Question: Error message on cufflinks: ImportError
0
gravatar for florian.laforets
14 months ago by
florian.laforets0 wrote:

Hello,

I couldn't find the answer for this elsewhere on the forum. I have run .bam files (between 8 bg and 15 gb each, uploaded via FTP client) analysis with Cufflinks, using a genome reference (not as guide), and with the multi-read correct option selected. My first few analysis worked well. I then loaded another batch of .bam files, and perfomed the same operation. However, in these cases I obtained a error message:

**Traceback (most recent call last):   File "/jetstream/scratch0/main/jobs/19873177/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**

I have tried running the jobs again, but got the same error message. I don't see what can be wrong, especially since I couldn't find a difference between the first and second batch of files.

If you need more details regarding this, just let me know. Any help would be very appreciated!

Many thanks,

Flo.

rna-seq cufflinks • 582 views
ADD COMMENTlink modified 14 months ago by Kevin Blighe46k • written 14 months ago by florian.laforets0

Were you using a different Python version or virtual environment for the first batch? And did you change anything regarding the Python packages in between. It seems it cannot import a package.

ADD REPLYlink written 14 months ago by Gungor Budak230

Thanks for your answer, Gundor. I forgot to mention I was running this on Galaxy.org. I therefore did not change any Python version (at least no intentionally) nor the virtual environnement. I did not change anything regarding the Python packages in between either.

ADD REPLYlink written 14 months ago by florian.laforets0
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