Error in which PASA scripts/assembly_db_loader.dbi can't connect to SQLite database

[Kris Alavattam]

Hi Brian,

I'm encountering an error after trying to relaunch PASA: the scripts/assembly_db_loader.dbi will not connect to the sqlite database. However, the database exists at the path listed below and is not an empty file. Do you have any advice on this?

Thanks,

Kris

Final portion of STDERR:

* [Tue Dec 27 08:54:15 2022] Running CMD: /usr/local/src/PASApipeline/scripts/assembly_db_loader.dbi -M '/home/kalavatt/tsukiyamalab/kalavatt/2022_transcriptome-construction/results/2022-1201/files_PASA_un_trim_trim-rcor_stringent-alignment-overlap-50.0/trinity_5781-5782_Q_IP_merged.un_multi-hit-mode_10_Local/trinity_5781-5782_Q_IP_merged.un_multi-hit-mode_10_Local.pasa.sqlite' > pasa_run.log.dir/alignment_assembly_loading.out
DBI connect('database=/home/kalavatt/tsukiyamalab/kalavatt/2022_transcriptome-construction/results/2022-1201/files_PASA_un_trim_trim-rcor_stringent-alignment-overlap-50.0/trinity_5781-5782_Q_IP_merged.un_multi-hit-mode_10_Local/trinity_5781-5782_Q_IP_merged.un_multi-hit-mode_10_Local.pasa.sqlite;host=localhost','root',...) failed: unable to open database file at /usr/local/src/PASApipeline/PerlLib/DB_connect.pm line 72.
Cannot connect to /home/kalavatt/tsukiyamalab/kalavatt/2022_transcriptome-construction/results/2022-1201/files_PASA_un_trim_trim-rcor_stringent-alignment-overlap-50.0/trinity_5781-5782_Q_IP_merged.un_multi-hit-mode_10_Local/trinity_5781-5782_Q_IP_merged.un_multi-hit-mode_10_Local.pasa.sqlite: unable to open database file at /usr/local/src/PASApipeline/scripts/assembly_db_loader.dbi line 51.
Error, cmd: /usr/local/src/PASApipeline/scripts/assembly_db_loader.dbi -M '/home/kalavatt/tsukiyamalab/kalavatt/2022_transcriptome-construction/results/2022-1201/files_PASA_un_trim_trim-rcor_stringent-alignment-overlap-50.0/trinity_5781-5782_Q_IP_merged.un_multi-hit-mode_10_Local/trinity_5781-5782_Q_IP_merged.un_multi-hit-mode_10_Local.pasa.sqlite' > pasa_run.log.dir/alignment_assembly_loading.out died with ret 65280 No such file or directory at /usr/local/src/PASApipeline/PerlLib/Pipeliner.pm line 187.
        Pipeliner::run(Pipeliner=HASH(0x55d8719355c0)) called at /usr/local/src/PASApipeline/Launch_PASA_pipeline.pl line 1047

[Brian Haas]

Hi Kris,

so if you run:

   ls /home/kalavatt/tsukiyamalab/kalavatt/2022_transcriptome-construction/results/2022-1201/files_PASA_un_trim_trim-rcor_stringent-alignment-overlap-50.0/trinity_5781-5782_Q_IP_merged.un_multi-hit-mode_10_Local/trinity_5781-5782_Q_IP_merged.un_multi-hit-mode_10_Local.pasa.sqlite

does it show the file?

If yes, then maybe the path is too long for it.  Try copying the file to /tmp and see if it'll find it there.

best,

~b

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