olgabot
commented
7 years ago Thank you for reporting this! You write really good bug reports. This is a problem that will be fixed by the new command line interface I'm working on to make all the arguments more explicit. Still working on it..
On Thu, Apr 20, 2017, 16:24 navarrereed notifications@github.com wrote:
Description
Ran outrigger validate on successful outrigger index results, crashed with ValueError: File "./outrigger_output/index/mxe/exon1.bed" does not exist. outrigger index ran successfully on a test dataset but found no mxe events in the truncated data. Consequently no exon1.bed file was written, which crashed outrigger validate. Skipped exon events were, however, validated and generated output. Steps to Reproduce
Successful outrigger index output: https://gist.github.com/navarrereed/afa45cde46027f2aa83fbd7825ea5db9 Failed outrigger validate output: https://gist.github.com/navarrereed/cd460498ca2c581c55057952139b080b
Expected behavior: Successful validation of existing se results in outrigger_output.
Actual behavior: Crash due to lack of mxe results in outrigger_output. Versions
outrigger --version outrigger 1.0.0
python --version Python 3.5.3
conda --version conda 4.3.16
OS: Ubuntu 14.04
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Olga Botvinnik PhD Program in Bioinformatics and Systems Biology http://bioinformatics.ucsd.edu/ Gene Yeo Laboratory http://yeolab.ucsd.edu/yeolab/Home.html | Sanford Consortium for Regenerative Medicine http://www.sanfordconsortium.org/ University of California, San Diego http://ucsd.edu/ www http://olgabotvinnik.com/ | blog http://blog.olgabotvinnik.com/ | github http://github.com/olgabot | twitter http://twitter.com/olgabot | linkedin http://www.linkedin.com/in/olgabotvinnik
leezx
Description
Ran outrigger validate on successful outrigger index results, crashed with ValueError: File "./outrigger_output/index/mxe/exon1.bed" does not exist. outrigger index ran successfully on a test dataset but found no mxe events in the truncated data. Consequently no exon1.bed file was written, which crashed outrigger validate. Skipped exon events were, however, validated and generated output before crash.
Steps to Reproduce
outrigger_output minus /gtf: https://www.dropbox.com/sh/k5waom8ueaspoeo/AAB4dGttyLiWG4RGfbgzXKzWa?dl=0 Successful outrigger index output: https://gist.github.com/navarrereed/afa45cde46027f2aa83fbd7825ea5db9 Failed outrigger validate output: https://gist.github.com/navarrereed/cd460498ca2c581c55057952139b080b
Expected behavior: Successful validation of outrigger_output. Outrigger appears to have written "se" results before crashing, graceful exit when no mxe events are detected.
Actual behavior: Crash due to lack of mxe results in outrigger_output.
Versions
outrigger --version outrigger 1.0.0
python --version Python 3.5.3
conda --version conda 4.3.16
OS: Ubuntu 14.04