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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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How to use --func-annot #106

Closed aslangabriel closed 1 year ago

aslangabriel commented 1 year ago

Describe your problem I want to test the annotation function with customized hmm database, To Reproduce Steps to reproduce the behavior:

  1. Download the latest AMR.LIB

  2. run the docker editon with the command docker run -v $PWD:/home/IF --user $(id -u):$(id -g) 431219fdaa50 --func_annot /home/shpc_1100038/AMR.LIB --local-max --circ --keep-tmp JSAHVC25.fasta The error information was listed as follows:

    2

    Thanks a lot

OS:

Linux

Integron_Finder Version:

V2.0

Additional context Add any other context about the problem here.

jeanrjc commented 1 year ago

You need to use --func_annot which tells IF whether it runs functional annotation or not and --path-func-annot with a file containing path to your library. Because func_annot does not expect an argument, IF thinks that the path to your lib is the replicon, and thus fails. Besides, it seems the path to your lib is wrong. (no such file or directory)

You can read more here : https://integronfinder.readthedocs.io/en/latest/user_guide/tutorial.html#functional-annotation