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Gaius-Augustus / BRAKER

BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes
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ERROR in file .conda/envs/braker3/bin/braker.pl at line 5333 #838

Open kinoppyi opened 2 weeks ago

kinoppyi commented 2 weeks ago

Hello, I am encountering several issues trying to launch braker3 on my server. I have installed BRAKER3 using conda.

I have followed the instructions and I am trying to run the command on the test files located in the test folder.

This is the error I am receiving: Thu Jun 13 14:16:25 2024: Log information is stored in file /global/scratch/users/edoardoscali/Software/BRAKER/example/tests/test1/braker.log ERROR in file /global/home/users/edoardoscali/.conda/envs/braker3/bin/braker.pl at line 5333 Failed to execute: /global/home/users/edoardoscali/.conda/envs/braker3/bin/perl /global/home/groups/consultsw/sl-7.x86_64/modules/genemark-es-et/4.33/gmes_petap.pl --verbose --sequence=/global/scratch/users/edoardoscali/Software/BRAKER/example/tests/test1/genome.fa --ET=/global/scratch/users/edoardoscali/Software/BRAKER/example/tests/test1/genemark_hintsfile.gff --cores=8 --gc_donor 0.001 --soft_mask auto --max_intergenic=10000 1>/global/scratch/users/edoardoscali/Software/BRAKER/example/tests/test1/GeneMark-ET.stdout 2>/global/scratch/users/edoardoscali/Software/BRAKER/example/tests/test1/errors/GeneMark-ET.stderr Failed to execute: /global/home/users/edoardoscali/.conda/envs/braker3/bin/perl /global/home/groups/consultsw/sl-7.x86_64/modules/genemark-es-et/4.33/gmes_petap.pl --verbose --sequence=/global/scratch/users/edoardoscali/Software/BRAKER/example/tests/test1/genome.fa --ET=/global/scratch/users/edoardoscali/Software/BRAKER/example/tests/test1/genemark_hintsfile.gff --cores=8 --gc_donor 0.001 --soft_mask auto --max_intergenic=10000 1>/global/scratch/users/edoardoscali/Software/BRAKER/example/tests/test1/GeneMark-ET.stdout 2>/global/scratch/users/edoardoscali/Software/BRAKER/example/tests/test1/errors/GeneMark-ET.stderr !

If I open the braker.log file I can see: 

                          RUNNING GENEMARK-EX

Thu Jun 13 14:16:45 2024: Checking whether file /global/scratch/users/edoardoscali/Software/BRAKER/example/tests/test1/genemark_hintsfile.gff contains enough hints and sufficient multiplicity information... Thu Jun 13 14:16:45 2024: Executing GeneMark-ET Thu Jun 13 14:16:45 2024: changing into GeneMark-ET directory /global/scratch/users/edoardoscali/Software/BRAKER/example/tests/test1/GeneMark-ET cd /global/scratch/users/edoardoscali/Software/BRAKER/example/tests/test1/GeneMark-ET Thu Jun 13 14:16:45 2024: Executing gmes_petap.pl /global/home/users/edoardoscali/.conda/envs/braker3/bin/perl /global/home/groups/consultsw/sl-7.x86_64/modules/genemark-es-et/4.33/gmes_petap.pl --verbose --sequence=/global/scratch/users/edoardoscali/Software/BRAKER/example/tests/test1/genome.fa --ET=/global/scratch/users/edoardoscali/Software/BRAKER/example/tests/test1/genemark_hintsfile.gff --cores=8 --gc_donor 0.001 --soft_mask auto --max_intergenic=10000 1>/global/scratch/users/edoardoscali/Software/BRAKER/example/tests/test1/GeneMark-ET.stdout 2>/global/scratch/users/edoardoscali/Software/BRAKER/example/tests/test1/errors/GeneMark-ET.stderr

I followed the instruction in the section "GeneMark-ETP" 1) My server has genemark already installed in this path: /global/home/users/edoardoscali/.conda/envs/braker3/bin/perl /global/home/groups/consultsw/sl-7.x86_64/modules/genemark-es-et/4.33/gmes_petap.pl 2) I have installed Genemark-ETP 3) when I run braker I am using this comand: braker.pl --genome=../genome.fa --bam=../RNAseq.bam --workingdir=$wd --threads 8 --gm_max_intergenic 10000 --skipOptimize --GENEMARK_PATH=/global/scratch/users/edoardoscali/Software/GeneMark-ETP/bin/

From the error I can see that even if I am specifying the --GENEMARK_PATH with the version that I have installed, braker tryes to run the genemark installed on my server.

4) I also tryed perl change_path_in_perl_scripts.pl "/usr/bin/env perl"

5) "you can check whether GeneMark-ES/ET/EP is installed properly by running the check_install.bash and/or executing examples in GeneMark-E-tests directory." I did, and worked correctly.

Can someone help me solving this problem?? Thank you so much!

Can someone help me fixing this issue?

kinoppyi commented 2 weeks ago

Ok, I found the solution.

I added this: --GENEMARK_PATH=/global/scratch/users/edoardoscali/Software/GeneMark-ETP/bin/gmes to braker.pl comand, and now is running fine!

Thanks