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Question: Fatal error in StringTie
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gravatar for Carlos Andrés Caicedo
15 months ago by
Carlos Andrés Caicedo • 0
Colombia/Medellín
Carlos Andrés Caicedo • 0 wrote:

Dear all

I was running StringTie and I got this error message. 

    Fatal error: Exit code 1 ()
Traceback (most recent call last):
  File "/galaxy/main/deps/_conda/envs/__stringtie@1.3.3/bin/prepDE.py", line 85, in <module>
    t_id=RE_TRANSCRIPT_ID.search(v[len(v)-1]).group(1)
AttributeError: 'NoneType' object has no attribute 'group'

could someone help me to figure out where the error in my procedure is?

Regards
assembly rna-seq • 447 views
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modified 15 months ago by Jennifer Hillman Jackson ♦ 25k • written 15 months ago by Carlos Andrés Caicedo • 0
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gravatar for Jennifer Hillman Jackson
15 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

In the past, this problem has come up and these were the solutions. Check both to find out if the issue is coming from one or both:

  1. The GTF file is missing valid attributes for type=transcript features. Specifically, it is missing the transcript_id "XXX" expected nomenclature. The type=gene as also missing the proper attribute gene_id "XXXX", but that should not impact this particular tool usage (yet watch out for it being a problem downstream if gene is used as a filter input with summary tools).

  2. HISAT was run without specifying to output results in a way that Stringtie can interpret. This prior Biostars post shows to how set the option for Cufflinks. For your run, instead, use the option for Stringie present in the same menu. https://biostar.usegalaxy.org/p/23367/#23369

Try this out and see if it helps. If not, a bug report can be sent in for specific feedback if working at http://usegalaxy.org or the problem can be reproduced there.

Thanks, Jen, Galaxy team
ADD COMMENT • link written 15 months ago by Jennifer Hillman Jackson ♦ 25k
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