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arq5x / gemini

a lightweight db framework for exploring genetic variation.
http://gemini.readthedocs.org
MIT License
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Problem loading VCF when include PED file #370

Open landyk01 opened 9 years ago

landyk01 commented 9 years ago

Hello,

I am having a problem loading a PED file into my gemini.db. I am using the following command:

gemini load -v /path/to/annotated/snpeff/vcf -t snpEff -p /path/to/ped /path/to/gemini.db

I am getting the following output/error:

Traceback (most recent call last): File "/hpc/users/lindem03/packages/gemini/master/bin/gemini", line 6, in gemini.gemini_main.main() File "/hpc/users/lindem03/packages/gemini/master/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 1104, in main args.func(parser, args) File "/hpc/users/lindem03/packages/gemini/master/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 135, in load_fn gemini_load.load(parser, args) File "/hpc/users/lindem03/packages/gemini/master/anaconda/lib/python2.7/site-packages/gemini/gemini_load.py", line 52, in load load_singlecore(args) File "/hpc/users/lindem03/packages/gemini/master/anaconda/lib/python2.7/site-packages/gemini/gemini_load.py", line 57, in load_singlecore gemini_loader = GeminiLoader(args) File "/hpc/users/lindem03/packages/gemini/master/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 46, in init self._prepare_samples() File "/hpc/users/lindem03/packages/gemini/master/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 549, in _prepare_samples self.ped_hash = load_ped_file(self.args.ped_file) File "/hpc/users/lindem03/packages/gemini/master/anaconda/lib/python2.7/site-packages/gemini/ped.py", line 26, in load_ped_file ped_dict[fields[1]] = fields IndexError: list index out of range

When I load just the VCF without the -p option it loads correctly.

Help and suggestions would be greatly appreciated! Thanks!

arq5x commented 9 years ago

Could you share the contents of your PED file? This will be tough to diagnose without it.

landyk01 commented 9 years ago

Here is the PED file I am trying to load.

Family_ID Individual_ID Paternal_ID Maternal_ID Sex Phenotype

1-00025 1-00025 1-00025-02 1-00025-01 -9 2 1-00025 1-00025-01 -9 -9 1 1 1-00025 1-00025-02 -9 -9 2 1

Thanks for your help!

arq5x commented 9 years ago

Unfortuantely, I can't replicate this with the current version. Can you confirm you are using the current version, and if so, could you also send me the first 1000 lines of your VCF file?

landyk01 commented 9 years ago

I am using version 0.11.0 - I believe that is the latest version.

What is the best way to send you the vcf file?

Thanks!