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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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some major and common problems #81

Closed hongyuan-zheng closed 3 years ago

hongyuan-zheng commented 3 years ago

Version of Integron_Finder:

Linux

Expected behavior

verify integrons in some strains which have been assembled to contigs

Actual behavior

integron_finder --local-max --func-annot --cpu 5 --gbk mysequence.fa

Steps to reproduce behavior

Relevant logs and/or screenshots

1. if the parameter --gbk was added ,the error below often occured: Traceback (most recent call last): File "/User/zhenghy/software/conda/miniconda/envs/IFv2/bin/integron_finder", line 10, in sys.exit(main()) File "/User/zhenghy/software/conda/miniconda/envs/IFv2/lib/python3.6/site-packages/integron_finder/scripts/finder.py", line 595, in main integron_res, summary = find_integron_in_one_replicon(replicon, config) File "/User/zhenghy/software/conda/miniconda/envs/IFv2/lib/python3.6/site-packages/integron_finder/scripts/finder.py", line 392, in find_integron_in_one_replicon add_feature(replicon, integrons_report, protein_db, config.distance_threshold) File "/User/zhenghy/software/conda/miniconda/envs/IFv2/lib/python3.6/site-packages/integron_finder/annotation.py", line 183, in add_feature f1 = SeqFeature.FeatureLocation(start_integron_1 - 1, end_integron_1) File "/User/zhenghy/software/conda/miniconda/envs/IFv2/lib/python3.6/site-packages/Bio/SeqFeature.py", line 750, in init self.start)) ValueError: End location (1532003) must be greater than or equal to start location (1900396) I did nothing except inputted the multi-fasta file as the input file.

2. if the input file was a multi-fasta ,the error below often occured: Traceback (most recent call last): File "/User/zhenghy/software/conda/miniconda/envs/IFv2/bin/integron_finder", line 10, in sys.exit(main()) File "/User/zhenghy/software/conda/miniconda/envs/IFv2/lib/python3.6/site-packages/integron_finder/scripts/finder.py", line 595, in main integron_res, summary = find_integron_in_one_replicon(replicon, config) File "/User/zhenghy/software/conda/miniconda/envs/IFv2/lib/python3.6/site-packages/integron_finder/scripts/finder.py", line 332, in find_integron_in_one_replicon evalue_attc=config.evalue_attc) File "/User/zhenghy/software/conda/miniconda/envs/IFv2/lib/python3.6/site-packages/integron_finder/attc.py", line 213, in find_attc_max go_left = (full_element[full_element.type_elt == "attC"].pos_beg.values[0] - df_max.pos_end.values[0] IndexError: index 0 is out of bounds for axis 0 with size 0 also, I did nothing except inputted the multi-fasta file as the input file.

3. what dose the third column "element" mean in the output file "mysequence.integrons" ?? 4. whould you please output a file of the fasta sequence of the verified integrons ??

jeanrjc commented 3 years ago

Hello, Sorry I did not see your issue when you posted it.

  1. If you could share the sequence causing the issue, it will be easier for us to debug.
  2. See error #73 and see whether it solve your issue.
  3. elements are the identifiers of different types of element (in column type_elt), such as attC/I sites, promoters, or proteins.
  4. IntegronFinder does not output fasta files, but gbk files (which should work normally). You can easily reconstruct fasta file from your input sequence and the table of positions. Feel free to propose a merge request to add this feature.

Best

jeanrjc commented 3 years ago

Without more details, I'm closing this issue. Feel free to add the details, and I'll reopen it.