MUSCLE in ShortBRED

Question

[a.mostafa5050]

Hi,

I have installed ShortBRED yesterday by conda

conda install -c biobakery shortbread

When I was trying to run shortbred_identify.py to create markers out of CARD database by

conda activate /cluster/projects/nn8021k/Conda-env/my_shortbred

shortbred_identify.py --goi /cluster/projects/nn8021k/Databases/CARD_327/markers_shortbred/protein_homolog_model.fasta
--ref /cluster/projects/nn8021k/Databases/humann_database/uniref/uniref90.fasta
--threads 32 --clustid 0.95 --markers /cluster/projects/nn8021k/Databases/CARD_327/markers_shortbred/CARD_markers.faa
--tmp /cluster/projects/nn8021k/Databases/CARD_327/markers_shortbred/Temp

I got this error

Invalid command line Unknown option in

Checking dependencies... Checking to make sure that installed version of usearch can make databases... Traceback (most recent call last):   File "/cluster/projects/nn8021k/Conda-env/my_shortbred/bin/shortbred_identify.py", line 274, in <module>
    pb.ClusterFams(dirClust, args.dClustID,strClustFile,args.dConsThresh,args.strMUSCLE )   File "/cluster/projects/nn8021k/Conda-env/my_shortbred/bin/src/process_blast.py", line 320, in ClusterFams
    subprocess.check_call([strMUSCLE, "-in", str(fileFasta), "-out", str(fileAlign)])   File "/cluster/projects/nn8021k/Conda-env/my_shortbred/lib/python2.7/subprocess.py", line 190, in check_call
    raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['muscle', '-in', '/cluster/projects/nn8021k/Databases/CARD_327/markers_shortbred/Temp/clust/fams/gb|AEZ36150.1|ARO:3000448|QepA1.faa', '-out', '/cluster/projects/nn8021k/Databases/CARD_327/markers_shortbred/Temp/clust/fams/gb|AEZ36150.1|ARO:3000448|QepA1.faa.aln']' returned non-zero exit status 1

Can you please help me with this?

[GenoMax]

ShortBREAD requires

BLASTP
USEARCH
MUSCLE
CD-HIT

Do you know if these are installed

[a.mostafa5050]

Thanks for the reply! Yes, all of them are installed

1. BLASTP version is blastp: 2.5.0+
2. USEARCH version is usearch v11.0.667_i86linux32
3. MUSCLE version is muscle 5.1.linux64
4. CD-HIT version is CD-HIT version 4.8.1 (built on Apr 7 2021)