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bcbio / bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
https://bcbio-nextgen.readthedocs.io
MIT License
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Errors when loading GEMINI files produced by the pipeline #143

Closed lbeltrame closed 10 years ago

lbeltrame commented 10 years ago

It looks like one of the runs produced non-functional GEMINI files:

gemini interactions Sample_174-varscan.db 
Traceback (most recent call last):
  File "/usr/bin/gemini", line 5, in <module>
    pkg_resources.run_script('gemini==0.6.3a', 'gemini')
  File "/usr/lib/python2.7/site-packages/pkg_resources.py", line 492, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/usr/lib/python2.7/site-packages/pkg_resources.py", line 1350, in run_script
    execfile(script_filename, namespace, namespace)
  File "/usr/lib/python2.7/site-packages/gemini-0.6.3a-py2.7.egg/EGG-INFO/scripts/gemini", line 5, in <module>
    gemini.gemini_main.main()
  File "/usr/lib/python2.7/site-packages/gemini-0.6.3a-py2.7.egg/gemini/gemini_main.py", line 748, in main
    args.func(parser, args)
  File "/usr/lib/python2.7/site-packages/gemini-0.6.3a-py2.7.egg/gemini/tool_interactions.py", line 285, in genequery
    sample_variants(c, args)
  File "/usr/lib/python2.7/site-packages/gemini-0.6.3a-py2.7.egg/gemini/tool_interactions.py", line 231, in sample_variants
    idx_to_sample = util.map_indicies_to_samples(c)
  File "/usr/lib/python2.7/site-packages/gemini-0.6.3a-py2.7.egg/gemini/gemini_utils.py", line 24, in map_indicies_to_samples
    c.execute("select sample_id, name from samples")
sqlite3.OperationalError: no such table: samples

In fact, there is no samples table in the SQLite database (checked with the command line sqlite3). I'm running another analysis to be sure.

lbeltrame commented 10 years ago

I also get errors (during the run) about "PRIMARY_KEY must be unique":

[2013-10-14 13:23] uni29: Traceback (most recent call last):
[2013-10-14 13:23] uni29:   File "/usr/local/bin/gemini", line 5, in <module>
[2013-10-14 13:23] uni29:     pkg_resources.run_script('gemini==0.6.3a', 'gemini')
[2013-10-14 13:23] uni29:   File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 540, in run_script
[2013-10-14 13:23] uni29:     dist.insert_on(self.entries, entry)
[2013-10-14 13:23] uni29:   File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 1455, in run_script
[2013-10-14 13:23] uni29:     size = zip_stat.file_size
[2013-10-14 13:23] uni29:   File "/usr/local/lib/python2.7/dist-packages/gemini-0.6.3a-py2.7.egg/EGG-INFO/scripts/gemini", line 5, in <module>
[2013-10-14 13:23] uni29:     gemini.gemini_main.main()
[2013-10-14 13:23] uni29:   File "/usr/local/lib/python2.7/dist-packages/gemini-0.6.3a-py2.7.egg/gemini/gemini_main.py", line 748, in main
[2013-10-14 13:23] uni29:     args.func(parser, args)
[2013-10-14 13:23] uni29:   File "/usr/local/lib/python2.7/dist-packages/gemini-0.6.3a-py2.7.egg/gemini/gemini_merge_chunks.py", line 157, in merge_chunks
[2013-10-14 13:23] uni29:     merge_db_chunks(args)
[2013-10-14 13:23] uni29:   File "/usr/local/lib/python2.7/dist-packages/gemini-0.6.3a-py2.7.egg/gemini/gemini_merge_chunks.py", line 145, in merge_db_chunks
[2013-10-14 13:23] uni29:     append_sample_info(main_curr, db)
[2013-10-14 13:23] uni29:   File "/usr/local/lib/python2.7/dist-packages/gemini-0.6.3a-py2.7.egg/gemini/gemini_merge_chunks.py", line 52, in append_sample_info
[2013-10-14 13:23] uni29:     main_curr.execute(cmd)
[2013-10-14 13:23] uni29: sqlite3.IntegrityError: PRIMARY KEY must be unique
lbeltrame commented 10 years ago

Further investigation shows that GEMINI fails to load the merged VCFs properly, but I'm not sure if it's a GEMINI bug or an improper VCF.

lbeltrame commented 10 years ago

It's likely that https://github.com/arq5x/gemini/commit/970b1619453aefa06bcd4e14eb6ae6e09b30c05f fixed this - I'll update and report back.

lbeltrame commented 10 years ago

It indeed fixed it. Upstream problem then: closing report.

roryk commented 10 years ago

Hi Luca,

Sorry for the trouble, yup I introduced that bug this month, nice catch.

vivekraj2007 commented 9 years ago

[root@localhost home]# gemini -v Traceback (most recent call last): File "/usr/bin/gemini", line 4, in import pkg_resources File "/usr/lib/python2.6/site-packages/pkg_resources.py", line 2659, in parse_requirements(requires), Environment() File "/usr/lib/python2.6/site-packages/pkg_resources.py", line 546, in resolve raise DistributionNotFound(req) pkg_resources.DistributionNotFound: numexpr>=2.4.3