Comments (3)
@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.
from gel-coverage.
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
from gel-coverage.
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.
from gel-coverage.
Related Issues (20)
- Compute coverage statistics at gene level using the union transcript HOT 1
- Compute coverage statistics at panel level HOT 1
- Parametrize the configuration file HOT 1
- Automate test data download by making it available in OpenCGA
- Stress test: run the analysis on a whole genome file HOT 2
- Add GRCh38 support to wrapper script HOT 6
- Add whole genome metric of coverage uneveness
- Report not sequenced regions HOT 1
- Support NonN regions bed file for the whole genome coverage analysis HOT 1
- Add statistics at chromosome level for whole genome and exome regions HOT 2
- Coverage pipeline usage of different chromosome identifiers conventions HOT 1
- Add support for chromosome chr prefix on cellbase helper HOT 1
- support for multiple panels HOT 2
- Uneveness of coverage metric is not being weighted and the result might be biased HOT 4
- Segmentation fault for GRCh38 coverage analysis HOT 5
- Calculate standard deviation at several genomic levels HOT 1
- Error when all transcripts are filtered out HOT 1
- Requirements meeting HOT 9
- Include a parametrizable number of bases up and downstream of each exon HOT 1
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from gel-coverage.