_out.
------------------------------Reference databases-------------------------------
Traceback (most recent call last):
File "/Users/andre/vcontact2/bin/vcontact2", line 794, in <module>
main(options)
File "/Users/andre/vcontact2/bin/vcontact2", line 339, in main
if os.path.exists(gene2genome_fp):
File "/Users/andre/miniconda3/lib/python3.9/genericpath.py", line 19, in exists
os.stat(path)
TypeError: stat: path should be string, bytes, os.PathLike or integer, not NoneType
Not sure what I'm doing wrong here.
vContact2 was installed directly from Bitbucket and with pip.
Thanks in advance.
Comments (3)
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I’m getting the exact same error. Did anyone already find a solution?
I installed through conda and have updated vContact to 0.9.22.
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You need to specify the gene2genome file via “--proteins-fp”
-Ben
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Sorry - did things a bit too fast. It was me who posted this, feel free to add me as author or similar? Thanks again.