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gatech-genemark / ProtHint

Protein hint generation pipeline for gene finding in eukaryotic genomes
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error, file not found parse_set.pl: set.out #35

Open mictadlo opened 2 years ago

mictadlo commented 2 years ago

Hello,

$ python prothint.py ../../NbLab330.genome.softmasked.fasta ../../NbenthamianaGenbankAA.fasta 

warning on: /mnt/OneTB/annotation/NlabProt/ProtHint/dependencies/GeneMarkES/gmhmme3  -m /mnt/OneTB/annotation/NlabProt/ProtHint/bin/GeneMark_ES/run/ES_ini/es_ini.mod   -f tr  -d /mnt/OneTB/annotation/NlabProt/ProtHint/bin/GeneMark_ES/run/ES_A_1/plus_hmm.gff  -k -0.03  -o /mnt/OneTB/annotation/NlabProt/ProtHint/bin/GeneMark_ES/run/ES_A_1/hmmout/dna.fa_7283.out  /mnt/OneTB/annotation/NlabProt/ProtHint/bin/GeneMark_ES/data/training/dna.fa_7283
concatenate predictions: /mnt/OneTB/annotation/NlabProt/ProtHint/bin/GeneMark_ES/run/ES_A_1
training level ES_A: /mnt/OneTB/annotation/NlabProt/ProtHint/bin/GeneMark_ES/run/ES_A_1
error, file not found /mnt/OneTB/annotation/NlabProt/ProtHint/dependencies/GeneMarkES/parse_set.pl: set.out
error on call: /mnt/OneTB/annotation/NlabProt/ProtHint/dependencies/GeneMarkES/parse_set.pl --section ES_A --cfg  /mnt/OneTB/annotation/NlabProt/ProtHint/bin/GeneMark_ES/run.cfg  --v 
[Tue Oct 19 01:35:46 2021] error: ProtHint exited due to an error in command: /mnt/OneTB/annotation/NlabProt/ProtHint/bin/../dependencies/GeneMarkES/gmes_petap.pl --verbose --cores 32 --ES --seq /mnt/OneTB/annotation/NlabProt/NbLab330.genome.softmasked.fasta --soft auto

What did I miss?

Thank you in advance,

Michal

tomasbruna commented 2 years ago

Hi Michal,

does the problem persist? I see you opened a BRAKER2 issue 2 days ago so I wonder whether you were able to resolve it. If so, can you please share what the issue was?

If not, I will look into this.

Tomas

mictadlo commented 2 years ago

Hi, Yes, the error still persists. By any chance, do you know why I got the above error?

Because of the error, I was not able to use your tool yet to train Augustus, GlimmerHMM and SNAP. After all annotation tools are finished then I would like to merge them with EvidenceModeller. I found here how to train SNAP. They provide a script to convert GFF3 to SNAP's ZFF format (gff3_to_zff.pl). By any chance, do you know how to train GlimmerHMM?

Thank you in advance, Michal

tomasbruna commented 2 years ago

Hi Michal,

sorry, I do not have any experience with training GlimmerHMM.

About the GeneMark error, did you try to run the check_install.bash in GeneMark's directory? Does that work without errors? One common issue with GeneMark is a segmentation fault on new Linux systems. GeneMark now has a version (LINUX 64 kernel 4) that solves this problem.

Best, Tomas

mictadlo commented 2 years ago

Hi, Thank you for your message. I got the following message:

$ uname -a
Linux appdev 5.10.0-9-amd64 #1 SMP Debian 5.10.70-1 (2021-09-30) x86_64 GNU/Linux

ProtHint-2.6.0/dependencies/GeneMarkES$ ./check_install.bash
Checking GeneMark-ES installation
Checking Perl setup
All required Perl modules were found
Checking GeneMark.hmm setup
GeneMark.hmm was found
GeneMark.hmm is set
Error, unexpected condition was detected

What did I miss?

Thank you in advance,

Michal

tomasbruna commented 2 years ago

Hi, this could be the error I mentioned (One common issue with GeneMark is a segmentation fault on new Linux systems).

Did you try downloading the LINUX 64 kernel 4 version from http://exon.gatech.edu/GeneMark/license_download.cgi?

Tomas