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License: GNU Affero General Public License v3.0
Bioinfromatic application for the detection of RREs in protein sequences of interest
License: GNU Affero General Public License v3.0
The following error shows when running program in exploratory mode:
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'
Can you help to solve it?
Hi guys, giving your tool a shot, looks pretty exciting!
Just a heads-up: the environment YAML file is missing the biopython
package, I needed to install it manually.
Cheers,
David
I just installed RREFinder for a quick testrun and was successful with fasta files, but not with genbank files. It looks to me like something about how biopython parses seq records from gbk files has changed? I only installed up to the point where I can run the precision mode. Full disclosure - I also commented out the line '- ld_impl_linux-64=2.34=h53a641e_0' in the RREfinder.yml file as it caused issues when installing, so there is the obvious chance that I'm causing problems...
Files used:
protein fasta:
https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/017/068/035/GCF_017068035.1_ASM1706803v1/GCF_017068035.1_ASM1706803v1_protein.faa.gz
gbk:
https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/017/068/035/GCF_017068035.1_ASM1706803v1/GCF_017068035.1_ASM1706803v1_genomic.gbff.gz
Commands used:
protein fasta:
python RRE.py --infile path/to/GCF_017068035.1_ASM1706803v1_protein.faa --intype fasta --outputfolder path/to/outfiles/ --cores 4 --mode --verbosity 2 precision RRE_test_faa
genbank:
python RRE.py --infile path/to/GCF_017068035.1_ASM1706803v1_genomic.gbff --intype genbank --outputfolder path/to/outfiles/ --cores 4 --mode precision --verbosity 2 RRE_test_gbk
Output for genbank:
Parse failed (sequence file ../outfiles/RRE_test_gbk/fastas/fasta_all.fasta):
Line 72: illegal character :
Looking at the vicinity of line 72 of the fasta_all.fasta file showed the following:
I tried it with a few different genbank files and end up running into the same problem sooner or later.
Hi,
It seems that we have a directory issue, supposedly due to a missing file in exploratory mode. This problem might have shown up before in previous issue, but applying the suggested solution (which is installing HHsuite in the same conda environment) did not solve the problem.
Any suggestion is appreciated. Thank you very much. Here is the log.
(RREfinder) ~/RREFinder$ python2 RRE.py -v2 -t fasta -c 10 -i test.fasta -m exploratory abcxyz
Warning! Output folder with name abcxyz already found - results may be overwritten
Reading in file test.fasta
Continuing with 6 queries
Skipped 0 genes
Rewriting fasta
Resubmitting 3 found RREs
hhblits -cpu 10 -d data/database/RRE_v5_iter_3 -i output/abcxyz/fastas/NonB_RRE.fasta -oa3m output/abcxyz/fastas/NonB_RRE_expalign.a3m -o output/abcxyz/fastas/NonB_RRE_expalign.hhr -v 0 -n 3
addss.pl output/abcxyz/fastas/NonB_RRE_expalign.a3m output/abcxyz/fastas/NonB_RRE_expalign_ss.a3m -a3m
Traceback (most recent call last):
File "RRE.py", line 1298, in
res,parsed_data_dict = main(settings)
File "RRE.py", line 1129, in main
all_groups = rrefinder_main(settings,RRE_targets,all_groups)
File "RRE.py", line 896, in rrefinder_main
resubmit_all(all_groups,RRE_targets,settings)
File "RRE.py", line 520, in resubmit_all
resubmit_group(group,RRE_targets,settings,settings.cores)
File "RRE.py", line 461, in resubmit_group
add_ss(group,settings,resubmit=True)
File "RRE.py", line 258, in add_ss
p = Popen(cmds,stdout=PIPE,stderr=PIPE)
File "/usr/lib/python2.7/subprocess.py", line 394, in init
errread, errwrite)
File "/usr/lib/python2.7/subprocess.py", line 1047, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
Hi,
I work on the bioinformatics platform ABiMS in Roscoff, France.
We are interested in your tool RREFinder. To follow our installation policies (we use Conda env), I would like to add your tool as a package on the bioconda channel. I started a PR here: bioconda/bioconda-recipes#33650
But for that, I miss a release of the tool with a version number and a tar.gz archive. Would it be possible to tag a release in your Github repo ?
Also feel free to push commits or comment in the PR !
Regards,
Loraine Guéguen
Hi,
I was trying to run the the exploratory mode with Uniclust database, as described in 3rd step of "Use RREFinder to detect RREs with the uniclust30 database (Advanced)" section:
resubmit_database=path/to/uniclust30
expand_database=path/to/uniclust30
But eventually the following error arises:
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.
And there are no _fas.ffindex in Uniclust30 database.
Best,
Pavlo
Hi, I noticed you are using the old antiSMASH output format, where the final file ends with .final.gbk
. Are you planning to support the new version as well?
In version 5.0, the output of antiSMASH has changed: https://github.com/antismash/antismash
Here is an example antiSMASH output file:
mibig_example_antismash_5.1.0.gbk.gz
The clusters are now provided in a more detailed form:
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"
You can contact the authors for more info.
Hi,
I tried the both installation methods - automatic and manual, but the following error arise:
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'
The problem could be connected to the addss.pl
script error:
$ 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>
Best,
Pavlo
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