Why does braker stop without any error output?
0
0
Entering edit mode
13 months ago
eennadi • 0

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

**************************

PREDICTING GENES WITH AUGUSTUS (NO UTRS)

**************************

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 ..

Fri Oct 30 17:57:42 2020: Running AUGUSTUS jobs from /mnt/data/emmanuel/braker_annotation_08092020/braker/hints.job.lst

Fri Oct 30 17:57:42 2020: Running AUGUSTUS job 1

software error • 365 views
ADD COMMENT

Login before adding your answer.

Traffic: 2102 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6