VFDB Parse the cluster output and tabulate the results using the specific Virulence gene DB compatible script:

[aslangabriel]

When I run this step: the error indicated that "File "mybin/VFDB_cdhit_to_csv.py", line 68, in
sys.exit(main())
File "mybin/VFDB_cdhit_to_csv.py", line 29, in main
outfile = file(args.outfile,"w")
NameError: name 'file' is not defined
'

[HumbiFred]

Hi,

I am facing the same problem. Is there maybe a solution out yet?

Thank you for your help in advance :)

Kind regards

[katholt]

This looks like a python3 issue - note srst2 is written for python2.

[HumbiFred]

Thank you! That's it. Now its workinge perfectly.

Could have figured that out myself, so sorry for bothering.