Closed anastazie closed 7 years ago
brentp
commented
7 years ago thanks for the PR.
can you give the full traceback that you saw? and if you have an example variant or vcf, that'd be great. I want to make this just a prominent error message rather than an exception.
anastazie
commented
7 years ago Hi, sure, below is part with error. I was running bcbio-nextgen on multiple samples and only third ended up with an error.
[2016-08-14T15:37Z] tabix index 1266-16-freebayes-decompose.vcf.gz
[2016-08-14T15:37Z] snpEff effects : 1266-16
[2016-08-14T15:38Z] tabix index 1266-16-freebayes-decompose-effects.vcf.gz
[2016-08-14T15:38Z] Create gemini database for /stgdata/bcbio/output/FirstRun-merged/work/gemini/1266-16-freebayes-decompose-effects.vcf.gz : 1266-16
[2016-08-14T15:39Z] Traceback (most recent call last):
[2016-08-14T15:39Z] File "/usr/local/bin/gemini", line 6, in <module>
[2016-08-14T15:39Z] gemini.gemini_main.main()
[2016-08-14T15:39Z] File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 1227, in main
[2016-08-14T15:39Z] args.func(parser, args)
[2016-08-14T15:39Z] File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 298, in loadchunk_fn
[2016-08-14T15:39Z] gemini_load_chunk.load(parser, args)
[2016-08-14T15:39Z] File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 843, in load
[2016-08-14T15:39Z] gemini_loader.populate_from_vcf()
[2016-08-14T15:39Z] File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 201, in populate_from_vcf
[2016-08-14T15:39Z] (variant, variant_impacts, extra_fields) = self._prepare_variation(var, anno_keys)
[2016-08-14T15:39Z] File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 525, in _prepare_variation
[2016-08-14T15:39Z] impact_so=impact.so, impact_severity=impact.effect_severity,
[2016-08-14T15:39Z] File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/geneimpacts/effect.py", line 330, in effect_severity
[2016-08-14T15:39Z] return self.impact_severity
[2016-08-14T15:39Z] File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/geneimpacts/effect.py", line 364, in impact_severity
[2016-08-14T15:39Z] return ['xxx', 'LOW', 'MED', 'HIGH'][self.severity]
[2016-08-14T15:39Z] File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/geneimpacts/effect.py", line 355, in severity
[2016-08-14T15:39Z] v = max(lookup[sev[csq]] for csq in self.consequences)
[2016-08-14T15:39Z] File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/geneimpacts/effect.py", line 355, in <genexpr>
[2016-08-14T15:39Z] v = max(lookup[sev[csq]] for csq in self.consequences)
[2016-08-14T15:39Z] KeyError: 'gene_fusion'
[2016-08-14T15:39Z] pid 71342: 9999 variants processed.
[2016-08-14T15:40Z] pid 71283: 9999 variants processed.
[2016-08-14T15:40Z] pid 71292: 9999 variants processed.
[2016-08-14T15:40Z] pid 71289: 9999 variants processed.
[2016-08-14T15:41Z] pid 71342: 17592 variants processed.
[2016-08-14T15:41Z] pid 71342: 124 skipped due to having the FILTER field set.
[2016-08-14T15:41Z] pid 71283: 17646 variants processed.
[2016-08-14T15:41Z] pid 71283: 66 skipped due to having the FILTER field set.
[2016-08-14T15:41Z] pid 71292: 17642 variants processed.
[2016-08-14T15:41Z] pid 71292: 70 skipped due to having the FILTER field set.
[2016-08-14T15:41Z] pid 71289: 17644 variants processed.
[2016-08-14T15:41Z] pid 71289: 68 skipped due to having the FILTER field set.
[2016-08-14T15:41Z] Indexing /stgdata/bcbio/output/FirstRun-merged/work/gemini/1266-16-freebayes-decompose-effects.vcf.gz with grabix.
[2016-08-14T15:41Z] Loading 88564 variants.
[2016-08-14T15:41Z] Breaking /stgdata/bcbio/output/FirstRun-merged/work/gemini/1266-16-freebayes-decompose-effects.vcf.gz into 5 chunks.
[2016-08-14T15:41Z] Loading chunk 0.
[2016-08-14T15:41Z] Loading chunk 1.
[2016-08-14T15:41Z] Loading chunk 2.
[2016-08-14T15:41Z] Loading chunk 3.
[2016-08-14T15:41Z] Loading chunk 4.
[2016-08-14T15:41Z] Traceback (most recent call last):
[2016-08-14T15:41Z] File "/usr/local/share/bcbio/anaconda/bin/gemini", line 6, in <module>
[2016-08-14T15:41Z] gemini.gemini_main.main()
[2016-08-14T15:41Z] File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 1227, in main
[2016-08-14T15:41Z] args.func(parser, args)
[2016-08-14T15:41Z] File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 198, in load_fn
[2016-08-14T15:41Z] gemini_load.load(parser, args)
[2016-08-14T15:41Z] File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/gemini/gemini_load.py", line 48, in load
[2016-08-14T15:41Z] load_multicore(args)
[2016-08-14T15:41Z] File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/gemini/gemini_load.py", line 92, in load_multicore
[2016-08-14T15:41Z] chunks = load_chunks_multicore(grabix_file, args)
[2016-08-14T15:41Z] File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/gemini/gemini_load.py", line 258, in load_chunks_multicore
[2016-08-14T15:41Z] wait_until_finished(procs)
[2016-08-14T15:41Z] File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/gemini/gemini_load.py", line 349, in wait_until_finished
[2016-08-14T15:41Z] raise ValueError("Processing failed on GEMINI chunk load")
[2016-08-14T15:41Z] ValueError: Processing failed on GEMINI chunk load
[2016-08-14T15:41Z] Uncaught exception occurred
Traceback (most recent call last):
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run
_do_run(cmd, checks, log_stdout)
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run
raise subprocess.CalledProcessError(exitcode, error_msg)
CalledProcessError: Command 'set -o pipefail; /usr/local/share/bcbio/anaconda/bin/gemini load --passonly --skip-cadd --skip-gerp-bp -v /stgdata/bcbio/output/FirstRun-merged/work/gemini/1266-16-freebayes-decompose-effects.vcf.gz -t snpEff --cores 5 --tempdir /stgdata/bcbio/output/FirstRun-merged/work/gemini/tx/tmpPKQXIO /stgdata/bcbio/output/FirstRun-merged/work/gemini/tx/tmpPKQXIO/1266-16-freebayes.db
Traceback (most recent call last):
File "/usr/local/bin/gemini", line 6, in <module>
gemini.gemini_main.main()
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 1227, in main
args.func(parser, args)
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 298, in loadchunk_fn
gemini_load_chunk.load(parser, args)
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 843, in load
gemini_loader.populate_from_vcf()
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 201, in populate_from_vcf
(variant, variant_impacts, extra_fields) = self._prepare_variation(var, anno_keys)
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 525, in _prepare_variation
impact_so=impact.so, impact_severity=impact.effect_severity,
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/geneimpacts/effect.py", line 330, in effect_severity
return self.impact_severity
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/geneimpacts/effect.py", line 364, in impact_severity
return ['xxx', 'LOW', 'MED', 'HIGH'][self.severity]
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/geneimpacts/effect.py", line 355, in severity
v = max(lookup[sev[csq]] for csq in self.consequences)
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/geneimpacts/effect.py", line 355, in <genexpr>
v = max(lookup[sev[csq]] for csq in self.consequences)
KeyError: 'gene_fusion'
pid 71342: 9999 variants processed.
pid 71283: 9999 variants processed.
pid 71292: 9999 variants processed.
pid 71289: 9999 variants processed.
pid 71342: 17592 variants processed.
pid 71342: 124 skipped due to having the FILTER field set.
pid 71283: 17646 variants processed.
pid 71283: 66 skipped due to having the FILTER field set.
pid 71292: 17642 variants processed.
pid 71292: 70 skipped due to having the FILTER field set.
pid 71289: 17644 variants processed.
pid 71289: 68 skipped due to having the FILTER field set.
Indexing /stgdata/bcbio/output/FirstRun-merged/work/gemini/1266-16-freebayes-decompose-effects.vcf.gz with grabix.
Loading 88564 variants.
Breaking /stgdata/bcbio/output/FirstRun-merged/work/gemini/1266-16-freebayes-decompose-effects.vcf.gz into 5 chunks.
Loading chunk 0.
Loading chunk 1.
Loading chunk 2.
Loading chunk 3.
Loading chunk 4.
Traceback (most recent call last):
File "/usr/local/share/bcbio/anaconda/bin/gemini", line 6, in <module>
gemini.gemini_main.main()
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 1227, in main
args.func(parser, args)
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 198, in load_fn
gemini_load.load(parser, args)
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/gemini/gemini_load.py", line 48, in load
load_multicore(args)
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/gemini/gemini_load.py", line 92, in load_multicore
chunks = load_chunks_multicore(grabix_file, args)
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/gemini/gemini_load.py", line 258, in load_chunks_multicore
wait_until_finished(procs)
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/gemini/gemini_load.py", line 349, in wait_until_finished
raise ValueError("Processing failed on GEMINI chunk load")
ValueError: Processing failed on GEMINI chunk load
' returned non-zero exit status 1thank you.
Hi, thanks for the tool! Here is one impact addition 'gene_fusion'. It has caused KeyError during gemimi database creation using bcbio-nextgen.
Cheers, Nastia