Question: Error with Gemini
0
gravatar for always_learning
5.0 years ago by
Doha, Qatar
always_learning980 wrote:

Hi All,

I am trying to use Gemini for my annotation purpose too. here is command I am using:gemini load -v example_snpeff.vcf -t snpEff my.db where example_snpeff is file generated by snpEff.

But I am getting this error


CADD scores are being loaded (to skip use:--skip-cadd).
GERP per bp is being loaded (to skip use:--skip-gerp-bp).
Traceback (most recent call last):
  File "/usr/local/bin/gemini", line 6, in <module>
    gemini.gemini_main.main()
  File "/usr/local/share/gemini/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 981, in main
    args.func(parser, args)
  File "/usr/local/share/gemini/anaconda/lib/python2.7/site-packages/gemini/gemini_load.py", line 51, in load
    load_singlecore(args)
  File "/usr/local/share/gemini/anaconda/lib/python2.7/site-packages/gemini/gemini_load.py", line 59, in load_singlecore
    gemini_loader.populate_from_vcf()
  File "/usr/local/share/gemini/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 99, in populate_from_vcf
    (variant, variant_impacts, extra_fields) = self._prepare_variation(var)
  File "/usr/local/share/gemini/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 313, in _prepare_variation
    gerp_bp = annotations.get_gerp_bp(var)
  File "/usr/local/share/gemini/anaconda/lib/python2.7/site-packages/gemini/annotations.py", line 355, in get_gerp_bp
    gerp = bigwig_summary(var, "gerp_bp")
  File "/usr/local/share/gemini/anaconda/lib/python2.7/site-packages/gemini/annotations.py", line 291, in bigwig_summary
    return _get_bw_summary(coords, anno)
  File "/usr/local/share/gemini/anaconda/lib/python2.7/site-packages/gemini/annotations.py", line 217, in _get_bw_summary
    return annotation.summarize(str(chrom), start, end, end-start).min_val[0]
  File "bbi_file.pyx", line 177, in bx.bbi.bbi_file.BBIFile.summarize (lib/bx/bbi/bbi_file.c:5316)
OverflowError: can't convert negative value to unsigned int

Any suggestion please !!

 

gemini • 1.7k views
ADD COMMENTlink modified 5.0 years ago • written 5.0 years ago by always_learning980
0
gravatar for always_learning
5.0 years ago by
Doha, Qatar
always_learning980 wrote:

No reply yet !! :( :(

ADD COMMENTlink written 5.0 years ago by always_learning980
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