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genomicsengland / gel-coverage

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SystemError: Input gene list is not correct #34

Open enricserra opened 7 years ago

enricserra commented 7 years ago

When running:

sh ./run_coverage_analysis.sh /genomes/analysis/by_date/2015-10-23/0000074602/LP2000860-DNA_B04/coverage/LP2000860-DNA_B04.bw /genomes/analysis/by_date/2015-10-23/0000074602/LP2000860-DNA_B04/coverage/LP2000860-DNA_B04.bw_558c24a2bb5a166f63868678_1.0.json

We get :

558c24a2bb5a166f63868678 1.0 DEBUG:requests.packages.urllib3.connectionpool:Starting new HTTP connection (1): bioinfo.hpc.cam.ac.uk DEBUG:requests.packages.urllib3.connectionpool:http://bioinfo.hpc.cam.ac.uk:80 "HEAD /cellbase HTTP/1.1" 302 0 DEBUG:requests.packages.urllib3.connectionpool:Starting new HTTP connection (1): 10.5.8.201 DEBUG:requests.packages.urllib3.connectionpool:http://10.5.8.201:8080 "HEAD /cellbase-4.5.0-rc HTTP/1.1" 302 0 DEBUG:root:Getting gene list from PanelApp... DEBUG:root:Gene list obtained from PanelApp of 0! INFO:root:Gene list to analyse: INFO:root:0 genes to analyse DEBUG:root:Creating the BigWig reader... DEBUG:root:BigWig reader created! INFO:root:Sanity checks on the configuration OK! INFO:root:Starting coverage analysis INFO:root:Building gene annotations bed file from CellBase... Traceback (most recent call last): File "/genomes/software/apps/gel-coverage/scripts/bigwig_analyser", line 103, in <module> main() File "/genomes/software/apps/gel-coverage/scripts/bigwig_analyser", line 88, in main (results, bed) = gel_coverage_engine.run() File "/genomes/software/apps/python2.7-tiering/lib/python2.7/site-packages/gelcoverage/runner.py", line 419, in run bed = self.cellbase_helper.make_exons_bed(self.gene_list, has_chr_prefix=self.bigwig_reader.has_chr_prefix) File "/genomes/software/apps/python2.7-tiering/lib/python2.7/site-packages/gelcoverage/tools/cellbase_helper.py", line 169, in make_exons_bed raise SystemError("Input gene list is not correct") SystemError: Input gene list is not correct

On the 8th of February 2017

priesgo commented 7 years ago

@enricserra CellBase was down also yesterday, so everything points to that. Could you rerun this job now? In any case, better error management is required to indicate CellBase not being reachable instead of this cryptic message.

enricserra commented 7 years ago

Getting this :

sh ./run_coverage_analysis.sh /genomes/analysis/by_date/2015-10-23/0000074602/LP2000860-DNA_B04/coverage/LP2000860-DNA_B04.bw /genomes/analysis/by_date/2015-10-23/0000074602/LP2000860-DNA_B04/coverage/LP2000860-DNA_B04.bw_558c24a2bb5a166f63868678_1.0.json 558c24a2bb5a166f63868678 1.0

DEBUG:requests.packages.urllib3.connectionpool:Starting new HTTP connection (1): bioinfo.hpc.cam.ac.uk
DEBUG:requests.packages.urllib3.connectionpool:http://bioinfo.hpc.cam.ac.uk:80 "HEAD /cellbase HTTP/1.1" 302 0
DEBUG:requests.packages.urllib3.connectionpool:Starting new HTTP connection (1): 10.5.8.201
DEBUG:requests.packages.urllib3.connectionpool:http://10.5.8.201:8080 "HEAD /cellbase-4.5.0-rc HTTP/1.1" 302 0
DEBUG:root:Getting gene list from PanelApp...
DEBUG:root:Gene list obtained from PanelApp of 0!
INFO:root:Gene list to analyse: 
INFO:root:0 genes to analyse
DEBUG:root:Creating the BigWig reader...
DEBUG:root:BigWig reader created!
INFO:root:Sanity checks on the configuration OK!
INFO:root:Starting coverage analysis
INFO:root:Building gene annotations bed file from CellBase...
Traceback (most recent call last):
  File "/genomes/software/apps/gel-coverage/scripts/bigwig_analyser", line 103, in <module>
    main()
  File "/genomes/software/apps/gel-coverage/scripts/bigwig_analyser", line 88, in main
    (results, bed) = gel_coverage_engine.run()
  File "/genomes/software/apps/python2.7-tiering/lib/python2.7/site-packages/gelcoverage/runner.py", line 419, in run
    bed = self.cellbase_helper.make_exons_bed(self.gene_list, has_chr_prefix=self.bigwig_reader.has_chr_prefix)
  File "/genomes/software/apps/python2.7-tiering/lib/python2.7/site-packages/gelcoverage/tools/cellbase_helper.py", line 169, in make_exons_bed
    raise SystemError("Input gene list is not correct")
SystemError: Input gene list is not correct

9-2-2017

priesgo commented 7 years ago

This is caused by a panel having 0 genes after gene filtering. This is somewhat incorrect input as there is no genes to analyse. In any case, the fail needs to be softer and provide the user with a proper warning.