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NCI-CCR-GB / serpentine

Serpentine is a growing collection of rules and workflows for NGS data processing.
https://github.com/NCI-CCR-GB/serpentine
MIT License
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seqtool error in seqtool vcf melt (for snpEff 4.0) #12

Open zhujack opened 9 years ago

zhujack commented 9 years ago

During vcf2txt using seqtool error vcf melt, there was an error:

pkg_resources.DistributionNotFound: pylev

Details please see below

module load R/3.0.0; cat SUBJECT/RMS2096/RMS2096blood_DNA/human_g1k_v37.novo/unifieldgenotyper/RMS2096blood_DNA.unifieldgenotyper.annotated.vcf | seqtool vcf melt -i -o SUBJECT/RMS2096/RMS2096blood_DNA/human_g1k_v37.novo/unifieldgenotyper/RMS2096blood_DNA.unifieldgenotyper.annotated.txt -s  RMS2096blood_DNA

 Traceback (most recent call last):
  File "/data/ngs/virtualenv/snakemake/bin/seqtool", line 4, in <module>
   import pkg_resources
  File "/data/ngs/virtualenv/snakemake/lib/python3.3/site-packages/pkg_resources.py", line 3007, in   <module>
working_set.require(__requires__)
  File "/data/ngs/virtualenv/snakemake/lib/python3.3/site-packages/pkg_resources.py", line 728, in require
needed = self.resolve(parse_requirements(requirements))
  File "/data/ngs/virtualenv/snakemake/lib/python3.3/site-packages/pkg_resources.py", line 626, in resolve
raise DistributionNotFound(req)
 pkg_resources.DistributionNotFound: pylev
seandavi commented 9 years ago

Filed this under seqtools on github.

On Thu, Dec 11, 2014 at 9:48 PM, Jack notifications@github.com wrote:

During vcf2txt using seqtool error vcf melt, there was an error:

pkg_resources.DistributionNotFound: pylev

Details please see below: $ module load R/3.0.0; cat SUBJECT/RMS2096/RMS2096blood_DNA/human_g1k_v37.novo/unifieldgenotyper/RMS2096blood_DNA.unifieldgenotyper.annotated.vcf | seqtool vcf melt -i -o SUBJECT/RMS2096/RMS2096blood_DNA/human_g1k_v37.novo/unifieldgenotyper/RMS2096blood_DNA.unifieldgenotyper.annotated.txt -s RMS2096blood_DNA

Traceback (most recent call last): File "/data/ngs/virtualenv/snakemake/bin/seqtool", line 4, in import pkg_resources File "/data/ngs/virtualenv/snakemake/lib/python3.3/site-packages/pkg_resources.py", line 3007, in working_set.require(requires) File "/data/ngs/virtualenv/snakemake/lib/python3.3/site-packages/pkg_resources.py", line 728, in require needed = self.resolve(parse_requirements(requirements)) File "/data/ngs/virtualenv/snakemake/lib/python3.3/site-packages/pkg_resources.py", line 626, in resolve raise DistributionNotFound(req) pkg_resources.DistributionNotFound: pylev

— Reply to this email directly or view it on GitHub https://github.com/NCI-CCR-GB/serpentine/issues/12.