Hi all!
Running this command with a CEGMA created training file
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autoAug.pl --species=An.07c14.C20k20.2.SSP3.0.bow.sharp --genome=An.07c14.C20k20.2.500bp.SCUBAT_140G_SSP3.0.bow.sharp.final.scaffolds.fasta --trainingset=An.07c14.C20k20.2.500bp.SCUBAT_140G_SSP3.0.bow.sharp.final.scaffolds.cegma.augustus-training.gff --useexisting -v --singleCPU --optrounds=3 &>augustus.out.txt
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2 Excuting "augustus --species=An.07c14.C20k20.2.SSP3.0 /work/Ananus/o.10.lc.90.j.cap3.m.90/sspace_scaffs/An.07c14.C20k20.2.500bp.SCUBAT_140G_SSP3.0/autoAug/autoAugTrain/training/training.gb.test > /work/Ananus/o.10.lc.90.j.cap3.m.90/sspa
ce_scaffs/An.07c14.C20k20.2.500bp.SCUBAT_140G_SSP3.0/autoAug/autoAugTrain/training/test/augustus.1.out" ... Finished!
1 Ab initio prediction accuracy of AUGUSTUS without optimizing, without UTRs, is: 0.409366666666667
1 Optimizing meta parameters of AUGUSTUS
2 Excuting "perl /home/philipp/bioProgs/augustus-3.0.1/config/../scripts/optimize_augustus.pl --rounds=3 --species=An.07c14.C20k20.2.SSP3.0 /work/Ananus/o.10.lc.90.j.cap3.m.90/sspace_scaffs/An.07c14.C20k20.2.500bp.SCUBAT_140G_SSP3.0/autoAug/autoAugTrain/training/training.gb.train.test --onlytrain=/work/Ananus/o.10.lc.90.j.cap3.m.90/sspace_scaffs/An.07c14.C20k20.2.500bp.SCUBAT_140G_SSP3.0/autoAug/autoAugTrain/training/training.gb.onlytrain --metapars=/home/philipp/bioProgs/augustus-3.0.1/config/species/An.07c14.C20k20.2.SSP3.0/An.07c14.C20k20.2.SSP3.0_metapars.cfg > optimize.out" ...
augustus: ERROR
IgenicModel::readAllParameters: Error reading file /home/philipp/bioProgs/augustus-3.0.1/config/species/An.07c14.C20k20.2.SSP3.0/An.07c14.C20k20.2.SSP3.0_igenic_probs.pbl. Truncated?
augustus: ERROR
IgenicModel::readAllParameters: Error reading file /home/philipp/bioProgs/augustus-3.0.1/config/species/An.07c14.C20k20.2.SSP3.0/An.07c14.C20k20.2.SSP3.0_igenic_probs.pbl. Truncated?
augustus: ERROR
IgenicModel::readAllParameters: Error reading file /home/philipp/bioProgs/augustus-3.0.1/config/species/An.07c14.C20k20.2.SSP3.0/An.07c14.C20k20.2.SSP3.0_igenic_probs.pbl. Truncated?
augustus: ERROR
ExonModel::readProbabilities: Error reading file /home/philipp/bioProgs/augustus-3.0.1/config/species/An.07c14.C20k20.2.SSP3.0/An.07c14.C20k20.2.SSP3.0_exon_probs.pbl at EMISSION, pattern TTTTT
augustus: ERROR
Invalid nucleotide '^@' encountered.
Could not read the accuracy values out of predictions.txt when processing bucket 1. at /home/philipp/bioProgs/augustus-3.0.1/config/../scripts/optimize_augustus.pl line 744.
failed to execute: perl /home/philipp/bioProgs/augustus-3.0.1/config/../scripts/optimize_augustus.pl --rounds=3 --species=An.07c14.C20k20.2.SSP3.0 /work/Ananus/o.10.lc.90.j.cap3.m.90/sspace_scaffs/An.07c14.C20k20.2.500bp.SCUBAT_140G_SSP3.0/autoAug/autoAugTrain/training/training.gb.train.test --onlytrain=/work/Ananus/o.10.lc.90.j.cap3.m.90/sspace_scaffs/An.07c14.C20k20.2.500bp.SCUBAT_140G_SSP3.0/autoAug/autoAugTrain/training/training.gb.onlytrain --metapars=/home/philipp/bioProgs/augustus-3.0.1/config/species/An.07c14.C20k20.2.SSP3.0/An.07c14.C20k20.2.SSP3.0_metapars.cfg > optimize.out!
failed to execute: No such file or directory
autoAug/autoAugTrain/training
and I can't find no "@" in my fasta file.
Any help with this would be highly appreciated.
Best regards
Philipp