ERROR in file /opt/BRAKER/scripts/braker.pl at line 10092, Failed to open directory ${workingdir}

[yyliang12]

Hi,

Thanks for developing such a power annotation pipeline!

When I run the BRAKER program, I get an error during the file deleting phase:

......
# Thu Apr 18 16:41:27 2024: find /home/yanyang_liang/ProgramFiles/2024/03_Aco_Annotation/02_Gene_Annotation/02_BRAKER3/P1_hap1 -empty
# Thu Apr 18 08:41:54 2024: deleting job lst files (if existing)

↑Those are the final records of braker.log

The STDERR of the braker.pl program is:

ERROR in file /opt/BRAKER/scripts/braker.pl at line 10092
Failed to open directory /home/yanyang_liang/ProgramFiles/2024/03_Aco_Annotation/02_Gene_Annotation/02_BRAKER3/P1_hap1!

The command I ran braker.pl was:

singularity exec -B /home/yanyang_liang:/home/yanyang_liang --writable braker3_sandbox braker.pl \
--gff3 \
--workingdir /home/yanyang_liang/ProgramFiles/2024/03_Aco_Annotation/02_Gene_Annotation/02_BRAKER3/P1_hap1 \
--AUGUSTUS_CONFIG_PATH ${AUGUSTUS_Config_Dir} \
--species ${Species_Name} \
--useexisting \
--threads ${threads} \
--genome ${Soft_Masked_Genome} \
--prot_seq ${Protein_Seq} \
--bam ${BAM_File} > ${log} 2>&1

What is more strange is that the test data can be completed through the same command properly without any errors popped out. Why would this happen?

Thanks, Yanyang.

[KatharinaHoff]

I have no idea why it happened, but it's part of the cleanup function. You should have all results available, already.

[yyliang12]

I have no idea why it happened, but it's part of the cleanup function. You should have all results available, already.

Hi Dr. Hoff,

Thanks for answering anyway!

I think it might be the some problems with the Snakemake script cuz I executed the BRAKER singularity image via Snakemake:

rule BRAKER:
    input:
    output:
    singularity:
        braker.sif
    shell:
        """
        braker.pl
        """

I just test the same data using a Bash script with all input files under ${PWD} path,

#!/bin/bash
singularity exec -B ${PWD}:${PWD} braker.pl

, turns out the whole braker.pl pipeline can be finished completely.

Thanks, Yanyang.