autoAug.pl(Augustus)-PASA pipeline error

Hi,

I attempt to obtain training gene sets for my new species using autoAug.pl on RNAseq data. I am sure I installed prerequisite software of PASA (http://pasapipeline.github.io/#A_sii) and I installed latest version of PASA.

This is a command I ran:

autoAug.pl --genome=genome.fasta --species=mySpecies -v -v --cdna=RNAseq.fasta

Then I got this message:

...failed to execute:perl pasa_asmbls_to_training_set.dbi -M "my_pasadb:localhost" -p "readonly:readonly" -g ./autoAug/seq/genome_clean.fa

This problem is resulted from use of unexpected version of PASA? Your help would be much appreciated.

augustus genome pasa software-error

• 3,391 views • link

updated 3.9 years ago by Ram

• written 10.8 years ago by freddiejung •

2 answers

Have you tried to manually run the command that fails to see what it complains about?

perl pasa_asmbls_to_training_set.dbi -M "my_pasadb:localhost" -p "readonly:readonly" -g ./autoAug/seq/genome_clean.fa

I wouldn't be surprised if the MySQL instance wasn't switched on, or the user you've supplied can't read or write to the database, or the database "my_pasadb" wasn't initialized yet (run "CREATE DATABASE my_pasadb" inside MySQL to initialize it). A quick skim of the manual shows that there are no steps on properly setting up the database and users.

• 0 views • link

written 10.8 years ago by Philipp Bayer

hi .i met the same error message.i think the reason is the version of PASA.i am going to change the parameters in autoAUG.pl

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written 9.0 years ago by wn1364 •