Problem converting trainingSetComplete.gff to trainingSetComplete.gb in autoAug.pl
Posted: Thu Nov 19, 2015 8:02 pm
Originally posted in the old forum by willj on 19.08.2013 - 09:04
Hi guys,
I am trying to run autoAug.pl and have run into a problem:
2 Running "grep -f pasa.complete.lst ../pasa/trainingSetCandidates.gff3 >trainingSetComplete.temp.gff" ... Finished!
2 Running "cat trainingSetComplete.temp.gff | perl -pe 's/\t\S*(asmbl_\d+).*/\t$1/' | sort -n -k 4 | sort -s -k 9 | sort -s -k 1,1 > trainingSetComplete.gff" ... Finished!
1 Average gene length in the training set is 1.00
2 The length of flanking DNA is set as 1000 accordingly.
3 Found script /home/will/devel/bioinfo/augustus.2.7/config/../scripts/gff2gbSmallDNA.pl.
3 perl /home/will/devel/bioinfo/augustus.2.7/config/../scripts/gff2gbSmallDNA.pl trainingSetComplete.gff /work/will/bin/augustus/autoAug/seq/genome_clean.fa 1000 trainingSetComplete.gb 1>gff2gbSmallDNA.stdout 2>gff2gbSmallDNA.stderr
1 The training set trainingSetComplete.gb contains 0 entries
2 Now trying to find out whether the CDS in the training set contain or exclude the stop codon.
3 cd /home/will/devel/bioinfo/augustus.2.7/config/species/generic
3 cat generic_parameters.cfg | perl -pe 's/(stopCodonExcludedFromCDS )(s+) /true /' > temp_1
3 mv temp_1 generic_parameters.cfg
3 Set value of "stopCodonExcludedFromCDS" in generic_parameters.cfg to "true"
3 cd /work/will/Puccinia_striiformis/bin/augustus/autoAug/trainingSet/training
3 Running "etraining --species=generic trainingSetComplete.gb 1>train.out 2>train.err" ...
failed to execute:
The problem seems to occur when it tries to run gff2gbSmallDNA.pl, because it says "1 The training set trainingSetComplete.gb contains 0 entries".
But the stderr and stdout for this step are empty:
$ cat gff2gbSmallDNA.stderr
$
$ cat gff2gbSmallDNA.stdout
$
So I don't know what is going wrong. Any thoughts?
Thanks very much
Will
Hi guys,
I am trying to run autoAug.pl and have run into a problem:
2 Running "grep -f pasa.complete.lst ../pasa/trainingSetCandidates.gff3 >trainingSetComplete.temp.gff" ... Finished!
2 Running "cat trainingSetComplete.temp.gff | perl -pe 's/\t\S*(asmbl_\d+).*/\t$1/' | sort -n -k 4 | sort -s -k 9 | sort -s -k 1,1 > trainingSetComplete.gff" ... Finished!
1 Average gene length in the training set is 1.00
2 The length of flanking DNA is set as 1000 accordingly.
3 Found script /home/will/devel/bioinfo/augustus.2.7/config/../scripts/gff2gbSmallDNA.pl.
3 perl /home/will/devel/bioinfo/augustus.2.7/config/../scripts/gff2gbSmallDNA.pl trainingSetComplete.gff /work/will/bin/augustus/autoAug/seq/genome_clean.fa 1000 trainingSetComplete.gb 1>gff2gbSmallDNA.stdout 2>gff2gbSmallDNA.stderr
1 The training set trainingSetComplete.gb contains 0 entries
2 Now trying to find out whether the CDS in the training set contain or exclude the stop codon.
3 cd /home/will/devel/bioinfo/augustus.2.7/config/species/generic
3 cat generic_parameters.cfg | perl -pe 's/(stopCodonExcludedFromCDS )(s+) /true /' > temp_1
3 mv temp_1 generic_parameters.cfg
3 Set value of "stopCodonExcludedFromCDS" in generic_parameters.cfg to "true"
3 cd /work/will/Puccinia_striiformis/bin/augustus/autoAug/trainingSet/training
3 Running "etraining --species=generic trainingSetComplete.gb 1>train.out 2>train.err" ...
failed to execute:
The problem seems to occur when it tries to run gff2gbSmallDNA.pl, because it says "1 The training set trainingSetComplete.gb contains 0 entries".
But the stderr and stdout for this step are empty:
$ cat gff2gbSmallDNA.stderr
$
$ cat gff2gbSmallDNA.stdout
$
So I don't know what is going wrong. Any thoughts?
Thanks very much
Will