gem-pasteur / Integron_Finder

Bioinformatics tool to find integrons in bacterial genomes
GNU General Public License v3.0
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[BUG] IF crashes with --gbk option in a specific caase #104

Closed eloilit closed 4 months ago

eloilit commented 2 years ago

Describe the bug When using the --gbk option, IF crashes if a feature (e.g. cassette, attC site) spans over both borders of a replicon.

To Reproduce Steps to reproduce the behavior: With the attached files

  1. integron_finder --local-max --mute --outdir ./IFResults --gembase --gembase-path ./Gembase --gbk ./Gembase/Replicons/KLPN001.0321.00476.P003.fst
  2. See error

Expected behavior

Finish without error and produce output files

Screenshots

image

Please complete the following information):

OS:

Integron_Finder Version:

integron_finder version 2.0.2 Using:

Additional context Not a big issue, as it works properly if we remove the --gbk option

eloilit commented 2 years ago

Gembase.zip

jeanrjc commented 2 years ago

a feature (e.g. cassette, attC site) spans over both borders of a replicon

You mean, that the feature exists in the circular replicon and is cut in 2 in the linear sequence ?

eloilit commented 2 years ago

Yes ! Here's an extraction of the .integrons file in my specific case. You can see that the last protein detected begins at position 190392 and ends at position 299 image