Entering edit mode
3.4 years ago
ErickW
•
0
I'm utilizing the michigan server and the provided checkVCF.py code that checks vcf.gz validity; however, when I run the python script, I get this error:
Python version is [ 2.7.5.final.0 ]
Begin checking vcfFile [ vcf1.vcf.gz ]
VCF checking failed at line [ 0 ]
Traceback (most recent call last):
File "checkVCF.py", line 291, in <module>
print >> logger, " [ %s ... ] " % ln[:50]
NameError: name 'ln' is not defined
Looking at the source code on Github, I see that 'ln' refers to the accompanying .fai file that comes in the zip folder; however, I tested the script with the example.vcf.gz file and I got the expected output.
Does anyone have any idea on why this is happening? Any insights?
