Hi everybody. First of all, gemini is a great tool.
I am having a problem loading a full genome vcf from a trio (father, mother and son).
I am using gemini devel version 0.30
the comand is this
gemini load -v filtered_normalized_annotated.vcf -p P_Trio.ped -t snpEff --cores 3 Trio_1.db
Everything goes smoothly until this error arises
pid 8503: 239999 variants processed.
pid 8506: 239999 variants processed.
pid 8509: 249999 variants processed.
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 311, in loadchunk_fn
gemini_load_chunk.load(parser, args)
File "/usr/local/share/gemini/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 918, in load
gemini_loader.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 407, in _prepare_variation
clinvar_info = annotations.get_clinvar_info(var)
File "/usr/local/share/gemini/anaconda/lib/python2.7/site-packages/gemini/annotations.py", line 648, in get_clinvar_info
clinvar.clinvar_sig = info_map['CLNSIG'].lower()
KeyError: 'CLNSIG'
pid 8506: 249999 variants processed.
pid 8509: 259999 variants processed.
pid 8506: 259999 variants processed.
It looks like that the chunk that is processed in pid 8503, fails completely and is not resumed in the process.
I have the lastest versions of the annotations databases from gemini (update --dataonly). I have used other vcf from other trios (exome instead of genome), and this problem did not appear.
Could it be a problem within the vcf (a problematic snp?) or a bug in the devel version of gemini?
I am completely lost.
As i said before, i have used the same thing with other trios vcfs (from exome) without any problem.
Hi everybody. First of all, gemini is a great tool.
I am having a problem loading a full genome vcf from a trio (father, mother and son).
I am using gemini devel version 0.30
the comand is this
gemini load -v filtered_normalized_annotated.vcf -p P_Trio.ped -t snpEff --cores 3 Trio_1.db
Everything goes smoothly until this error arises
pid 8503: 239999 variants processed.
pid 8506: 239999 variants processed.
pid 8509: 249999 variants processed.
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 311, in loadchunk_fn
gemini_load_chunk.load(parser, args)
File "/usr/local/share/gemini/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 918, in load
gemini_loader.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 407, in _prepare_variation
clinvar_info = annotations.get_clinvar_info(var)
File "/usr/local/share/gemini/anaconda/lib/python2.7/site-packages/gemini/annotations.py", line 648, in get_clinvar_info
clinvar.clinvar_sig = info_map['CLNSIG'].lower()
KeyError: 'CLNSIG'
pid 8506: 249999 variants processed.
pid 8509: 259999 variants processed.
pid 8506: 259999 variants processed.
It looks like that the chunk that is processed in pid 8503, fails completely and is not resumed in the process.
I have the lastest versions of the annotations databases from gemini (update --dataonly). I have used other vcf from other trios (exome instead of genome), and this problem did not appear.
Could it be a problem within the vcf (a problematic snp?) or a bug in the devel version of gemini?
I am completely lost.
As i said before, i have used the same thing with other trios vcfs (from exome) without any problem.