Problem on following the post-assembly-QC-workflow

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Hi!

I met a problem when following the post-assembly-QC-workflow: Hands-on: ERGA post-assembly QC / ERGA post-assembly QC / Assembly

Here is the error message when I runed the BlobToolKit within this workflow:
Traceback (most recent call last):
File “/opt/conda/envs/btk_env/bin/blobtools”, line 8, in
sys.exit(cli())
File “/opt/conda/envs/btk_env/lib/python3.9/site-packages/blobtools/blobtools.py”, line 105, in cli
sys.exit(subcommand())
File “/opt/conda/envs/btk_env/lib/python3.9/site-packages/blobtools/lib/add.py”, line 203, in cli
main(args)
File “/opt/conda/envs/btk_env/lib/python3.9/site-packages/blobtools/lib/add.py”, line 149, in main
parsed = field[“module”].parse(
File “/opt/conda/envs/btk_env/lib/python3.9/site-packages/blobtools/lib/hits.py”, line 541, in parse
blast = parse_blast(
File “/opt/conda/envs/btk_env/lib/python3.9/site-packages/blobtools/lib/hits.py”, line 83, in parse_blast
taxid = row[cols[“staxids”]]
IndexError: list index out of range

Here is my history: Galaxy
It seems that this error is related to the output of the diamond in the last step.
Could you help me find a solution? Thank you very mcuh!

Cheers,

Chuan

1 Like
2

Hi @chuan_zhai

I’m reviewing the history, more feedback soon.

Xref: BlobToolKit problem

3

Hi @chuan_zhai

The Diamond hits that do not have a taxonomy assignment are empty in the 7th column … and that is failing the BlobToolKit tool.

Try running this on your Diamond output to get rid of those lines →

tool: Select lines that match an expression
option: NOT Matching
expression: .*\t$

Now, the BlobToolKit tool can’t use those rows anyway but I don’t think their presence should fail the tool. I’ve reported this for a bug fix consideration here → Blobtoolkit can have trouble parsing raw Diamond results · Issue #1456 · bgruening/galaxytools · GitHub

Thanks for reporting the problem! :slight_smile:

1 Like
4

Hi jennaj!

Your solution worked! Thank you!

Cheers,

Chuan