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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 /opt/BRAKER/scripts/braker.pl at line 4490 #798

Closed Wangray123 closed 2 months ago

Wangray123 commented 2 months ago

Hello! I am running Braker v2.1.5 in singularity to annotate the genomic data of fungi with RNA data, then, I get this error message: ERROR: in file /opt/BRAKER/scripts/braker.pl at line 4490 Genome file /home/data/t150418/workspace/1511Genome/07Braker/1511.genome.fa.masked --softmasking does not exist.

I'm sure the file name and path correctly. And I keep getting this error that i dont really know how to troubleshoot. So hope someone can help.

Details are as follows：

BRAKER CALL: /opt/BRAKER/scripts/braker.pl --cores 12 --species=Myspecies --genome=/home/data/t150418/workspace/1511Genome/07Braker/1511.genome.fa.masked --softmasking --fungus --bam=/home/data/t150418/workspace/1511Genome/06hisat2/WTrnaseq.bam --gff3

Mon Apr 8 21:32:13 2024: braker.pl version 2.1.5

Mon Apr 8 21:32:13 2024: Configuring of BRAKER for using external tools...

Mon Apr 8 21:32:13 2024: Found environment variable $AUGUSTUS_CONFIG_PATH. Setting $AUGUSTUS_CONFIG_PATH to /home/data/t150418/augustus_config

Mon Apr 8 21:32:13 2024: Found environment variable $AUGUSTUS_BIN_PATH. Setting $AUGUSTUS_BIN_PATH to /opt/augustus/bin

Mon Apr 8 21:32:13 2024: Found environment variable $AUGUSTUS_SCRIPTS_PATH. Setting $AUGUSTUS_SCRIPTS_PATH to /opt/augustus/scripts

Mon Apr 8 21:32:13 2024: Found environment variable $GENEMARK_PATH. Setting $GENEMARK_PATH to /opt/GeneMark-ET/gmes_linux_64

Mon Apr 8 21:32:13 2024: Found environment variable $BAMTOOLS_PATH. Setting $BAMTOOLS_PATH to /opt/bamtools/bin**

Mon Apr 8 21:32:13 2024: Found environment variable $SAMTOOLS_PATH. Setting $SAMTOOLS_PATH to /opt/samtools

Mon Apr 8 21:32:13 2024: Found environment variable $DIAMOND_PATH. Setting $DIAMOND_PATH to /opt/Diamond

Mon Apr 8 21:32:13 2024: Did not find environment variable $PYTHON3_PATH

Mon Apr 8 21:32:13 2024: Trying to guess $PYTHON3_PATH from location of python3 executable that is available in your $PATH

Mon Apr 8 21:32:13 2024: Setting $PYTHON3_PATH to /usr/bin

Mon Apr 8 21:32:13 2024: Did not find environment variable $CDBTOOLS_PATH

Mon Apr 8 21:32:13 2024: Trying to guess $CDBTOOLS_PATH from location of cdbfasta executable that is available in your $PATH

Mon Apr 8 21:32:13 2024: Setting $CDBTOOLS_PATH to /usr/bin

Mon Apr 8 21:32:13 2024: ERROR: in file /opt/BRAKER/scripts/braker.pl at line 4490

Genome file /home/data/t150418/workspace/1511Genome/07Braker/1511.genome.fa.masked --softmasking does not exist.

KatharinaHoff commented 2 months ago

softmasking is default, now. Just delete the option --softmasking.

On Mon, Apr 8, 2024 at 5:02 PM Wangray123 @.***> wrote:

Hello! I am running Braker v2.1.5 in singularity to annotate the genomic data of fungi with RNA data, then, I get this error message: ERROR: in file /opt/BRAKER/scripts/braker.pl at line 4490 Genome file /home/data/t150418/workspace/1511Genome/07Braker/1511.genome.fa.masked --softmasking does not exist.

I'm sure the file name and path correctly. And I keep getting this error that i dont really know how to troubleshoot. So hope someone can help.

Details are as follows： BRAKER CALL: /opt/BRAKER/scripts/braker.pl --cores 12 --species=Myspecies --genome=/home/data/t150418/workspace/1511Genome/07Braker/1511.genome.fa.masked --softmasking --fungus --bam=/home/data/t150418/workspace/1511Genome/06hisat2/WTrnaseq.bam --gff3 Mon Apr 8 21:32:13 2024: braker.pl version 2.1.5 Mon Apr 8 21:32:13 2024: Configuring of BRAKER for using external tools... Mon Apr 8 21:32:13 2024: Found environment variable $AUGUSTUS_CONFIG_PATH. Setting $AUGUSTUS_CONFIG_PATH to /home/data/t150418/augustus_config Mon Apr 8 21:32:13 2024: Found environment variable $AUGUSTUS_BIN_PATH. Setting $AUGUSTUS_BIN_PATH to /opt/augustus/bin Mon Apr 8 21:32:13 2024: Found environment variable $AUGUSTUS_SCRIPTS_PATH. Setting $AUGUSTUS_SCRIPTS_PATH to /opt/augustus/scripts Mon Apr 8 21:32:13 2024: Found environment variable $GENEMARK_PATH. Setting $GENEMARK_PATH to /opt/GeneMark-ET/gmes_linux_64 Mon Apr 8 21:32:13 2024: Found environment variable $BAMTOOLS_PATH. Setting $BAMTOOLS_PATH to /opt/bamtools/bin** Mon Apr 8 21:32:13 2024: Found environment variable $SAMTOOLS_PATH. Setting $SAMTOOLS_PATH to /opt/samtools Mon Apr 8 21:32:13 2024: Found environment variable $DIAMOND_PATH. Setting $DIAMOND_PATH to /opt/Diamond Mon Apr 8 21:32:13 2024: Did not find environment variable $PYTHON3_PATH Mon Apr 8 21:32:13 2024: Trying to guess $PYTHON3_PATH from location of python3 executable that is available in your $PATH Mon Apr 8 21:32:13 2024: Setting $PYTHON3_PATH to /usr/bin Mon Apr 8 21:32:13 2024: Did not find environment variable $CDBTOOLS_PATH Mon Apr 8 21:32:13 2024: Trying to guess $CDBTOOLS_PATH from location of cdbfasta executable that is available in your $PATH Mon Apr 8 21:32:13 2024: Setting $CDBTOOLS_PATH to /usr/bin Mon Apr 8 21:32:13 2024: ERROR: in file /opt/BRAKER/scripts/braker.pl at line 4490

Genome file /home/data/t150418/workspace/1511Genome/07Braker/1511.genome.fa.masked --softmasking does not exist.

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Wangray123 commented 2 months ago

Solved now. Thanks a lot！