I am waiting to hear back from the developer of Augustus, but I wanted to see if anyone else had experience with the error message I received.
First try with etraining: etraining --species=1371E14H2 training.gb.train >train.out ...sh: line 1: 118112 Segmentation fault etraining --species=1371E14H2 training.gb.train > train.out 2> train.err
failed to execute:
failed to execute: No such file or directory
I am confused, is it saying I do not have the directory it is trying to write into? Or is this saying something is wrong with augustus executing etraining?
I looked into the train.err and train.out files and nothing was listed.
Not sure if it helps, but here is what my script looks like:
perl /work/Geomicrobiology/msobol/bin/augustus/scripts/autoAug.pl --genome=/work/Geomicrobiology/msobol/IODP_329_SPG/1371E14H2/repeatmasker/1371E_14H2_contigs.fasta.masked --species=1371E14H2 --trainingset=/work/Geomicrobiology/msobol/IODP_329_SPG/1371E14H2/maker/1371E_14H2_contigs.fasta.maker.output/augustus.train.gff3 --useexisting -v --optrounds=3 --workingdir=/work/Geomicrobiology/msobol/IODP_329_SPG/1371E14H2/augustus/