Entering edit mode
4.9 years ago
Morgan S. ▴ 80
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/
/work/- are you sure about this? You have a directory titled
workunder the root directory?
Yes. This is now the HPC cluster is set up at my university. The autoAug.pl script works fine up until the part where it tries etraining. So I do not think there is anything wrong with how I am calling the autoAug script.
Did you check with your HPC folks? They can tell you if something attempted by the software crossed limits set by the HPC system.