SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Start genome at origin shadow19c Bioinformatics 0 07-01-2015 05:26 AM
Trinity fail to start lupid Bioinformatics 20 05-03-2015 04:41 AM
Where does the read start? Ingeneious Illumina/Solexa 3 12-10-2014 12:13 PM
Trinity - de novo: how to start Pol8 Bioinformatics 1 10-12-2014 02:32 PM
Where to start nullabee General 4 04-01-2010 05:29 PM

Reply
 
Thread Tools
Old 08-28-2015, 01:06 AM   #1
dep
Junior Member
 
Location: Russia

Join Date: Apr 2015
Posts: 7
Default 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.
dep is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 05:54 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO