Hi, I am running shortBRED on metagenomic samples to determine the number of hits of antibiotic resistance genes in each sample. However, when I look at the .tsv files generated by shortBRED, all of the hits are “zero” for each gene in every sample that I look at.
Here is an example of a tsv file from one sample, where the first value is the count, second is the hits, and third is total marker length. The first and second values are always zero in all of my files.
|Family|Count|Hits|TotMarkerLength|
|gb|AAA03550_1|ARO_3002523|AAC(2_)-Ia|0.0|0|178|
|gb|AAA16194_1|ARO_3002540|AAC(3)-VIa|0.0|0|299|
|gb|AAA19882_1|ARO_3003562|TLE|0.0|0|52|
|gb|AAA20116_1|ARO_3000180|tetA(P)|0.0|0|104|
|gb|AAA20117_1|ARO_3000195|tetB(P)|0.0|0|103|
|gb|AAA21532_1|ARO_3003559|cepA|0.0|0|137|
|gb|AAA21889_1|ARO_3002554|AAC(6_)-Ig|0.0|0|50|
|gb|AAA22081_1|ARO_3002670|cat|0.0|0|48|
|gb|AAA22277_1|ARO_3003007|bmr|0.0|0|172|
|gb|AAA22289_1|ARO_3002672|cat86|0.0|0|133|
|gb|AAA22562_1|ARO_3002878|BcII|0.0|0|59|
|gb|AAA22597_1|ARO_3000495|ErmD|0.0|0|167|
|gb|AAA22851_1|ARO_3000179|tet(L)|0.0|0|49|
|gb|AAA22904_1|ARO_3000578|CcrA|0.0|0|249|
Here is the command that I am using (in a conda environment with shortBRED and all dependencies installed):
shortbred_quantify.py --markers /home/bfranc10/scratch4-jsuez1/shared_databases/shortbred_materials/ShortBRED_CARD_2017_markers.faa --wgs /home/bfranc10/scratch4-jsuez1/reprocessed_data/suez2022paper_processed/megahit_out_day21/fastas/ERR10083398.contigs.fasta --results /home/bfranc10/scratch4-jsuez1/bfranc_work/programs/shortbred_programs/results/day21/ERR10083398_shortbred_results.tsv --tmp example_quantify --usearch /home/bfranc10/scratch4-jsuez1/shared_databases/shortbred_materials/usearch
I am using the 2017 CARD markers from the Huttenhower Lab website. Am I missing a step? Was there anything I needed to do after downloading the markers?