HMM search failed error

[GeoMicroSoares]

Dear @EllaRan - thanks for creating this tool! We're really excited to use it but have come across an error that we can't figure out how to get past, would you mind helping out?

Using the following command:

$ python /mnt/cephfs1/projects/Linda_test/Dramma_Out/DRAMMA/run_DRAMMA_pipeline.py --dif_format_paths /mnt/cephfs1/projects/Linda_test/Dramma_Out/dramma_input/P_2-5_SV21-Z1-C10_MG_P_2-5_SE_S26_min1000.genes.faa /mnt/cephfs1/projects/Linda_test/Dramma_Out/dramma_input/P_2-5_SV21-Z1-C10_MG_P_2-5_SE_S26_min1000.genes.gff /mnt/cephfs1/projects/Linda_test/Dramma_Out/dramma_input/P_2-5_SV21-Z1-C10_MG_P_2-5_SE_S26_min1000.genes /mnt/cephfs1/projects/Linda_test/Dramma_Out/dramma_input/P_2-5_SV21-Z1-C10_MG_P_2-5_SE_S26_min1000.fasta -out /mnt/cephfs1/projects/Linda_test/Dramma_output --tmhmm /home/llabecka/software/tmhmm-2.0c/bin/tmhmm --model /mnt/cephfs1/projects/Linda_test/models/DRAMMA_AMR_model.pkl --feature_dir /mnt/cephfs1/projects/Linda_test/Dramma_output/features --ncpus 10

we get the error below, and I can't figure out what might be going wrong.

fasta file is: /mnt/cephfs1/projects/Linda_test/Dramma_Out/dramma_input/P_2-5_SV21-Z1-C10_MG_P_2-5_SE_S26_min1000.genes.faa
hmmsearch --cpu 9 --tblout /mnt/cephfs1/projects/Linda_test/Dramma_Out/DRAMMA/P_2-5_SV21-Z1-C10_MG_P_2-5_SE_S26_min1000.genes.faa.VS.DRAMMA_ARG_DB.tblout /mnt/cephfs1/projects/Linda_test/Dramma_Out/DRAMMA/data/feature_extraction/hmms_for_proximity_features/DRAMMA_ARG_DB.hmm /mnt/cephfs1/projects/Linda_test/Dramma_Out/dramma_input/P_2-5_SV21-Z1-C10_MG_P_2-5_SE_S26_min1000.genes.faa
/bin/sh: 1: None: not found
Failed running hmmsearch of /mnt/cephfs1/projects/Linda_test/Dramma_Out/dramma_input/P_2-5_SV21-Z1-C10_MG_P_2-5_SE_S26_min1000.genes.faa on /mnt/cephfs1/projects/Linda_test/Dramma_Out/DRAMMA/data/feature_extraction/hmms_for_proximity_features/DRAMMA_ARG_DB.hmm.
Traceback (most recent call last):
  File "/mnt/cephfs1/projects/Linda_test/Dramma_Out/DRAMMA/run_DRAMMA_pipeline.py", line 116, in <module>
    main(args)
  File "/mnt/cephfs1/projects/Linda_test/Dramma_Out/DRAMMA/run_DRAMMA_pipeline.py", line 71, in main
    res = single_sample_pipeline(args, feature_lst)
  File "/mnt/cephfs1/projects/Linda_test/Dramma_Out/DRAMMA/run_DRAMMA_pipeline.py", line 28, in single_sample_pipeline
    feature_lst.run_features(*args.dif_format_paths, out_dir=args.feature_dir)
  File "/mnt/cephfs1/projects/Linda_test/Dramma_Out/DRAMMA/feature_extraction/feature_list.py", line 44, in run_features
    feature.run_feature_to_file(protein_fasta, gff, fa, ids, data, out_dir)
  File "/mnt/cephfs1/projects/Linda_test/Dramma_Out/DRAMMA/feature_extraction/labeling.py", line 36, in run_feature_to_file
    feature_to_file(self.res_name, dir_path=out_dir)(self.get_features)(protein_fasta, ids)
  File "/mnt/cephfs1/projects/Linda_test/Dramma_Out/DRAMMA/utilities.py", line 271, in wrapper
    df = func(*args, **kwargs)
  File "/mnt/cephfs1/projects/Linda_test/Dramma_Out/DRAMMA/feature_extraction/labeling.py", line 17, in get_features
    hmm_tblout = get_tblout_file(self.hmmer_path, self.hmm_db, fasta_file, cpu=self.n_cpus)  # returns HMM search results
  File "/mnt/cephfs1/projects/Linda_test/Dramma_Out/DRAMMA/feature_extraction/create_tblout_file.py", line 33, in get_tblout_file
    raise Exception(f"HMM search failed for {fasta_file} with errorcode: {sp.returncode}")
Exception: HMM search failed for /mnt/cephfs1/projects/Linda_test/Dramma_Out/dramma_input/P_2-5_SV21-Z1-C10_MG_P_2-5_SE_S26_min1000.genes.faa with errorcode: 127

Please let me know what other information you might need to help us figure this out. Keep up the good work!

[EllaRan]

Dear GeoMicroSoares,

It seems like you didn't include the --hmmer_path argument in your command, therefore the hmm search fails and raises that exception.

Let me know if it works for you.