Could not read the accuracy values out of predictions.txt

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katharina
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Could not read the accuracy values out of predictions.txt

Post by katharina »

Originally posted in the old forum by Philipp Schiffer on 05.04.2014 - 17:12
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
I get the following error

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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
However I find a filed called predictions.txt in
autoAug/autoAugTrain/training
and I can't find no "@" in my fasta file.
Any help with this would be highly appreciated.
Best regards
Philipp
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katharina
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Re: Could not read the accuracy values out of predictions.txt

Post by katharina »

by katharina on 07.04.2014 - 11:30
The weird @-sign might originate from a windows newline character. Check your files for those. Maybe removing those characters will solve the entire problem.
Otherwise, if AUGUSTUS keeps complaining about truncated parameter files, I'd start training fresh, with a clean (and complete) parameter set.
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Re: Could not read the accuracy values out of predictions.txt

Post by katharina »

by Philipp Schiffer on 14.04.2014 - 13:58
solved with dos2unix
Hi Katharina,
thanks for that. Obviously should have thought of doing a dos2unix myself, but as the data had never seen a Windows computer I didn’t think of it. I am still puzzled by that. My best guess would be that the perl scripts in the SSPACE scaffolder somehow introduced the weird characters (all on Linux machines though).
Anyway, it worked after the dos2unix
Cheers
Philipp
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