Resume PASA alignment Assembly

[Zin Win Latt]

Hello Brian,

Is there a way to resume Pasa Alignment Assembly pipeline? Previously, I ran the following scripts and somehow, Putty cause inactive because of the internet connection. I think the pipeline is still generating PolyAsites.fasta by cdbyank ( I think it is the last step of Pasa alignment assembly). 

~/PASApipeline.v2.4.1/Launch_PASA_pipeline.pl \

   -c alignAssembly.config -C -R -g Gbi_chr.fa \

   -t transcripts.fasta.clean -T -u transcripts.fasta \

   --ALIGNERS gmap --CPU 20 \

   --TDN tdn.accs

If I want to resume, which parameter should i get rid of from above scripts (or) which parameter should i add? Could someone help me to fix this? Thank you.

Regards,

Zin

[Zin Win Latt]

When I re-ran the above script, I found the following error.

-- Skipping CMD: /home/zwl/PASApipeline.v2.4.1/scripts/PASA_transcripts_and_assemblies_to_GFF3.dbi -M '/tmp/mydb_pasa.sqlite' -f -A -P gmap -T  > mydb_pasa.sqlite.failed_gmap_alignments.gtf, checkpoint [/home/zwl/test/__pasa_mydb_pasa.sqlite_SQLite_chkpts/mydb_pasa.sqlite.failed_gmap_alignments.gtf.ok] exists.
* [Fri Aug  6 16:49:52 2021] Running CMD: /home/zwl/PASApipeline.v2.4.1/scripts/polyA_site_transcript_mapper.dbi -M '/tmp/mydb_pasa.sqlite' -c transcripts.fasta.cln -g Gbi_chr.fa -t transcripts.fasta > pasa_run.log.dir/polyAsite_analysis.out
DBD::SQLite::db do failed: no such table: transcriptPolyA at /home/zwl/PASApipeline.v2.4.1/PerlLib/DB_connect.pm line 221.
failed query: <delete from transcriptPolyA >    values:
Errors: no such table: transcriptPolyA
 at /home/zwl/PASApipeline.v2.4.1/PerlLib/DB_connect.pm line 233.
        DB_connect::RunMod(DB_connect=HASH(0x2af9af4cf428), "delete from transcriptPolyA ") called at /home/zwl/PASApipeline.v2.4.1/scripts/polyA_site_transcript_mapper.dbi line 507
        main::clear_polyA_db_tables() called at /home/zwl/PASApipeline.v2.4.1/scripts/polyA_site_transcript_mapper.dbi line 76
Error, cmd: /home/zwl/PASApipeline.v2.4.1/scripts/polyA_site_transcript_mapper.dbi -M '/tmp/mydb_pasa.sqlite' -c transcripts.fasta.cln -g Gbi_chr.fa -t transcripts.fasta > pasa_run.log.dir/polyAsite_analysis.out died with ret 512 No such file or directory at /home/zwl/PASApipeline.v2.4.1/PerlLib/Pipeliner.pm line 187.
        Pipeliner::run(Pipeliner=HASH(0x2b2b70103070)) called at /home/zwl/PASApipeline.v2.4.1/Launch_PASA_pipeline.pl line 1044

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[Brian Haas]

hi - it looks like it's not finding the database that should be listed in the config file.  For sqlite, make sure it's a /full/path/to/your/pasa_db.sqlite file.

hope this helps,

~brian

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Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas