KatharinaHoff
commented
12 months ago There were several changes between different GeneMark versions. I recommend that you use the exact version that is distributed with the BRAKER3 container (Docker/Singularity) to run BRAKER3. You don't have to install a separate key file if you use this version.
On Sat, Sep 9, 2023 at 1:49 AM ytter96 @.***> wrote:
Hi! I'm new to this and I have no idea what is wrong. GeneMarkES/ST is an application in my university's HPC system, so I did not download the GeneMarkES program on my own computer (my genome files are also in the HPC system, not local). That may be why many solutions found here can't be applied to me (or I've no idea how to get to that path).
My GeneMark-ES.stderr file says error, file not found: data/training.fna
My job's output slurm file says this: ERROR in file /opt/BRAKER/scripts/braker.pl at line 5147 Failed to execute: /usr/bin/perl /opt/ETP/bin/gmes//gmes_petap.pl --verbose --cores=1 --ES --gc_donor 0.001 --sequence=/home/ytter/junonia/jun_coe_output/genome.fa --soft_mask auto 1>/home/ytter/junonia/jun_coe_output/GeneMark-ES.stdout 2>/home/ytter/junonia/jun_coe_output/errors/GeneMark-ES.stderr The most common problem is an expired or not present file ~/.gm_key!
*** I have a .gm_key, and it has not expired since I got it a few days ago.
And the gmes.log says this: /opt/ETP/bin/gmes/gmes_petap.pl : [Thu Sep 7 22:56:26 2023] /opt/ETP/bin/gmes/probuild --reformat_fasta --uppercase --allow_x --letters_per_line 60 --out data/dna.fna --label _dna --trace info/dna.trace --in /home/ytter/junonia/jun_coe_output/genome.fa --mask_soft 100 --mask_margin 0 --low2gff data/in_mask.gff /opt/ETP/bin/gmes/gmes_petap.pl : [Thu Sep 7 22:56:26 2023] cat in_mask.gff >> plus.gff /opt/ETP/bin/gmes/gmes_petap.pl : [Thu Sep 7 22:56:49 2023] /opt/ETP/bin/gmes/probuild --seq data/dna.fna --allow_x --stat info/dna.general --details /opt/ETP/bin/gmes/gmes_petap.pl : [Thu Sep 7 22:57:19 2023] /opt/ETP/bin/gmes/probuild --seq data/dna.fna --allow_x --stat_fasta info/dna.multi_fasta /opt/ETP/bin/gmes/ gmes_petap.pl : [Thu Sep 7 22:57:32 2023] /opt/ETP/bin/gmes/probuild --seq data/dna.fna --allow_x --substring_n_distr info/dna.gap_distr /opt/ETP/bin/gmes/gmes_petap.pl : [Thu Sep 7 22:57:55 2023] /opt/ETP/bin/gmes/gc_distr.pl --in data/dna.fna --out info/dna.gc.csv --w 1000,8000 /opt/ETP/bin/gmes/gmes_petap.pl : [Thu Sep 7 22:58:18 2023] /opt/ETP/bin/gmes/probuild --seq /home/ytter/junonia/jun_coe_output/GeneMark-ES/data/dna.fna --split dna.fa --max_contig 5000000 --min_contig 50000 --letters_per_line 100 --split_at_n 5000 --split_at_x 5000 --allow_x --x_to_n --trace ../../info/training.trace
From the output slurm file, it seems like they cant execute my gmes_petap.pl file? I can't find that file since GeneMarkES/4 is not on my local computer, but the school's HPC/ remote system. Is there a way I can access the application and see whether ETP/bin/gmes//gmes_petap.pl exists? Is the double // in the path the problem?
Thank you! This is my first time posting an issue on github, so if I'm missing any important information, please let me know!
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Hi! I'm new to this and I have no idea what is wrong. GeneMarkES/ST is an application in my university's HPC system, so I did not download the GeneMarkES program on my own computer (my genome files are also in the HPC system, not local). That may be why many solutions found here can't be applied to me (or I've no idea how to get to that path).
My GeneMark-ES.stderr file says
error, file not found: data/training.fnaMy job's output slurm file says this:
ERROR in file /opt/BRAKER/scripts/braker.pl at line 5147 Failed to execute: /usr/bin/perl /opt/ETP/bin/gmes//gmes_petap.pl --verbose --cores=1 --ES --gc_donor 0.001 --sequence=/home/ytter/junonia/jun_coe_output/genome.fa --soft_mask auto 1>/home/ytter/junonia/jun_coe_output/GeneMark-ES.stdout 2>/home/ytter/junonia/jun_coe_output/errors/GeneMark-ES.stderr The most common problem is an expired or not present file ~/.gm_key!*** I have a .gm_key, and it has not expired since I got it a few days ago.
And the gmes.log says this:
/opt/ETP/bin/gmes/gmes_petap.pl : [Thu Sep 7 22:56:26 2023] /opt/ETP/bin/gmes/probuild --reformat_fasta --uppercase --allow_x --letters_per_line 60 --out data/dna.fna --label _dna --trace info/dna.trace --in /home/ytter/junonia/jun_coe_output/genome.fa --mask_soft 100 --mask_margin 0 --low2gff data/in_mask.gff /opt/ETP/bin/gmes/gmes_petap.pl : [Thu Sep 7 22:56:26 2023] cat in_mask.gff >> plus.gff /opt/ETP/bin/gmes/gmes_petap.pl : [Thu Sep 7 22:56:49 2023] /opt/ETP/bin/gmes/probuild --seq data/dna.fna --allow_x --stat info/dna.general --details /opt/ETP/bin/gmes/gmes_petap.pl : [Thu Sep 7 22:57:19 2023] /opt/ETP/bin/gmes/probuild --seq data/dna.fna --allow_x --stat_fasta info/dna.multi_fasta /opt/ETP/bin/gmes/gmes_petap.pl : [Thu Sep 7 22:57:32 2023] /opt/ETP/bin/gmes/probuild --seq data/dna.fna --allow_x --substring_n_distr info/dna.gap_distr /opt/ETP/bin/gmes/gmes_petap.pl : [Thu Sep 7 22:57:55 2023] /opt/ETP/bin/gmes/gc_distr.pl --in data/dna.fna --out info/dna.gc.csv --w 1000,8000 /opt/ETP/bin/gmes/gmes_petap.pl : [Thu Sep 7 22:58:18 2023] /opt/ETP/bin/gmes/probuild --seq /home/ytter/junonia/jun_coe_output/GeneMark-ES/data/dna.fna --split dna.fa --max_contig 5000000 --min_contig 50000 --letters_per_line 100 --split_at_n 5000 --split_at_x 5000 --allow_x --x_to_n --trace ../../info/training.traceFrom the output slurm file, it seems like they cant execute my gmes_petap.pl file? I can't find that file since GeneMarkES/4 is not on my local computer, but the school's HPC/ remote system. Is there a way I can access the application and see whether ETP/bin/gmes//gmes_petap.pl exists? Is the double // in the path the problem?
Thank you! This is my first time posting an issue on github, so if I'm missing any important information, please let me know!