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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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GeneMark-ETP didn't receive enough evidence from the input data, in this case #851

Open xuyinnnan opened 3 weeks ago

xuyinnnan commented 3 weeks ago

Hi, run command :

singularity exec -B $PWD:$PWD braker3.sif braker.pl --useexisting --species Brachymystax_lenok1 --genome ./s3_repeats_screen/A1.genome.masked.final.fasta --prot_seq ./s1_input_data/homologs/Merged.pep.fasta --rnaseq_sets_ids A_brain,A_gonad,A_heart,A_liver,A_muscle --rnaseq_sets_dir ./s1_input_data/RNA_seq/hisat2_aln/ --nocleanup --threads 64 --gff3 --workingdir ./braker3/

then I got these error： ERROR in file /opt/BRAKER/scripts/braker.pl at line 5578 Failed to execute: /usr/bin/perl /opt/ETP/bin/gmetp.pl --cfg ./singularity/braker3/GeneMark-ETP/etp_config.yaml --workdir ./singularity/braker3/GeneMark-ETP --bam ./singularity/braker3/GeneMark-ETP/etp_data/ --cores 64 --softmask 1>./singularity/braker3/errors/GeneMark-ETP.stdout 2>./singularity/braker3/errors/GeneMark-ETP.stderr Failed to execute: /usr/bin/perl /opt/ETP/bin/gmetp.pl --cfg ./singularity/braker3/GeneMark-ETP/etp_config.yaml --workdir ./singularity/braker3/GeneMark-ETP --bam ./singularity/braker3/GeneMark-ETP/etp_data/ --cores 64 --softmask 1>./singularity/braker3/errors/GeneMark-ETP.stdout 2>./singularity/braker3/errors/GeneMark-ETP.stderr The most common problem is that GeneMark-ETP didn't receive enough evidence from the input data, in this case, see errors/GeneMark-ETP.stderr!

This is this question

thanks ！

xuyinnnan commented 3 weeks ago

supplement ：

less GeneMark-ETP.stderr: FASTA index file ./singularity/braker3/GeneMark-ETP/data/genome.softmasked.fasta.fai created. error, file/folder not found: transcripts_merged.fasta.gff

Any suggestion on a solution?