Integron_Finder
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gem-pasteur
[BUG] if crash during annotaion phase
Describe the bug A clear and concise description of what the bug is.
whith the last gembase (version 0523) is used (--gembase) and there is a pseudogene (gene indicated as CDS in LSTINf but no proteins in prot file) and we ask for the functionnal annotation (--func_annot) IF crash
To Reproduce
Integrons integron_finder --gembase --cpu 20 --func-annot --keep-tmp --local-max --calin-threshold 1 /pasteur/zeus/projets/p02/Gembase/Current/ALL_DB/test_Replicons/ACBA001.0523.00041.fna
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| || | | | || __/ (_| | | | (_) | | | | | _| | | | | | (_| | __/ |
|___|_| |_|\__\___|\__, |_| \___/|_| |_| |_| |_|_| |_|\__,_|\___|_|
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integron_finder version 2.0.5
Using:
- Python 3.12.9 | packaged by conda-forge | (main, Feb 14 2025, 08:00:06) [GCC 13.3.0]
- numpy 1.26.4
- pandas 2.2.3
- matplolib 3.8.2
- biopython 1.85
- Prodigal V2.6.3: February, 2016
- INFERNAL 1.1.4 (Dec 2020)
- HMMER 3.3.2 (Nov 2020); http://hmmer.org/
Authors:
- Jean Cury, Bertrand Neron, Eduardo Rocha,
Citation:
Néron, B.; Littner, E.; Haudiquet, M.; Perrin, A.; Cury, J.; Rocha, E.P.C.
IntegronFinder 2.0: Identification and Analysis of Integrons across Bacteria, with a Focus on Antibiotic Resistance in Klebsiella.
Microorganisms 2022, 10, 700. https://doi.org/10.3390/microorganisms10040700
If you use --func-annot in conjunction with file NCBIfam-AMRFinder.hmm please also cite
Haft, DH et al., Nucleic Acids Res. 2018 Jan 4;46(D1):D851-D860
PMID: 29112715
=======================
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it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
integron_finder is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program (COPYING file).
If not, see [<http://www.gnu.org/licenses/>](http://www.gnu.org/licenses/).
=======================
command used: integron_finder --gembase --cpu 20 --func-annot --keep-tmp --local-max --calin-threshold 1 /pasteur/zeus/projets/p02/Gembase/Current/ALL_DB/test_Replicons/ACBA001.0523.00041.fna
=======================
INFO : ############ Processing replicon ACBA001.0523.00041.001C (1/2) ############
...
WARNING : Sequence describe in LSTINF file ACBA001.0523.00041.001C_02479 is not present in /pasteur/zeus/projets/p02/Gembase/Releases/2023/Microbial_0523/Proteins/ACBA001.0523.00041.prt
WARNING : Sequence describe in LSTINF file ACBA001.0523.00041.001C_02482 is not present in /pasteur/zeus/projets/p02/Gembase/Releases/2023/Microbial_0523/Proteins/ACBA001.0523.00041.prt
WARNING : Sequence describe in LSTINF file ACBA001.0523.00041.001C_02485 is not present in /pasteur/zeus/projets/p02/Gembase/Releases/2023/Microbial_0523/Proteins/ACBA001.0523.00041.prt
...
INFO : Starting Default search ... :
INFO : Default search done... :
INFO : In replicon ACBA001.0523.00041.001C, there are:
INFO : - 0 complete integron(s) found with a total 0 attC site(s)
INFO : - 1 CALIN element(s) found with a total of 3 attC site(s)
INFO : - 0 In0 element(s) found with a total of 0 attC site
INFO : Starting search with local_max...:
INFO : Search with local_max was already done, continue... :
INFO : In replicon ACBA001.0523.00041.001C, there are:
INFO : - 0 complete integron(s) found with a total 0 attC site(s)
INFO : - 1 CALIN element(s) found with a total of 3 attC site(s)
INFO : - 0 In0 element(s) found with a total of 0 attC site
INFO : Adding proteins ... :
INFO : Starting functional annotation ...:
Traceback (most recent call last):
File "/pasteur/zeus/projets/p01/MDM/MDM_conda/mdm_base_env3.12/bin/integron_finder", line 10, in <module>
sys.exit(main())
^^^^^^
File "/pasteur/zeus/projets/p01/MDM/MDM_conda/mdm_base_env3.12/lib/python3.12/site-packages/integron_finder/scripts/finder.py", line 653, in main
integron_res, summary = find_integron_in_one_replicon(replicon, config)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/pasteur/zeus/projets/p01/MDM/MDM_conda/mdm_base_env3.12/lib/python3.12/site-packages/integron_finder/scripts/finder.py", line 410, in find_integron_in_one_replicon
func_annot(integrons, replicon, protein_db, fa_hmm, config, result_tmp_dir)
File "/pasteur/zeus/projets/p01/MDM/MDM_conda/mdm_base_env3.12/lib/python3.12/site-packages/integron_finder/annotation.py", line 90, in func_annot
prot_to_annotate.append(prot_db[prot_id])
~~~~~~~^^^^^^^^^
File "/pasteur/zeus/projets/p01/MDM/MDM_conda/mdm_base_env3.12/lib/python3.12/site-packages/integron_finder/prot_db.py", line 583, in __getitem__
return self._prot_db[prot_seq_id]
~~~~~~~~~~~~~^^^^^^^^^^^^^
File "/pasteur/zeus/projets/p01/MDM/MDM_conda/mdm_base_env3.12/lib/python3.12/site-packages/Bio/File.py", line 238, in __getitem__
record = self._proxy.get(self._offsets[key])
~~~~~~~~~~~~~^^^^^
KeyError: 'ACBA001.0523.00041.001C_02482'
/!\ please share your input file so we can reproduce the problem
Expected behavior
do try to perform the functional annotation on pseud genes
Screenshots
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Please complete the following information):
OS:
- [x] Linux
- [ ] Windows
- [x ] Mac
Integron_Finder Version:
copy/paste here the output of integron_finder --version
Additional context Add any other context about the problem here.
