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gem-pasteur / Integron_Finder

Bioinformatics tool to find integrons in bacterial genomes
GNU General Public License v3.0
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Error related to prodigal: RuntimeError("{0} failed returncode = {1}".format(prodigal_cmd, returncode)) #79

Closed sasonbol closed 3 years ago

sasonbol commented 4 years ago

Hello, I used to work with intgeron finder version 2 on a virtual environment smoothly, but now I am always getting an error related to prodigal which I cannot resolve

Version of Integron_Finder:

integron_finder version 2-2020-10-04 Using:

OS

Expected behavior

integron_finder was expected to run normally as I used it before with similar sequences with no errors. Now it is always generating this error

Actual behavior

cannot process the replicon, getting an error: raise RuntimeError("{0} failed returncode = {1}".format(prodigal_cmd, returncode))

Relevant logs and/or screenshots

Here is what I get exactly:

          INFO     :  ############ Processing replicon NZ_CP050695.1 (1/1) ############

Unknown option.

Usage: prodigal [-a trans_file] [-c] [-d nuc_file] [-f output_type] [-g tr_table] [-h] [-i input_file] [-m] [-n] [-o output_file] [-p mode] [-q] [-s start_file] [-t training_file] [-v]

Do 'prodigal -h' for more information.

Traceback (most recent call last): File "/home/sarah/Integron_Finder/bin/integron_finder", line 11, in load_entry_point('integron-finder', 'console_scripts', 'integron_finder')()

File "/home/sarah/src/Integron_Finder/integron_finder/scripts/finder.py", line 601, in main integron_res, summary = find_integron_in_one_replicon(replicon, config)

File "/home/sarah/src/Integron_Finder/integron_finder/scripts/finder.py", line 303, in find_integron_in_one_replicon protein_db = ProdigalDB(replicon, config)

File "/home/sarah/src/Integron_Finder/integron_finder/prot_db.py", line 64, in init self._prot_file = self._make_protfile()

File "/home/sarah/src/Integron_Finder/integron_finder/prot_db.py", line 403, in _make_protfile

raise RuntimeError("{0} failed returncode = {1}".format(prodigal_cmd, returncode))

RuntimeError: /usr/bin/prodigal -i /media/sarah/06422813422809CF/Updated PhD_work/hypersaline_environments_assemblies/Halophiles/arch-complete/Natrialbaceae_archeaon/Results_Integron_Finder_Natrialbaceae/tmp_NZ_CP050695.1/NZ_CP050695.1.fst -a /media/sarah/06422813422809CF/Updated PhD_work/hypersaline_environments_assemblies/Halophiles/arch-complete/Natrialbaceae_archeaon/Results_Integron_Finder_Natrialbaceae/tmp_NZ_CP050695.1/NZ_CP050695.1.prt -o /dev/null -q failed returncode = 15

I would be grateful if you could help me out to solve this problem, Best, Sarah

bneron commented 3 years ago

can you tell me which version of prodigal you run?

nwalas commented 3 years ago

I am also receiving this error and I tried with both prodigal 2.6.3 and 2.6.2 (which I believe is the minimum for the program). I am operating in miniconda on mac ios catalaina.

Any help would be greatly appreciated thank you! Niko

bneron commented 3 years ago

can you run just prodigal on your data without the -o option ?

bneron commented 3 years ago

prodigal -i /media/sarah/06422813422809CF/Updated PhD_work/hypersaline_environments_assemblies/Halophiles/arch-complete/Natrialbaceae_archeaon/Results_Integron_Finder_Natrialbaceae/tmp_NZ_CP050695.1/NZ_CP050695.1.fst -a /media/sarah/06422813422809CF/Updated PhD_work/hypersaline_environments_assemblies/Halophiles/arch-complete/Natrialbaceae_archeaon/Results_Integron_Finder_Natrialbaceae/tmp_NZ_CP050695.1/NZ_CP050695.1.prt

nwalas commented 3 years ago

Hi, when I run with any commands for prodigal like:

integron_finder test_assembled.fasta --local-max prodigal -i users/nikolinawalas/miniconda3/envs/integron_finder/bin/prodigal

I am returned the error: unrecognized arguments: prodigal -i

Isn't integron_finder meant to manually command the attached databases?

Thanks!

nwalas commented 3 years ago

I also tried just running: % prodigal -i mygenes.fasta -o mygenesoutput.tsv

it does in fact find the genes and produce an output file; it also runs it fine if I do not specify an output file

nwalas commented 3 years ago

Hi all; I have resolved this issue. For me, it seemed to be an issue with my fasta file. It included short read sequences, I needed to remove all ">seq" line breaks in my fasta file for integron finder to recognize it as one sequence. Hope this helps!

sasonbol commented 3 years ago

I am using Prodigal V2.6.3 I am also using a complete circular genome so I don't really have short reads. I am also having the same error with sequences that I have used before butt it is giving me the same error although it worked before with those sequences

sasonbol commented 3 years ago

I am not using --prodigal command in my command line and I have never used it before but I understand that it works by default.

sasonbol commented 3 years ago

The following command is not working as there is no prt file created. The tmp folder only has a fasta file (.fst) at wihich this command can work on: prodigal -i /media/sarah/06422813422809CF/Updated PhD_work/hypersaline_environments_assemblies/Halophiles/arch-complete/Natrialbaceae_archeaon/Results_Integron_Finder_Natrialbaceae/tmp_NZ_CP050695.1/NZ_CP050695.1.fst -a /media/sarah/06422813422809CF/Updated PhD_work/hypersaline_environments_assemblies/Halophiles/arch-complete/Natrialbaceae_archeaon/Results_Integron_Finder_Natrialbaceae/tmp_NZ_CP050695.1/NZ_CP050695.1.prt

jeanrjc commented 3 years ago

Hello @sasonbol,

What is the output of the command you just showed ?

sasonbol commented 3 years ago

PRODIGAL v2.6.3 [February, 2016]
Univ of Tenn / Oak Ridge National Lab Doug Hyatt, Loren Hauser, et al.

Error: can't open input file NZ_CP050695.1.prt.

(This is the output that I got)

jeanrjc commented 3 years ago

The .prt should be the output file, not the input one. Can you make sure that the .fst is the input (-i) and the .prt the output (-a). Can you show also all your terminal session when doing the following : 

cd "/media/sarah/06422813422809CF/Updated PhD_work/hypersaline_environments_assemblies/Halophiles/arch-complete/Natrialbaceae_archeaon/Results_Integron_Finder_Natrialbaceae/tmp_NZ_CP050695.1/"
ls -lh
prodigal -i NZ_CP050695.1.fst -a NZ_CP050695.1.prt

(make sure the path for changing directory with cd is correct)

sasonbol commented 3 years ago

OK. I tried on another sequence which showed the same problem, and a prt file was created when I used the prodigal command, but it is still not working when I use the integron_finder command. I tried to run integron finder on the same sequence, but I got this error now: command used: integron_finder celeribacter-chromosome.fasta --circ --local-max -dt 8000 --promoter-attI --pdf --gbk

                 =======================

INFO : ############ Processing replicon NZ_CP004393.1 (1/1) ############

INFO : Starting Default search ... : Traceback (most recent call last): File "/home/sarah/Integron_Finder/bin/integron_finder", line 11, in load_entry_point('integron-finder', 'console_scripts', 'integron_finder')() File "/home/sarah/src/Integron_Finder/integron_finder/scripts/finder.py", line 601, in main integron_res, summary = find_integron_in_one_replicon(replicon, config) File "/home/sarah/src/Integron_Finder/integron_finder/scripts/finder.py", line 321, in find_integron_in_one_replicon cpu=config.cpu) File "/home/sarah/src/Integron_Finder/integron_finder/infernal.py", line 129, in find_attc raise RuntimeError("{0} failed returncode = {1}".format(cmsearch_cmd, returncode)) RuntimeError: /home/sarah/miniconda3/bin/cmsearch --cpu 1 -A /media/sarah/06422813422809CF/Updated PhD_work/hypersaline_environments_assemblies/Halophiles/bacteria-complete/new-complete/Celeribacter-indicus/Results_Integron_Finder_celeribacter-chromosome/tmp_NZ_CP004393.1/NZ_CP004393.1_attc.res --tblout /media/sarah/06422813422809CF/Updated PhD_work/hypersaline_environments_assemblies/Halophiles/bacteria-complete/new-complete/Celeribacter-indicus/Results_Integron_Finder_celeribacter-chromosome/tmp_NZ_CP004393.1/NZ_CP004393.1_attc_table.res -E 10 --incE 1.0 /home/sarah/src/Integron_Finder/data/Models/attc_4.cm /media/sarah/06422813422809CF/Updated PhD_work/hypersaline_environments_assemblies/Halophiles/bacteria-complete/new-complete/Celeribacter-indicus/Results_Integron_Finder_celeribacter-chromosome/tmp_NZ_CP004393.1/NZ_CP004393.1.fst failed returncode = 1

sasonbol commented 3 years ago

I uninstalled and reinstalled prodigal2.6.3, but the same problem still exists

jeanrjc commented 3 years ago

Closing because not able to reproduce the problem. I'll reopen if more details are brought showing that there might be a bug in IntegronFinder.