GEMINI ISSUE

[shwetanavle]

After using this command-$bash master=test.sh. I am getting the following error 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 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 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'

Help would be appreciated