outrigger validate fails when outrigger_output/index/mxe/exon1.bed does not exist

[ghost]

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

[olgabot]

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 ***@***.***> 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 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#82>, or mute the thread </~https://github.com/notifications/unsubscribe-auth/AAxNcOuiz5zR0Qk2KvW69PBOgYVjFXE9ks5rx-kjgaJpZM4NDsTa> .

-- --- 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]

I encountered the same problem. I used Esenmble gtf file. Could this be the reason?
ValueError: File "./outrigger_output/index/mxe/exon1.bed" does not exist