alexamk / rrefinder Goto Github PK

Reading in file ../rodeo2/region007.gbk
Continuing with 42 queries
Rewriting fasta
hmmsearch --cpu 1 -o output/tes5/results/RREfinder_hmm_results.txt --domtblout output/tes5/results/RREfinder_hmm_results.tbl -T 25 data/hmm/RRE_v7_phmms_3_iter.hmm output/tes5/fastas/fasta_all.fasta
Resubmitting 1 found RREs
- 12:41:59.246 ERROR: Input file (output/tes5/fastas/Contig253_7120-7474_kmtR_S1361_07170_RRE_expalign_ss.a3m) could not be opened!

Traceback (most recent call last):
  File "./RRE.py", line 1371, in <module>
    res,parsed_data_dict = main(settings)
  File "./RRE.py", line 1190, in main
    all_groups = rrefinder_main(settings,RRE_targets,all_groups)
  File "./RRE.py", line 945, in rrefinder_main
    resubmit_all(all_groups,RRE_targets,settings)
  File "./RRE.py", line 567, in resubmit_all
    resubmit_group(group,RRE_targets,settings,settings.cores)
  File "./RRE.py", line 515, in resubmit_group
    parse_hhpred_res(group,RRE_targets,settings,resubmit=True)
  File "./RRE.py", line 519, in parse_hhpred_res
    results = read_hhr(group.RRE_results_file)
  File "./RRE.py", line 365, in read_hhr
    with open(f) as inf:
FileNotFoundError: [Errno 2] No such file or directory: 'output/tes5/results/Contig253_7120-7474_kmtR_S1361_07170_RRE.hhr'

 resubmit_database=path/to/uniclust30
 expand_database=path/to/uniclust30

Traceback (most recent call last):
  File "RRE.py", line 1400, in <module>
    check_databases(settings)
  File "RRE.py", line 1374, in check_databases
    raise ValueError(f'File {file} for category {category} not found. Please make sure all required databases are downloaded and their paths indicated in the config file.')
ValueError: File UniRef30_2021_03_fas.ffindex for category exploratory_hhpred_resubmit_database not found. Please make sure all required databases are downloaded and their paths indicated in the config file.

     protocluster    1..16387
                     /aStool="rule-based-clusters"
                     /contig_edge="True"
                     /core_location="[0:15047]"
                     /cutoff="20000"
                     /detection_rule="((YcaO or TIGR03882) and ((thio_amide and
                     (PF06968 or PF04055 or PF07366)) or Lant_dehydr_C or
                     Lant_dehydr_N or PF07366 or PF06968 or PF04055) or
                     thiostrepton)"
                     /neighbourhood="10000"
                     /product="thiopeptide"
                     /protocluster_number="2"
                     /tool="antismash"
     proto_core      1..15047
                     /aStool="rule-based-clusters"
                     /tool="antismash"
                     /cutoff="20000"
                     /detection_rule="((YcaO or TIGR03882) and ((thio_amide and
                     (PF06968 or PF04055 or PF07366)) or Lant_dehydr_C or
                     Lant_dehydr_N or PF07366 or PF06968 or PF04055) or
                     thiostrepton)"
                     /neighbourhood="10000"
                     /product="thiopeptide"
                     /protocluster_number="2"
     cand_cluster    1..16387
                     /candidate_cluster_number="1"
                     /contig_edge="True"
                     /detection_rules="((YcaO or TIGR03882) and ((thio_amide and
                     (PF06968 or PF04055 or PF07366)) or Lant_dehydr_C or
                     Lant_dehydr_N or PF07366 or PF06968 or PF04055) or
                     thiostrepton)"
                     /detection_rules="((goadsporin_like or PF00881 or
                     TIGR03605) and (YcaO or TIGR03882))"
                     /kind="chemical_hybrid"
                     /product="thiopeptide"
                     /product="LAP"
                     /protoclusters="2"
                     /protoclusters="1"
                     /tool="antismash"

Reading in file ../../04_bgc_annotation/gb6/data/gb1_bin.48.strict_filtered_kept_contigs.fasta
Continuing with 2227 queries
Rewriting fasta
Resubmitting 5 found RREs
Traceback (most recent call last):
  File "RRE.py", line 1403, in <module>
    res,parsed_data_dict = main(settings)
  File "RRE.py", line 1184, in main
    all_groups = rrefinder_main(settings,RRE_targets,all_groups)
  File "RRE.py", line 939, in rrefinder_main
    resubmit_all(all_groups,RRE_targets,settings)
  File "RRE.py", line 561, in resubmit_all
    resubmit_group(group,RRE_targets,settings,settings.cores)
  File "RRE.py", line 502, in resubmit_group
    add_ss(group,settings,resubmit=True)
  File "RRE.py", line 296, in add_ss
    with open(infile) as handle:
FileNotFoundError: [Errno 2] No such file or directory: 'output/gb1/fastas/NIMADCBA_00820_Ferric_uptake_regulation_protein_RRE_expalign.a3m'

$ addss.pl --help
<normal output>
.
.
. 
Filtering alignment to diversity 7 ...                                                                                                                                                                             
$ hhfilter -v 1 -neff 7 -i /tmp/FySoZdSt9c/9q7oqmXpnV.in.a3m -o /tmp/FySoZdSt9c/9q7oqmXpnV.in.a3m                                                                                                                  
                                                                                                                                                                                                                   
Error: command 'hhfilter -v 1 -neff 7 -i /tmp/FySoZdSt9c/9q7oqmXpnV.in.a3m -o /tmp/FySoZdSt9c/9q7oqmXpnV.in.a3m' returned error code 0     
.
.
.
<several more errors arise, but this is the first one>