Author Topic: python error for vcf2bed  (Read 4064 times)

isthisthat

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python error for vcf2bed
« on: May 14, 2014, 08:40:40 AM »
Hello,
I'm running the following commandline:
vcf2bed < in.vcf > out.bed

and I'm getting this error:
Exception in thread Thread-1:
Traceback (most recent call last):
  File "/illumina/thirdparty/python/python-2.7.5/lib/python2.7/threading.py", line 808, in __bootstrap_inner
    self.run()
  File "/illumina/thirdparty/python/python-2.7.5/lib/python2.7/threading.py", line 761, in run
    self.__target(*self.__args, **self.__kwargs)
  File "/illumina/thirdparty/bedops/bedops_linux_x86_64-v2.4.2/bin/vcf2bed", line 192, in consumeVCF
    bed_line = convertVCFToBed(vcf_line, params, to_stream)
  File "/illumina/thirdparty/bedops/bedops_linux_x86_64-v2.4.2/bin/vcf2bed", line 222, in convertVCFToBed
    for columnIdx in range(len(params.columns)):
TypeError: object of type 'NoneType' has no len()

Thank you.

AlexReynolds

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Re: python error for vcf2bed
« Reply #1 on: May 14, 2014, 08:43:06 AM »
Sorry you're having problems. Can you post your VCF file somewhere for us to do testing on our end?