Failed run - ?syntax issue

[lflisboa]

New user here, having recurrent issues right after:

[11:46:13] Running: fasta_generate_regions.py reference/ref.fa.fai 147471 > reference/ref.txt 2>> snps.log
[11:46:13] Error running command, check /path/to/snps.log

Getting following .log:

snps.log

Tried .gbff, .fasta as reference, both ultimately failing.

Appreciate your help!

[tseemann]

It says it can't run fasta_generate_regions.py
This is part of most freebayes packages (but not all).
Do you have it?

[lflisboa]

Thanks for your quick reply - I do have freebayes v1.0.2-dirty

[tseemann]

Do you have snps.log file for the failed run?

if you type fasta_generate_regions.py what happens?

[lflisboa]

I get the same syntax error message as in the snps.log linked to my initial message:

File "/home/llisboa/miniconda3/bin/fasta_generate_regions.py", line 7
print "usage: ", sys.argv[0], " "
^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print("usage: ", sys.argv[0], " ")?

[lflisboa]

Problem solved it seems - @mcroxen figured it out - python3 was probably being called instead of python2.7, so creating an environment for snippy did the trick, but just for --ref .fasta, otherwise having same issue as #154 with snpeff