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-   -   autoAug.pl cannot start Launch_PASA_pipeline (http://seqanswers.com/forums/showthread.php?t=62306)

dep 08-28-2015 02:06 AM

autoAug.pl cannot start Launch_PASA_pipeline
 
Dear Colleagues!

Could someone advise me on Augustus?
I am trying to train Augustus for my fungus species using RNA-seq data. I believe I have installed all the programs it requires, but when I start it like this:

autoAug.pl --genome /path-to-genome.fasta --species=myspecies --cdna=/path-to-RNA-seq.fasta -v -v --pasa --useexisting --verbose --workingdir=/path-to-workingdir

it stops after trying to start Launch_PASA_pipeline. The CLI error says the following:

"Failed to execute, possible reasons could be:
1. There is already a database named "PASAmyspecies" 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 /path-to/Launch_PASA_pipeline.stderr for PASA error messages."

It is the same if I use the test training set.
Dropping the mysql database does not help.
slclust is installed and is in my PATH
I don't see how the headers could be not unique.



The Launch_PASA_pipeline.stderr says the following:
"Error, must specify at least one primary aligner via --ALIGNER or imported via --IMPORT... at /home/dmitrii/biotools/PASApipeline-2.0.2/scripts/Launch_PASA_pipeline.pl line 314."

I have no experience with PERL at all, but that line says smth about choosing between gmap and blat. I thought that blat was the default aligner and this did not have to be a problem. I could not find in manuals, which configuration file should I change to change the --ALIGNER parameter.

I would appreciate any suggestions.


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