Followed Exome-Seq tutorial, but Gemini Load not working

Question: Followed Exome-Seq tutorial, but Gemini Load not working

7 weeks ago by

kelseyca • 0 wrote:

Hello!

I am performing a study with data from 80 cancer patients, half of which showed one symptom and the other half did not. This is my first time trying exome-seq to find variants.

I followed this exome sequencing data tutorial and created a annotated, combined VCF file from all my samples. However, the gemini load tool is not working. It gives me the following error:

Fatal error: Exit code 1 ()
/cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-0ae1b02314661bbc0d5b3ad056661189eb8c84f903ed935d47dca50a820294df/lib/python2.7/site-packages/gemini/annotations.py:9: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from bx.bbi.bigwig_file import BigWigFile
/cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-0ae1b02314661bbc0d5b3ad056661189eb8c84f903ed935d47dca50a820294df/lib/python2.7/site-packages/cyvcf2/__init__.py:1: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from .cyvcf2 import (VCF, Variant, Writer, r_ as r_unphased, par_relatedness,
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-0ae1b02314661bbc0d5b3ad056661189eb8c84f903ed935d47dca50a820294df/bin/gemini", line 6, in <module>
    gemini.gemini_main.main()
  File "/cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-0ae1b02314661bbc0d5b3ad056661189eb8c84f903ed935d47dca50a820294df/lib/python2.7/site-packages/gemini/gemini_main.py", line 1177, in main
    args.func(parser, args)
  File "/cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-0ae1b02314661bbc0d5b3ad056661189eb8c84f903ed935d47dca50a820294df/lib/python2.7/site-packages/gemini/gemini_main.py", line 198, in load_fn
    gemini_load.load(parser, args)
  File "/cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-0ae1b02314661bbc0d5b3ad056661189eb8c84f903ed935d47dca50a820294df/lib/python2.7/site-packages/gemini/gemini_load.py", line 24, in load
    annos = annotations.get_anno_files(args)
  File "/cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-0ae1b02314661bbc0d5b3ad056661189eb8c84f903ed935d47dca50a820294df/lib/python2.7/site-packages/gemini/annotations.py", line 16, in get_anno_files
    config = read_gemini_config( args = args )
  File "/cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-0ae1b02314661bbc0d5b3ad056661189eb8c84f903ed935d47dca50a820294df/lib/python2.7/site-packages/gemini/config.py", line 52, in read_gemini_config
    fname = _get_config_file(dirs, use_globals=use_globals)
  File "/cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-0ae1b02314661bbc0d5b3ad056661189eb8c84f903ed935d47dca50a820294df/lib/python2.7/site-packages/gemini/config.py", line 47, in _get_config_file
    .format(CONFIG_FILE, dnames))
ValueError: GEMINI configuration file gemini-config.yaml not found in ['/usr/local/share/gemini', '/home/g2main/.gemini'].
Please ensure the GEMINI data is installed using the install-data.py script
http://gemini.readthedocs.org/en/latest/content/installation.html
WARNING:galaxy.datatypes.binary:<galaxy.datatypes.binary.GeminiSQLite object="" at="" 0x2b3ceb2936d0="">, set_meta Exception: no such table: version

Does anyone know why it might not have worked? It is because I didn't upload a PED file? I was under the impression that it is optional. As these patients are not family-related I thought it would not be useful to use a PED file. If the error is not occurring because of the PED file, I'm not sure what the problem might be!

Thank you so much in advance!

exome-seq variants usegalaxy.org analysis galaxy • 146 views

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modified 7 weeks ago by Jennifer Hillman Jackson ♦ 25k • written 7 weeks ago by kelseyca • 0

7 weeks ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hi,

Yes, the tool is problematic at https://usegalaxy.org. We just updated it and the dependent annotation database indexes have not been added yet. We'll be updating this. Ticket: https://github.com/galaxyproject/usegalaxy-playbook/issues/165

This tutorial is noted as working only at the EU public Galaxy server https://usegalaxy.eu on the GTN website under the gear icon for "Galaxy instances": http://galaxyproject.github.io/training-material/topics/variant-analysis/. I tested the tool there today and it works fine - just be certain to use the most current version of the tool and the annotation or you will run into more problems. Any other combinations will fail.

Thanks! Jen, Galaxy team

ADD COMMENT • link written 7 weeks ago by Jennifer Hillman Jackson ♦ 25k

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