Error with running autoAug.pl
Posted: Thu Nov 19, 2015 5:23 pm
Originally posted in the old forum by Yanpeng, Li on 15.11.2012 - 09:42
Hi all,
I first use augustus. Some problems occur:
muzi@muzi-laptop[examples] perl autoAug.pl --genome=genome.fa --species=HS04 --cdna=cdna.fa -v -v --pasa
2 checking for installed programs ... ok.
3 mkdir /home/muzi/biology/bioinformatics/soft/gene-prediction/augustus/augustus.2.6.1/examples/autoAug/trainingSet
3 mkdir seq
3 mkdir hints
3 mkdir cdna
3 mkdir gbrowse
3 mkdir pasa
3 mkdir training
2 All necessary directories have been created unter /home/muzi/biology/bioinformatics/soft/gene-prediction/augustus/augustus.2.6.1/examples/autoAug/trainingSet.
3 cd /home/muzi/biology/bioinformatics/soft/gene-prediction/augustus/augustus.2.6.1/examples/autoAug/seq
3 ln -s /home/muzi/biology/bioinformatics/soft/gene-prediction/augustus/augustus.2.6.1/examples/genome.fa genome.fa
3 Cleaning genome file from DOS whitespaces/linebreaks...
3 perl /home/muzi/biology/bioinformatics/soft/gene-prediction/augustus/augustus.2.6.1/config//../scripts/cleanDOSfasta.pl /home/muzi/biology/bioinformatics/soft/gene-prediction/augustus/augustus.2.6.1/examples/genome.fa > /home/muzi/biology/bioinformatics/soft/gene-prediction/augustus/augustus.2.6.1/examples/autoAug/seq/genome_clean.fa
1 ####### Step 0: Creating training set with genes using PASA #######
3 cd /home/muzi/biology/bioinformatics/soft/gene-prediction/augustus/augustus.2.6.1/examples/autoAug/trainingSet/pasa
3 ln -fs /home/muzi/biology/bioinformatics/soft/gene-prediction/augustus/augustus.2.6.1/examples/cdna.fa transcripts.fasta
2 Running perl /home/muzi/biology/bioinformatics/soft/gene-prediction/augustus/augustus-training/PASA/PASA_r2012-06-25/seqclean/seqclean/seqclean transcripts.fasta 1>seqclean.stdout 2>seqclean.stderr ... Finished!
3 cp /home/muzi/biology/bioinformatics/soft/gene-prediction/augustus/augustus-training/PASA/PASA_r2012-06-25/pasa_conf/pasa.alignAssembly.Template.txt alignAssembly.config
3 Setting appropriate values in alignAssembly.config
3 rm alignAssembly.config; mv temp alignAssembly.config; chmod a+x alignAssembly.config
3 Adjusted alignAssembly.config
3 ln -fs /home/muzi/biology/bioinformatics/soft/gene-prediction/augustus/augustus.2.6.1/examples/autoAug/seq/genome_clean.fa genome.fasta
3 Reading MySQL variables from /home/muzi/biology/bioinformatics/soft/gene-prediction/augustus/augustus-training/PASA/PASA_r2012-06-25/pasa_conf/
2 Executing the Alignment Assembly: perl /home/muzi/biology/bioinformatics/soft/gene-prediction/augustus/augustus-training/PASA/PASA_r2012-06-25/scripts/Launch_PASA_pipeline.pl -c alignAssembly.config -C -R -g /home/muzi/biology/bioinformatics/soft/gene-prediction/augustus/augustus.2.6.1/examples/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 "PASAHS04" in your mysql host.
2. The software "slclust" is not installed correctly, try to install it again (see the details in the PASA documentation).
Inspect /home/muzi/biology/bioinformatics/soft/gene-prediction/augustus/augustus.2.6.1/examples/autoAug/trainingSet/pasa/Launch_PASA_pipeline.stderr for PASA error messages.
I deleted the database named "PASAHS04" in your mysql host and reinstall slclust. The problems still occurred.
Can anyone help me with this?
Thanks,
Yanpeng,Li
Hi all,
I first use augustus. Some problems occur:
muzi@muzi-laptop[examples] perl autoAug.pl --genome=genome.fa --species=HS04 --cdna=cdna.fa -v -v --pasa
2 checking for installed programs ... ok.
3 mkdir /home/muzi/biology/bioinformatics/soft/gene-prediction/augustus/augustus.2.6.1/examples/autoAug/trainingSet
3 mkdir seq
3 mkdir hints
3 mkdir cdna
3 mkdir gbrowse
3 mkdir pasa
3 mkdir training
2 All necessary directories have been created unter /home/muzi/biology/bioinformatics/soft/gene-prediction/augustus/augustus.2.6.1/examples/autoAug/trainingSet.
3 cd /home/muzi/biology/bioinformatics/soft/gene-prediction/augustus/augustus.2.6.1/examples/autoAug/seq
3 ln -s /home/muzi/biology/bioinformatics/soft/gene-prediction/augustus/augustus.2.6.1/examples/genome.fa genome.fa
3 Cleaning genome file from DOS whitespaces/linebreaks...
3 perl /home/muzi/biology/bioinformatics/soft/gene-prediction/augustus/augustus.2.6.1/config//../scripts/cleanDOSfasta.pl /home/muzi/biology/bioinformatics/soft/gene-prediction/augustus/augustus.2.6.1/examples/genome.fa > /home/muzi/biology/bioinformatics/soft/gene-prediction/augustus/augustus.2.6.1/examples/autoAug/seq/genome_clean.fa
1 ####### Step 0: Creating training set with genes using PASA #######
3 cd /home/muzi/biology/bioinformatics/soft/gene-prediction/augustus/augustus.2.6.1/examples/autoAug/trainingSet/pasa
3 ln -fs /home/muzi/biology/bioinformatics/soft/gene-prediction/augustus/augustus.2.6.1/examples/cdna.fa transcripts.fasta
2 Running perl /home/muzi/biology/bioinformatics/soft/gene-prediction/augustus/augustus-training/PASA/PASA_r2012-06-25/seqclean/seqclean/seqclean transcripts.fasta 1>seqclean.stdout 2>seqclean.stderr ... Finished!
3 cp /home/muzi/biology/bioinformatics/soft/gene-prediction/augustus/augustus-training/PASA/PASA_r2012-06-25/pasa_conf/pasa.alignAssembly.Template.txt alignAssembly.config
3 Setting appropriate values in alignAssembly.config
3 rm alignAssembly.config; mv temp alignAssembly.config; chmod a+x alignAssembly.config
3 Adjusted alignAssembly.config
3 ln -fs /home/muzi/biology/bioinformatics/soft/gene-prediction/augustus/augustus.2.6.1/examples/autoAug/seq/genome_clean.fa genome.fasta
3 Reading MySQL variables from /home/muzi/biology/bioinformatics/soft/gene-prediction/augustus/augustus-training/PASA/PASA_r2012-06-25/pasa_conf/
2 Executing the Alignment Assembly: perl /home/muzi/biology/bioinformatics/soft/gene-prediction/augustus/augustus-training/PASA/PASA_r2012-06-25/scripts/Launch_PASA_pipeline.pl -c alignAssembly.config -C -R -g /home/muzi/biology/bioinformatics/soft/gene-prediction/augustus/augustus.2.6.1/examples/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 "PASAHS04" in your mysql host.
2. The software "slclust" is not installed correctly, try to install it again (see the details in the PASA documentation).
Inspect /home/muzi/biology/bioinformatics/soft/gene-prediction/augustus/augustus.2.6.1/examples/autoAug/trainingSet/pasa/Launch_PASA_pipeline.stderr for PASA error messages.
I deleted the database named "PASAHS04" in your mysql host and reinstall slclust. The problems still occurred.
Can anyone help me with this?
Thanks,
Yanpeng,Li