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arpcard / rgi

Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.
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UserWarning: sequence should be at least 100000 characters (47098 found) #214

Closed raphenya closed 10 months ago

raphenya commented 1 year ago

Describe the bug A clear and concise description of what the bug is.

Input rgi main -i homolog.fasta -o output --clean -g PYRODIGAL -a diamond --debug --num_threads 10 --local > run.log 2>&1

Input file

https://github.com/arpcard/rgi/blob/master/tests/inputs/homolog.fasta

Error log

INFO 2023-01-18 12:01:52,489 : /Users/amos/Desktop/test/homolog.fasta => None INFO 2023-01-18 12:01:52,515 : valid nucleotide fasta: {'A': 14771, 'T': 14410, 'G': 9084, 'C': 8833, 'N': 0, 'U': 0, 'W': 0, 'S': 0, 'M': 0, 'K': 0, 'R': 0, 'Y': 0, 'B': 0, 'D': 0, 'H': 0, 'V': 0} INFO 2023-01-18 12:01:52,746 : create blast DB. INFO 2023-01-18 12:01:53,596 : create diamond DB. /Users/amos/miniconda3/envs/rgiDev/lib/python3.7/site-packages/app/ORF.py:253: UserWarning: sequence should be at least 100000 characters (47098 found) orf_finder.train(*sequences, force_nonsd=True) INFO 2023-01-18 12:01:53,944 : work with file /Users/amos/Desktop/test/homolog.fasta.temp.contig.fsa INFO 2023-01-18 12:01:54,189 : done running diamond blastp -> /Users/amos/Desktop/test/localDB INFO 2023-01-18 12:01:54,189 : set blast xml file: [/Users/amos/Desktop/test/homolog.fasta.temp.contig.fsa.blastRes.xml] INFO 2023-01-18 12:01:54,189 : run filter INFO 2023-01-18 12:01:54,201 : homolog_worker started... INFO 2023-01-18 12:01:54,203 : variant_worker started... INFO 2023-01-18 12:01:54,204 : overexpression_worker started... INFO 2023-01-18 12:01:54,205 : rRNA process: contig INFO 2023-01-18 12:01:54,206 : rRNA process INFO 2023-01-18 12:01:54,207 : create_db_query INFO 2023-01-18 12:01:54,208 : DB from user query INFO 2023-01-18 12:01:54,522 : save variant results... INFO 2023-01-18 12:01:54,523 : save overexpression results... INFO 2023-01-18 12:01:54,524 : save homolog results... INFO 2023-01-18 12:01:54,616 : blast_reference_to_db_query INFO 2023-01-18 12:01:55,071 : done running blastn -> /Users/amos/Desktop/test/homolog.fasta.temp.db INFO 2023-01-18 12:01:55,343 : rRNA process Done. INFO 2023-01-18 12:01:55,361 : prepare output(s) for input: /Users/amos/Desktop/test/homolog.fasta INFO 2023-01-18 12:01:55,371 : Total running time 2.882s INFO 2023-01-18 12:01:55,373 : Cleaning up temporary files...output INFO 2023-01-18 12:01:55,373 : /Users/amos/Desktop/test INFO 2023-01-18 12:01:55,374 : Removed file: /Users/amos/Desktop/test/homolog.fasta.temp.db.nhr INFO 2023-01-18 12:01:55,375 : Removed file: /Users/amos/Desktop/test/homolog.fasta.temp.homolog.json INFO 2023-01-18 12:01:55,375 : Removed file: /Users/amos/Desktop/test/homolog.fasta.temp.rrna.json INFO 2023-01-18 12:01:55,375 : Removed file: /Users/amos/Desktop/test/homolog.fasta.temp.contigToORF.fsa INFO 2023-01-18 12:01:55,376 : Removed file: /Users/amos/Desktop/test/homolog.fasta.temp INFO 2023-01-18 12:01:55,376 : Removed file: /Users/amos/Desktop/test/homolog.fasta.temp.contig.fsa.blastRes.xml INFO 2023-01-18 12:01:55,376 : Removed file: /Users/amos/Desktop/test/homolog.fasta.temp.contig.fsa INFO 2023-01-18 12:01:55,377 : Removed file: /Users/amos/Desktop/test/homolog.fasta.temp.overexpression.json INFO 2023-01-18 12:01:55,377 : Removed file: /Users/amos/Desktop/test/homolog.fasta.temp.db.nsq INFO 2023-01-18 12:01:55,377 : Removed file: /Users/amos/Desktop/test/homolog.fasta.temp.predictedGenes.json INFO 2023-01-18 12:01:55,378 : Removed file: /Users/amos/Desktop/test/homolog.fasta.temp.predictedGenes.protein.json INFO 2023-01-18 12:01:55,378 : Removed file: /Users/amos/Desktop/test/homolog.fasta.temp.blastRes.rrna.xml INFO 2023-01-18 12:01:55,378 : Removed file: /Users/amos/Desktop/test/homolog.fasta.temp.variant.json INFO 2023-01-18 12:01:55,379 : Removed file: /Users/amos/Desktop/test/homolog.fasta.temp.db.nin INFO 2023-01-18 12:01:55,379 : /Users/amos/Desktop/test

CARD Version 3.2.5

RGI version 6.0.2 (latest commit: fd9847408158e5101cf33dc4a68bd263ca5bec4f)

Expected behavior I get UserWarning when using option -g PYRODIGAL but not with -g PRODIGAL

Desktop (please complete the following information):

Additional context

Results are not currently affected for this input file.

github-actions[bot] commented 10 months ago

Issue is stale and will be closed in 7 days unless there is new activity