I installed ShortBRED yesterday by Conda.
When I download the example files and tried it using the following command
shortbred_identify.py --goi input_prots.faa --ref ref_prots.faa --markers mytestmarkers.faa --tmp example_identify
Traceback (most recent call last):
File "/cluster/projects/nn8021k/Conda-env/my_shortbred/bin/shortbred_identify.py", line 281, in <module>
"-dbtype", "prot", "-logfile", dirTmp + os.sep + "goidb.log"])
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 '['makeblastdb', '-in', 'example_identify/clust/clust.faa', '-out', 'example_identify/clustdb/goidb', '-dbtype', 'prot', '-logfile', 'example_identify/goidb.log']' returned non-zero exit status 1
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