Question: Cufflinks Failure Error - Solution: use version 2.2.1.2 or later
0
gravatar for VY
3 months ago by
VY120
London
VY120 wrote:

Hello,

I've been trying to run cufflinks on my bam files for the last couple of house and keep getting the following tool error. Does anyone know if this is something to do with the bam files or is it an issue with galaxy? (Bam files were generated on the terminal using HISAT2 - not on galaxy).

Thanks! V

Traceback (most recent call last):
  File "/jetstream/scratch0/main/jobs/19882713/tool_files/cufflinks_wrapper.py", line 9, in <module>
    from galaxy.datatypes.util.gff_util import parse_gff_attributes, gff_attributes_to_str
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/util/gff_util.py", line 6, in <module>
    from bx.intervals.io import GenomicInterval, GenomicIntervalReader, MissingFieldError, NiceReaderWrapper, ParseError
ImportError: No module named bx.intervals.io
rna-seq cufflinks • 192 views
ADD COMMENTlink modified 3 months ago by Jennifer Hillman Jackson25k • written 3 months ago by VY120
0
gravatar for Jennifer Hillman Jackson
3 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

This is a brand new dependency issue (today) and we will be correcting it. Please follow progress here: https://github.com/galaxyproject/usegalaxy-playbook/issues/146

Meanwhile, you might want to consider using the updated tools/workflows for RNA-seq covered in the Galaxy tutorials (and avoid this tool): https://galaxyproject.org/learn/

Thanks for reporting the problem! Jen, Galaxy team

ADD COMMENTlink written 3 months ago by Jennifer Hillman Jackson25k

The problem is now fixed. Be sure to use the latest Cufflinks tool version (was just installed). Thanks!

ADD REPLYlink written 3 months ago by Jennifer Hillman Jackson25k

Hi Jen,

Thanks for your help. I've created new jobs with the updated cufflinks - some went through and finished alright but others crashed and gave this error, do you think it's another bug?

thanks! Val

  File "/jetstream/scratch0/main/jobs/19888009/tool_files/cufflinks_wrapper.py", line 169
    print cmd
            ^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print(cmd)?
ADD REPLYlink written 3 months ago by VY120

First, make sure that you are using the latest version of Cufflinks.

Next, try a rerun, or better, switch to using Stringtie. That tool and others are covered in the Galaxy tutorial's link I sent.

Thanks!

ADD REPLYlink written 3 months ago by Jennifer Hillman Jackson25k

I was unable to reproduce your problem (with any of the Cufflinks tool versions). You may be using a specific parameter that is buggy.

If you have time, please send in a bug report from the failed job and leave the inputs/outputs undeleted. Include a link to this Biostars thread for reference/link the two.

Even though Stringtie is an alternative tool, if there is a clear problem with this tool it would be good to characterize it.

How to send in the bug report: https://galaxyproject.org/issues/#usage-problem-reporting

ADD REPLYlink written 3 months ago by Jennifer Hillman Jackson25k

Hi Jen, I was unable to reproduce it either. I rerun cufflinks on the same files with the same parameters a second time and it went through fine so must have been a temporary glitch somewhere. Sorry.

ADD REPLYlink written 3 months ago by VY120

No problem, glad the rerun worked out. Your job may have been executing during the update (best guess!). Thanks!

ADD REPLYlink written 12 weeks ago by Jennifer Hillman Jackson25k
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