Error when running Galaxy on fasta sequences

Question: Error when running Galaxy on fasta sequences

3.1 years ago by

cerrirc • 0 wrote:

Hi all,

I am running Repeat Explorer on a fasta file with about 8.000 sequences

I am getting the following error when executing the Clustering tool for repeat discovery:

Traceback (most recent call last):

  File "/mnt/raid_galaxy/home/galaxy/galaxy-dist/tools/umbr_programs/seqclust2/programs/all2all_comparison.py", line 240, in <module>
    int(options.min_overlap))
  File "/mnt/raid_galaxy/home/galaxy/galaxy-dist/tools/umbr_programs/seqclust2/programs/all2all_comparison.py", line 207, in all2all_comparison
    clean_hitsort(mgblast_output_files, hitsort_file, ids)
  File "/mnt/raid_galaxy/home/galaxy/galaxy-dist/tools/umbr_programs/seqclust2/programs/all2all_comparison.py", line 145, in clean_hitsort
    ids_destination[line_items[0]].write(line)
KeyError: 'ARSiTERT00200003,'

Does anyone please know what it could be?

Regards,

Ricardo

software error galaxy • 624 views

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modified 3.1 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.1 years ago by cerrirc • 0

3.1 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

This is a python error. In the context of what I think this tool is doing, and the input types, I suggest double checking the format of the fasta identifiers plus ensuring that there are no duplicates. You might need to remove extra content from the description lines (leaving only the identifiers on the ">" fasta lines).

Just as a guess: it could be that extra content in the description lines is not parsed out completely by this tool (content after the ">", first word, and first whitespace). Meaning, what megablast parsed out as an identifier is a mismatch for the identifier otherwise indexed by the tool. Cycle the fasta file through Fasta-to-Tabular (breaking the description line into two fields), then Tabular-To-Fasta (selecting just the first field back for the "identifier", the third field back for the "sequence", leaving the second field of "extra description" content behind). Wrapping the fasta lines may also help.

I am not sure where you are working, but if this format change does not work - or it has already been done, contacting the instance owner or the tool author is the next step.

Thanks, Jen, Galaxy team

ADD COMMENT • link written 3.1 years ago by Jennifer Hillman Jackson ♦ 25k

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