eloilit
commented
2 years ago command used: integron_finder --local-max --mute --outdir ./IFResults --gembase --gembase-path ./VibrionaceaDBMarch2022_v2 --gbk ./VibrionaceaDBMarch2022_v2/Replicons/VIBR.0322.11443.0157.fna
@jeanrjc Here are the files to reproduce the error
Describe the bug IF crashes on a multiple contigs file, using the gembase format, in the middle of the contigs being processed.
To Reproduce Steps to reproduce the behavior:
I located the files to reproduce the error in /pasteur/appa/scratch/elittner/for_issue_IF_crashes Expected behavior
Normal completion
Screenshots
Traceback (most recent call last): File "/Users/eloi/Documents/Softwares/anaconda3/envs/IFv2.0.1/bin/integron_finder", line 10, in
sys.exit(main())
File "/Users/eloi/Documents/Softwares/anaconda3/envs/IFv2.0.1/lib/python3.9/site-packages/integron_finder/scripts/finder.py", line 648, in main
integron_res, summary = find_integron_in_one_replicon(replicon, config)
File "/Users/eloi/Documents/Softwares/anaconda3/envs/IFv2.0.1/lib/python3.9/site-packages/integron_finder/scripts/finder.py", line 385, in find_integron_in_one_replicon
integrons = find_integron(replicon, protein_db, integron_max, intI_file, phageI_file, config)
File "/Users/eloi/Documents/Softwares/anaconda3/envs/IFv2.0.1/lib/python3.9/site-packages/integron_finder/integron.py", line 150, in find_integron
attc_left = np.array([i_attc.pos_beg.values[0] for i_attc in attc_ac])
File "/Users/eloi/Documents/Softwares/anaconda3/envs/IFv2.0.1/lib/python3.9/site-packages/integron_finder/integron.py", line 150, in
attc_left = np.array([i_attc.pos_beg.values[0] for i_attc in attc_ac])
IndexError: index 0 is out of bounds for axis 0 with size 0
Please complete the following information):
OS:
Integron_Finder Version:
integron_finder version 2.0.2 Using:
Python 3.9.13 | packaged by conda-forge | (main, May 27 2022, 17:01:00) [Clang 13.0.1 ]
numpy 1.19.4
pandas 1.1.5
matplolib 3.3.3
biopython 1.78
Prodigal V2.6.3: February, 2016
INFERNAL 1.1.4 (Dec 2020)
HMMER 3.3.2 (Nov 2020); http://hmmer.org/
Additional context Only one example failing over a big dataset