autoAug.pl error
Posted: Thu Nov 19, 2015 5:16 pm
Originally posted in the old forum by willj on 25.07.2013 - 05:00
Hi guys,
I am trying to run autoAug.pl, but am getting an error:
2 checking for installed programs ... ok.
1 Checking fasta headers in file /work/will/genome/bin/augustus/APLG_003_scaff.fasta.masked...
1 Checking fasta headers in file /work/will/genome/bin/augustus/GG_Trinity_PASA_clean.fasta...
3 mkdir gbrowse
3 mkdir pasa
3 mkdir training
2 All necessary directories have been created unter /work/will/genome/bin/augustus/autoAug/trainingSet.
3 cd /work/will/genome/bin/augustus/autoAug/seq
3 Cleaning genome file from DOS whitespaces/linebreaks...
3 perl /home/will/devel/bioinfo/augustus.2.7/config/../scripts/cleanDOSfasta.pl /work/will/genome/bin/augustus/APLG_003_scaff.fasta.masked > /work/will/genome/bin/augustus/autoAug/seq/genome_clean.fa
1 ####### Step 0: Creating training set with genes using PASA #######
3 cd /work/will/genome/bin/augustus/autoAug/trainingSet/pasa
2 Skipping seqclean. Using existing transcripts.fasta.clean.
2 Using existing alignAssembly.config.
3 ln -fs /work/will/genome/bin/augustus/autoAug/seq/genome_clean.fa genome.fasta
3 Reading MySQL variables from /home/will/devel/bioinfo/PASA/PASA2/pasa_conf/
1 Dropping MySQL database PASAmygenome on host gdudev.anu.edu.au.
2 Executing the Alignment Assembly: perl /home/will/devel/bioinfo/PASA/PASA2/scripts/Launch_PASA_pipeline.pl -c alignAssembly.config -C -R -g /work/will/genome/bin/augustus/autoAug/seq/genome_clean.fa -t transcripts.fasta.clean -T -u transcripts.fasta 1>Launch_PASA_pipeline.stdout 2>Launch_PASA_pipeline.stderr ...2 A test output...
Failed to execute, possible reasons could be:
1. There is already a database named "PASAmygenome" in your mysql host.
2. The software "slclust" is not installed correctly, try to install it again (see the details in the PASA documentation).
3. The fasta headers in cDNA or genome file were not unique.
Inspect /work/will/genome/bin/augustus/autoAug/trainingSet/pasa/Launch_PASA_pipeline.stderr for PASA error messages.
The error I get in Launch_PASA_pipeline.stderr looks like this:
Error, must specify at least one primary aligner via --ALIGNER or imported via --IMPORT... at /home/will/devel/bioinfo/PASA/PASA2/scripts/Launch_PASA_pipeline.pl line 311.
Whereabouts do I specify --ALIGNER?
Thanks very much
Cheers
Will
Hi guys,
I am trying to run autoAug.pl, but am getting an error:
2 checking for installed programs ... ok.
1 Checking fasta headers in file /work/will/genome/bin/augustus/APLG_003_scaff.fasta.masked...
1 Checking fasta headers in file /work/will/genome/bin/augustus/GG_Trinity_PASA_clean.fasta...
3 mkdir gbrowse
3 mkdir pasa
3 mkdir training
2 All necessary directories have been created unter /work/will/genome/bin/augustus/autoAug/trainingSet.
3 cd /work/will/genome/bin/augustus/autoAug/seq
3 Cleaning genome file from DOS whitespaces/linebreaks...
3 perl /home/will/devel/bioinfo/augustus.2.7/config/../scripts/cleanDOSfasta.pl /work/will/genome/bin/augustus/APLG_003_scaff.fasta.masked > /work/will/genome/bin/augustus/autoAug/seq/genome_clean.fa
1 ####### Step 0: Creating training set with genes using PASA #######
3 cd /work/will/genome/bin/augustus/autoAug/trainingSet/pasa
2 Skipping seqclean. Using existing transcripts.fasta.clean.
2 Using existing alignAssembly.config.
3 ln -fs /work/will/genome/bin/augustus/autoAug/seq/genome_clean.fa genome.fasta
3 Reading MySQL variables from /home/will/devel/bioinfo/PASA/PASA2/pasa_conf/
1 Dropping MySQL database PASAmygenome on host gdudev.anu.edu.au.
2 Executing the Alignment Assembly: perl /home/will/devel/bioinfo/PASA/PASA2/scripts/Launch_PASA_pipeline.pl -c alignAssembly.config -C -R -g /work/will/genome/bin/augustus/autoAug/seq/genome_clean.fa -t transcripts.fasta.clean -T -u transcripts.fasta 1>Launch_PASA_pipeline.stdout 2>Launch_PASA_pipeline.stderr ...2 A test output...
Failed to execute, possible reasons could be:
1. There is already a database named "PASAmygenome" in your mysql host.
2. The software "slclust" is not installed correctly, try to install it again (see the details in the PASA documentation).
3. The fasta headers in cDNA or genome file were not unique.
Inspect /work/will/genome/bin/augustus/autoAug/trainingSet/pasa/Launch_PASA_pipeline.stderr for PASA error messages.
The error I get in Launch_PASA_pipeline.stderr looks like this:
Error, must specify at least one primary aligner via --ALIGNER or imported via --IMPORT... at /home/will/devel/bioinfo/PASA/PASA2/scripts/Launch_PASA_pipeline.pl line 311.
Whereabouts do I specify --ALIGNER?
Thanks very much
Cheers
Will