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