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oschwengers / referenceseeker

Rapid determination of appropriate reference genomes.
https://doi.org/10.21105/joss.01994
GNU General Public License v3.0
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[BUG] IndexError: list index out of range #13

Closed Jwebster89 closed 3 years ago

Jwebster89 commented 3 years ago

When running referenceseeker 1.6.3 (installed with conda) with a custom database I received an "IndexError: list index out of range".

Traceback (most recent call last): File "/home/user/miniconda3/envs/ref_seeker/bin/referenceseeker", line 10, in sys.exit(main()) File "/home/user/miniconda3/envs/ref_seeker/lib/python3.9/site-packages/referenceseeker/referenceseeker.py", line 96, in main ref_genomes = util.read_reference_genomes(config) File "/home/user/miniconda3/envs/ref_seeker/lib/python3.9/site-packages/referenceseeker/util.py", line 24, in read_reference_genomes 'name': cols[3]

I imported my genomes into the database without using the optional --organism flag and received this error. After checking the custom db.tsv and the util.py, it looks like I might have needed something in the name column other than the default "". Re-ran the database import with the --organism flag and it appears to be working now.

oschwengers commented 3 years ago

Hello @Jwebster89 , thanks for reporting! The issue should be fixed. ReferenceSeeker now sets a default organism strings to 'NA' if no organism name is provided. A patch release is out - it should make its way through the CD (PyPI/Docker/BioConda) soon.

I close the issue for now - please do not hesitate to reopen it, if the issue should somehow remain. Best regards!