Hello, I am running Braker on my genome but it keeps dying without any error output. Find part of the log file below
Please how can I also make braker to resume from where it stopped?
Fri Oct 30 17:57:20 2020: training AUGUSTUS
Fri Oct 30 17:57:20 2020: Copying optimized parameters to working directory /mnt/data/emmanuel/braker_annotation_08092020/braker/species
cp -r /home/emmanuel/miniconda3/envs/augustus/config/species/Mucuna_pruriens /mnt/data/emmanuel/braker_annotation_08092020/braker/species
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PREDICTING GENES WITH AUGUSTUS (NO UTRS)
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Fri Oct 30 17:57:20 2020: RUNNING AUGUSTUS
Fri Oct 30 17:57:20 2020: Preparing genome for running AUGUSTUS in parallel
Fri Oct 30 17:57:20 2020: Creating directory for storing AUGUSTUS files (hints, temporarily) /mnt/data/emmanuel/braker_annotation_08092020/braker/genome_split.
Fri Oct 30 17:57:20 2020: splitting genome file in smaller parts for parallel execution of AUGUSTUS prediction
perl /home/emmanuel/miniconda3/envs/augustus/bin/splitMfasta.pl /mnt/data/emmanuel/braker_annotation_08092020/braker/genome.fa --outputpath=/mnt/data/emmanuel/braker_annotation_0809
2020/braker/genome_split 2>/mnt/data/emmanuel/braker_annotation_08092020/braker/errors/splitMfasta.stderr
cd /mnt/data/emmanuel/braker_annotation_08092020/braker/genome_split; for f in genome.split.*; do NAME=grep ">" $f; mv $f ${NAME#>}.fa; done; cd ..
Fri Oct 30 17:57:36 2020: Split genome file in 546 parts, finished.
Fri Oct 30 17:57:36 2020: copy extrinsic file /home/emmanuel/miniconda3/envs/braker2/bin/cfg/rnaseq.cfg to working directory
cp /home/emmanuel/miniconda3/envs/braker2/bin/cfg/rnaseq.cfg /mnt/data/emmanuel/braker_annotation_08092020/braker/species/Mucuna_pruriens/ex1.cfg
Fri Oct 30 17:57:36 2020: Making AUGUSTUS jobs with hintsfile /mnt/data/emmanuel/braker_annotation_08092020/braker/hintsfile.gff, cfgFile /home/emmanuel/miniconda3/envs/braker2/bi
n/cfg/rnaseq.cfg, UTR status off, and hintId hints
Fri Oct 30 17:57:36 2020: Creating directory for storing AUGUSTUS files (hints, temporarily) /mnt/data/emmanuel/braker_annotation_08092020/braker/augustus_tmp.
Fri Oct 30 17:57:36 2020: creating /mnt/data/emmanuel/braker_annotation_08092020/braker/aug_hints.lst for AUGUSTUS jobs
Fri Oct 30 17:57:36 2020: creating AUGUSTUS jobs (with hints)
cd /mnt/data/emmanuel/braker_annotation_08092020/braker perl /home/emmanuel/miniconda3/envs/augustus/bin/createAugustusJoblist.pl --sequences=/mnt/data/emmanuel/braker_annotation_08092020/braker/aug_hints.lst --wrap="#!/bin/bash" --overl ap=5000 --chunksize=1252500 --outputdir=/mnt/data/emmanuel/braker_annotation_08092020/braker/augustus_tmp --joblist=/mnt/data/emmanuel/braker_annotation_08092020/braker/hints.job.ls t --jobprefix=aug_hints_ --partitionHints --command "/home/emmanuel/miniconda3/envs/augustus/bin/augustus --species=Mucuna_pruriens --AUGUSTUS_CONFIG_PATH=/home/emmanuel/miniconda3/ envs/augustus/config --extrinsicCfgFile=/home/emmanuel/miniconda3/envs/braker2/bin/cfg/rnaseq.cfg --alternatives-from-evidence=true --UTR=off --exonnames=on --codingseq=on --allow_h inted_splicesites=gcag,atac --softmasking=1" 2>/mnt/data/emmanuel/braker_annotation_08092020/braker/errors/createAugustusJoblist_hints.stderr cd ..
