autoAug.pl(Augustus)-PASA pipeline error

Question

[freddiejung]

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.

Answer 1

[Philipp Bayer]

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.

Answer 2

[wn1364]

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