Hello
I have used the Stringtie tool successfully to produce transcript assemblies and additional ballgown input files.
I wanted to also try the DeSeq2 tool so I tried to run Stringtie again with the same data and reference with default settings and changed the additional output to Deseq/EdgeR. But the jobs failed due to following error
"Fatal error: Exit code 1 () Traceback (most recent call last): File "/packages/galaxy/database/dependencies/_conda/envs/__stringtie@1.3.3/bin/prepDE.py", line 175, in <module> t_dict[t_id].setdefault(s, int(ceil(coverage*transcript_len/read_len))) NameError: name 'coverage' is not defined"
I am using Galaxy on the local server. I don't understand what went wrong this time as the input data is same and I previously ran succesful analysis with the same tool just with different additional output option.
Can someone kindly point out what seems to be the problem?
Dear all,
Another error with StringTie I just got, it looks very similar so I posted it here:
"0 sample1 Fatal error: Exit code 1 () Traceback (most recent call last): File "/galaxy/main/deps/_conda/envs/__stringtie@1.3.3/bin/prepDE.py", line 186, in <module> t_dict.setdefault(t_id, {}) NameError: name 't_id' is not defined"
Im using the Galaxy Main server if thats of any help.
Any help appreciated.
Cheers,
A
This is an error that comes up with when using particular output settings but only for certain datasets. We have been investigating but since this doesn't always result, it has been difficult to track down why (and how to avoid it). I see your bug report was sent in. More feedback soon. Thanks! Jen, Galaxy team
Hello,
A similar problem came up with the tool during other tests. That error cannot be reproduced with all use cases. Your reported error is new and we have no examples and cannot reproduce.
This is the prior ticket, that I closed out, but may reopen if the issue with this output selection can be clarified. https://github.com/galaxyproject/tools-iuc/issues/1322
If you have time to test to see if the problem can be reproduced at http://usegalaxy.org and then send in a bug report, that would be helpful.
Thanks for reporting the problem! Jen, Galaxy team
The current workaround addresses the "NameError: name 't_id' is not defined" error. We are not able to reproduce the error "NameError: name 'coverage' is not defined".
Would you be able to run a test at http://usegalaxy.org to see if the error can be reproduced there? If another usage issue is present, we want to learn about it and correct at the same time as the other issue is addressed. Both seem to be linked to the same output option selection and the problem is likely with the tool itself.
Be sure that you follow the workaround below first to prepare/groom the reference annotation unless you are already using Stringtie merge transcripts.