GEMINI ISSUE

Question

[shwetan]

Using gemini found at:

/usr/local/bin/gemini
/usr/local/share/gemini/anaconda/lib/python2.7/site-packages/gemini/config.py:61: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
  config = yaml.load(in_handle)
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 7, in <module>
    gemini_main.main()
  File "/usr/local/share/gemini/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 1249, in main
    args.func(parser, args)
  File "/usr/local/share/gemini/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 204, in load_fn
    gemini_load.load(parser, args)
  File "/usr/local/share/gemini/anaconda/lib/python2.7/site-packages/gemini/gemini_load.py", line 51, in load
    l = load_singlecore(args)
  File "/usr/local/share/gemini/anaconda/lib/python2.7/site-packages/gemini/gemini_load.py", line 86, in load_singlecore
    l.populate_from_vcf()
  File "/usr/local/share/gemini/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 223, in populate_from_vcf
    (variant, variant_impacts) = self._prepare_variation(var, anno_keys)
  File "/usr/local/share/gemini/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 406, in _prepare_variation
    rs_ids = annotations.get_dbsnp_info(var)
  File "/usr/local/share/gemini/anaconda/lib/python2.7/site-packages/gemini/annotations.py", line 664, in get_dbsnp_info
    for hit in annotations_in_vcf(var, "dbsnp", "vcf", "grch37"):
  File "/usr/local/share/gemini/anaconda/lib/python2.7/site-packages/gemini/annotations.py", line 422, in annotations_in_vcf
    if isinstance(h, (cyvcf2.Variant, pysam.VariantRecord)):
AttributeError: 'module' object has no attribute 'VariantRecord'
/usr/local/share/gemini/anaconda/lib/python2.7/site-packages/gemini/config.py:61: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
  config = yaml.load(in_handle)
Traceback (most recent call last):
  File "/usr/local/bin/gemini", line 7, in <module>
    gemini_main.main()
  File "/usr/local/share/gemini/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 1249, in main
    args.func(parser, args)
  File "/usr/local/share/gemini/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 204, in load_fn
    gemini_load.load(parser, args)
  File "/usr/local/share/gemini/anaconda/lib/python2.7/site-packages/gemini/gemini_load.py", line 51, in load
    l = load_singlecore(args)
  File "/usr/local/share/gemini/anaconda/lib/python2.7/site-packages/gemini/gemini_load.py", line 86, in load_singlecore
    l.populate_from_vcf()
  File "/usr/local/share/gemini/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 223, in populate_from_vcf
    (variant, variant_impacts) = self._prepare_variation(var, anno_keys)
  File "/usr/local/share/gemini/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 414, in _prepare_variation
    thousandG = annotations.get_1000G_info(var)
  File "/usr/local/share/gemini/anaconda/lib/python2.7/site-packages/gemini/annotations.py", line 737, in get_1000G_info
    for hit in annotations_in_vcf(var, "1000g", "vcf", "grch37"):
  File "/usr/local/share/gemini/anaconda/lib/python2.7/site-packages/gemini/annotations.py", line 422, in annotations_in_vcf
    if isinstance(h, (cyvcf2.Variant, pysam.VariantRecord)):
AttributeError: 'module' object has no attribute 'VariantRecord'

THank you in advance

[Potetos]

Same problem when loading vcf

Answer 1

[bioinformily]

Hi! The issue is solved by updating pysam.

conda update pysam

[Edmond]

Hi, I have the same issue, I followed the instructions of the docker container in the docs: https://gemini.readthedocs.io/en/latest/content/installation.html How can I update pysam in the docker ?

[adeizadavid]

conda update pysam

This code did not solve the problem for me. I used the pip alternative with no luck. Any luck to this issue with GEMINI

[adeizadavid]

updating pysam worked for me. Make sure there are no conflicting issues with the anaconda that comes with the Gemini installation. In my case, I had to remove miniconda and recreate the conda structure for bash.