Error on sample data

[Juan Cerda-Herrera]

Hello,

I am trying to run PASA on Docker with the sample data provided. I am using SQLite as I do not have MySQL. I am following the instructions from the wiki and this is the command I am running:

 docker run --rm -it -v $PWD/tmp:/tmp -v $PWD/sample_data:/home/bhaas/GITHUB/pasapipeline/sample_data pasapipeline/pasapipeline:latest bash -c 'cd /home/bhaas/GITHUB/pasapipeline/sample_data && /usr/local/src/PASApipeline/Launch_PASA_pipeline.pl -c alignAssembly.config -C -R --ALIGNER gmap -g genome_sample.fasta -t all_transcripts.fasta.clean'

This is the error I am getting:

[@viterbi work]$ docker run --rm -it -v $PWD/tmp:/tmp -v $PWD/sample_data:/home/bhaas/GITHUB/pasapipeline/sample_data pasapipeline/pasapipeline:latest bash -c 'cd /home/bhaas/GITHUB/pasapipeline/sample_data && /usr/local/src/PASApipeline/Launch_PASA_pipeline.pl -c alignAssembly.config -C -R --ALIGNER gmap -g genome_sample.fasta -t all_transcripts.fasta.clean'

-connecting to SQLite db: tmp/sample_mydb_pasa

-*** Running PASA pipeine:

* [Thu Sep  7 17:15:24 2023] Running CMD: /usr/local/src/PASApipeline/scripts/create_sqlite_cdnaassembly_db.dbi -c alignAssembly.config -S '/usr/local/src/PASApipeline/schema/cdna_alignment_sqliteschema'

DBI connect('dbname=tmp/sample_mydb_pasa','',...) failed: unable to open database file at /usr/local/src/PASApipeline/scripts/create_sqlite_cdnaassembly_db.dbi line 60.

Can't call method "do" on unblessed reference at /usr/local/src/PASApipeline/scripts/create_sqlite_cdnaassembly_db.dbi line 62.

Error, cmd: /usr/local/src/PASApipeline/scripts/create_sqlite_cdnaassembly_db.dbi -c alignAssembly.config -S '/usr/local/src/PASApipeline/schema/cdna_alignment_sqliteschema' died with ret 65280 No such file or directory at /usr/local/src/PASApipeline/PerlLib/Pipeliner.pm line 187.

Pipeliner::run(Pipeliner=HASH(0x55c95f769ac8)) called at /usr/local/src/PASApipeline/Launch_PASA_pipeline.pl line 1061

I should mentioned that I have installed and ran PASA from source, conda and now docker and ultimately I get this error. I have done this on two different servers as well. Could someone guide me through what is going on in here and how I can solve it?

Thanks! 

[Brian Haas]

Hi,

In your file alignAssembly.config, if the database is set to 

tmp/sample_mydb_pasa

please make it 

/tmp/sample_mydb_pasa

if that's not the issue, we can explore it further

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[Juan Cerda-Herrera]

It looks like that was indeed the error. I was able to run the sample data thought the pipeline, as well as the compare annotation pipeline, which was my primary goal. I want to annotate UTRs and after running it with my data, the files do not appear to annotate the UTRs and the gene models remain unchanged, even if the program finishes successfully. Any reason for that? Is there a specific flag I need to include to add UTRs?

Thanks!

[Brian Haas]

Hi Juan,

It sounds like maybe the identifiers in the annotated gff3 file and those in the genome fasta file used with PASA might not be matching up identically.

Also, be sure to first run the pasa alignment assembly pipeline before then loading in your gene annotations and running the annotation comparison/update steps.

Adding UTRs should be happening at the very least if it's all configured correctly.  

hope this helps,

~b

To view this discussion on the web visit https://groups.google.com/d/msgid/pasapipeline-users/b898f6d8-4e60-4701-87db-0ef4d57e52e9n%40googlegroups.com.