GEMINI ISSUE
1
0
Entering edit mode
3.7 years ago
shwetan • 0

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

GEMINI • 1.7k views
ADD COMMENT
0
Entering edit mode

Same problem when loading vcf

ADD REPLY
0
Entering edit mode
3.2 years ago

Hi! The issue is solved by updating pysam.

conda update pysam
ADD COMMENT
0
Entering edit mode

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 ?

ADD REPLY
0
Entering edit mode
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

ADD REPLY
0
Entering edit mode

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.

ADD REPLY

Login before adding your answer.

Traffic: 1529 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6