MUSCLE in ShortBRED

ahmedbar · August 3, 2023, 4:48pm

Hi,
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

I got the following error

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

When I tried ShorBRED with my data I got a similar 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?

franzosa · August 30, 2023, 6:42pm

Sorry for missing this. In both cases it looks like it’s having trouble calling binaries needed for processing the data. Can you verify that you have BLAST and MUSCLE installed and their versions?

ahmedbar · August 30, 2023, 7:05pm

Hi,

Thanks for reaching out.

I managed to run ShortBRED, but I have another weird error. I would be grateful if you helped me out.

I created markers from CARD database and mobile OG database.

I have a dataset of 400 samples. 395 samples succeeded (got the output table) and 5 failed in both analyses (resistome and mobilome).

I figured it might be because of a problem with my samples.

I ran ShortBRED against another dataset of around 70 samples. All the samples for resistome succeeded but for mobiloem one sample failed.

It means nothing wrong with the samples.
I also ran ShortBRED against the failed sample to exclude the memory as a factor in killing the process, but I got the same error message.
Also, I used another version of uearch but got the same error message.

Attached is the log file that contains the error message.
I hope to help me out ASAP.

I really looking forward to hearing from you very soon.

Best regards,
Ahmed Bargheet

(Attachment slurm-9094360.base is missing)

ahmedbar · August 30, 2023, 7:08pm

Hi,