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gem-pasteur / Integron_Finder

Bioinformatics tool to find integrons in bacterial genomes
GNU General Public License v3.0
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Prediction over sequence start with --linear #55

Closed johrollin closed 2 years ago

johrollin commented 6 years ago

Hello,

On few bacteria, integron_finder find an integron over the sequence start even if the "--linear" option is active.

FEATURES          Location/Qualifiers
    integron      join(1591485..1621862,1..7622)
                  /integron_id="integron_01"
                  /integron_type="complete"

If I understand the "--linear" option correctly this should not append, right ?

Here is the command line we used:

integron_finder $fnafile --local_max --cpu 1 --linear

Nothing very specific there, but we still use the "gembase workaround" (https://github.com/gem-pasteur/Integron_Finder/issues/35), I don't think it impact this issue.

If needed I can provide data for further test.

J.Rollin LABGeM/Génoscope

jeanrjc commented 6 years ago

Hello,

Indeed, it shouldn't happen. It might be already fixed in version 2.0 though. We'll let you know when it's fixed.

Best, Jean

duboism commented 4 years ago

Hello,

Any news on this bug ?

duboism commented 2 years ago

Hello,

IIUC, the bug is solved in version 2, right ?

bneron commented 2 years ago

Yes, I will very soon (one or two days) release a new version.