Augustus Segmentation fault error message
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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/

augustus gene prediction annotation • 1.8k views
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/work/ - are you sure about this? You have a directory titled work under the root directory?

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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.

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Did you check with your HPC folks? They can tell you if something attempted by the software crossed limits set by the HPC system.