Question: Stringtie tool failed with error "NameError: name 't_id' is not defined"
2
gravatar for tamrin.chowdhury
16 months ago by
tamrin.chowdhury40 wrote:

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?

ADD COMMENTlink modified 15 months ago by Jennifer Hillman Jackson25k • written 16 months ago by tamrin.chowdhury40
1

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

ADD REPLYlink written 15 months ago by aescalante10

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

ADD REPLYlink written 15 months ago by Jennifer Hillman Jackson25k

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

ADD REPLYlink modified 15 months ago • written 16 months ago by Jennifer Hillman Jackson25k

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.

ADD REPLYlink modified 15 months ago • written 15 months ago by Jennifer Hillman Jackson25k
0
gravatar for Jennifer Hillman Jackson
15 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Update 06-06-2017

We have isolated a specific usage issue with Stringtie and the option to output additional files for use with DESeq2/EdgeR. This is related to the error NameError: name 't_id' is not defined. To use a reference GTF, it is currently required that the reference annotation be prepared/groomed with the Stringtie merge transcripts tool. Even if that is the only reference annotation used.

The root cause of the error NameError: name 'coverage' is not defined has not been determined yet because it cannot be reproduced with testing. If you run into this particular error, please send in a bug report that includes a link to this post in the comments.

Work-around for now:

If using an external GTF source with Stringtie, and not currently using Stringtie merge transcripts, running just the external GTF dataset through the Stringtie merge transcripts tool (as an "input_gtf", leaving the input for "guide_gff" with no dataset selected) will produce a groomed version of the reference annotation that can be used by Stringtie.

Full ticket:

https://github.com/galaxyproject/tools-iuc/issues/1322

Thanks to everyone who reported the problem here and/or sent in bug reports! Jen, Galaxy team

ADD COMMENTlink modified 15 months ago • written 15 months ago by Jennifer Hillman Jackson25k
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