Closed sasonbol closed 3 years ago
can you tell me which version of prodigal you run?
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
can you run just prodigal on your data without the -o option ?
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
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!
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
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!
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
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.
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
Hello @sasonbol,
What is the output of the command you just showed ?
Error: can't open input file NZ_CP050695.1.prt.
(This is the output that I got)
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)
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
I uninstalled and reinstalled prodigal2.6.3, but the same problem still exists
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.
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:
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
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