Problem with PASA Pipeline Installation Configuration

Question

[jstevenson2256]

I've installed PASA and am trying to configure it for alignment assembly using the sample data supplied. I try running the pipeline using the commands given on the wiki (https://github.com/PASApipeline/PASApipeline/wiki/PASA_alignment_assembly):

$PASAHOME/Launch_PASA_pipeline.pl \
       -c alignAssembly.config -C -R -g genome_sample.fasta \
       -t all_transcripts.fasta.clean -T -u all_transcripts.fasta \
       -f FL_accs.txt --ALIGNERS blat,gmap --CPU 2

Unfortunately, I'm getting the following issue:

-connecting to SQLite db: /tmp/sample_mydb_pasa.sqlite
-*** Running PASA pipeine:
* Running CMD: /data/software/PASA/PASApipeline/scripts/create_sqlite_cdnaassembly_db.dbi -c sqlite.confs/alignAssembly.config -S '/data/software/PASA/PASApipeline/schema/cdna_alignment_sqliteschema'

DBD::SQLite::db do failed: table URL_templates already exists at /data/software/PASA/PASApipeline/scripts/create_sqlite_cdnaassembly_db.dbi line 62.

Error, invalid SQLite schema at /data/software/PASA/PASApipeline/scripts/create_sqlite_cdnaassembly_db.dbi line 62.

Error, cmd: /data/software/PASA/PASApipeline/scripts/create_sqlite_cdnaassembly_db.dbi -c sqlite.confs/alignAssembly.config -S '/data/software/PASA/PASApipeline/schema/cdna_alignment_sqliteschema' died with ret 512 No such file or directory at /data/software/PASA/PASApipeline/PerlLib/Pipeliner.pm line 186.
        Pipeliner::run(Pipeliner=HASH(0xc92b88)) called at ../Launch_PASA_pipeline.pl line 1044

I have no idea what this means nor how to fix it. The program is directed to the correct sample input files and the PerlLib that came with the installation. Help in fixing and/or understanding this would be greatly appreciated.

[ATpoint]

I would open an issue at Github, as this seems to be rather specific.

Answer 1

[jstevenson2256]

Issue fixed, see https://github.com/PASApipeline/PASApipeline/issues/104

[ATpoint]

Good to hear, thanks for following up :)