When I tried to run shortbred_quantify.py, I got the following errors:
subprocess.CalledProcessError: Command '['/home/ewissel2/scr4_jsuez1/shared_databases/shortbred_materials/usearch11.0.667_i86linux32', '--usearch_local', '/home/bfranc10/scratch4-jsuez1/reprocessed_data/suez2022paper_processed/megahit_out/fastas/ERR10083802.contigs.fasta', '--db', '/scratch4/jsuez1/bfranc_work/programs/shortbred_programs/shortbred/example_quantify/ShortBRED_CARD_2017_markers.faa.udb', '--id', '0.95', '--userout', '/scratch4/jsuez1/bfranc_work/programs/shortbred_programs/shortbred/example_quantify/wgsfull_results.tab', '--userfields', 'query+target+id+alnlen+mism+opens+qlo+qhi+tlo+thi+evalue+bits+ql+tl+qs+ts', '--maxaccepts', '1', '--maxrejects', '32', '--threads', '1']' returned non-zero exit status 1
KeyError: '6'
IndexError: list index out of range
I installed shortBRED 0.9.3 into a python 2.7.18 conda environment made with a yml file, and all of the dependencies (muscle, cd-hit, blast, biopython, usearch) installed.
The command that I used was:
shortbred_quantify.py --markers /home/ewissel2/scr4_jsuez1/shared_databases/shortbred_materials/ShortBRED_CARD_2017_markers.faa --wgs /home/bfranc10/scratch4-jsuez1/reprocessed_data/suez2022paper_processed/megahit_out/fastas/ERR10083753.contigs.fasta --results /home/bfranc10/scratch4-jsuez1/bfranc_work/programs/shortbred_programs/results/baseline/ERR10083753_shortbred_results.tsv --tmp example_quantify --usearch /home/ewissel2/scr4_jsuez1/shared_databases/shortbred_materials/usearch11.0.667_i86linux32