Question: Problem with PASA Pipeline Installation Configuration
0
gravatar for jstevenson2256
18 months ago by
jstevenson225610 wrote:

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.

ADD COMMENTlink modified 18 months ago • written 18 months ago by jstevenson225610

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

ADD REPLYlink written 18 months ago by ATpoint40k
1
gravatar for jstevenson2256
18 months ago by
jstevenson225610 wrote:

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

ADD COMMENTlink written 18 months ago by jstevenson225610

Good to hear, thanks for following up :)

ADD REPLYlink written 18 months ago by ATpoint40k
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