AutoAug.pl "No such file or directory"
Posted: Thu Nov 19, 2015 6:46 pm
Originally posted in the old forum by Clint Dalrymple on 01.02.2014 - 12:41
I've so far tried this with two different complete genomes, prepared with CEGMA 2.4.010312 and received the same error. This is on Scientific Linux 6.5, Augustus 3.0
[clint@genome test]$ autoAug.pl --Species=WPainted --genome=genome.fa --trainingset=augustus-training.gff --useexisting
2 checking for installed programs ... ok.
1 Checking fasta headers in file /home/clint/genomics/test/genome.fa...
2 All necessary directories have been created unter /home/clint/genomics/test/autoAug/trainingSet.
1 Using existing cDNA alignments and hints.
1 ####### Step 1: Training AUGUSTUS (no UTR models) #######
2 perl /home/clint/augustus-3.0/scripts/autoAugTrain.pl -t=/home/clint/genomics/test/augustus-training.gff -s=WPainted --useexisting -g=/home/clint/genomics/test/autoAug/seq/genome_clean.fa -w=/home/clint/genomics/test/autoAug -v -v --opt=1
2 Reusing existing training set training.gb.
2 Running command "perl /home/clint/augustus-3.0/config//../scripts/new_species.pl --species=WPainted --silent --ignore 1>new_species.stdout" to create AUGUSTUS config files for new species WPainted
2 Now training AUGUSTUS parameters for WPainted.
1 training.gb contains 378 sequences and 378 genes, each sequence contains 1 gene(s) on average.
1 test/evaluation set training.gb.test contains 37 sequences and 37 genes.
1 training set training.gb.train contains 341 sequences and 341 genes.
1 training.gb.train.test contains 300 sequences and 300 genes.
1 training.gb.onlytrain contains 41 sequences and 41 genes.
2 Seting value of "stopCodonExcludedFromCDS" in WPainted_parameters.cfg to "true"
2 First try with etraining: etraining --species=WPainted training.gb.train >train.out ...failed to execute:
failed to execute: No such file or directory
[clint@genome test]$ which etraining
~/augustus-3.0/bin/etraining
[clint@genome test]$
I've so far tried this with two different complete genomes, prepared with CEGMA 2.4.010312 and received the same error. This is on Scientific Linux 6.5, Augustus 3.0
[clint@genome test]$ autoAug.pl --Species=WPainted --genome=genome.fa --trainingset=augustus-training.gff --useexisting
2 checking for installed programs ... ok.
1 Checking fasta headers in file /home/clint/genomics/test/genome.fa...
2 All necessary directories have been created unter /home/clint/genomics/test/autoAug/trainingSet.
1 Using existing cDNA alignments and hints.
1 ####### Step 1: Training AUGUSTUS (no UTR models) #######
2 perl /home/clint/augustus-3.0/scripts/autoAugTrain.pl -t=/home/clint/genomics/test/augustus-training.gff -s=WPainted --useexisting -g=/home/clint/genomics/test/autoAug/seq/genome_clean.fa -w=/home/clint/genomics/test/autoAug -v -v --opt=1
2 Reusing existing training set training.gb.
2 Running command "perl /home/clint/augustus-3.0/config//../scripts/new_species.pl --species=WPainted --silent --ignore 1>new_species.stdout" to create AUGUSTUS config files for new species WPainted
2 Now training AUGUSTUS parameters for WPainted.
1 training.gb contains 378 sequences and 378 genes, each sequence contains 1 gene(s) on average.
1 test/evaluation set training.gb.test contains 37 sequences and 37 genes.
1 training set training.gb.train contains 341 sequences and 341 genes.
1 training.gb.train.test contains 300 sequences and 300 genes.
1 training.gb.onlytrain contains 41 sequences and 41 genes.
2 Seting value of "stopCodonExcludedFromCDS" in WPainted_parameters.cfg to "true"
2 First try with etraining: etraining --species=WPainted training.gb.train >train.out ...failed to execute:
failed to execute: No such file or directory
[clint@genome test]$ which etraining
~/augustus-3.0/bin/etraining
[clint@genome test]$