I encountered problem when I use the sample to run pasa

[wangzhe...@gmail.com]

Hi all,

       When I use sample data to run pasa, there is some problem, can you help me?

       I used the command line below:

     

       ../scripts/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

       And it's feedback is:

       ## Processing CMD:

09:33:44        CMD: /home/bio_soft/1-test/PASApipeline-2.0.2/scripts/..//scripts/create_mysql_cdnaassembly_db.dbi -c alignAssembly.config -S /home/bio_soft/1-test/PASApipeline-2.0.2/scripts/..//schema/cdna_alignment_mysqlschema

mysql: [Warning] Using a password on the command line interface can be insecure.

ERROR 1067 (42000) at line 111 in file: '/home/bio_soft/1-test/PASApipeline-2.0.2/schema/cdna_alignment_mysqlschema': Invalid default value for 'date'

CMD: /usr/bin/mysql  -uroot -pwangbuliao91 -hlocalhost -Dsample_mydb_pasa1 -e 'source /home/bio_soft/1-test/PASApipeline-2.0.2/scripts/..//schema/cdna_alignment_mysqlschema' failed.

Use of uninitialized value $index in concatenation (.) or string at ../scripts/Launch_PASA_pipeline.pl line 981.

Use of uninitialized value $index in concatenation (.) or string at ../scripts/Launch_PASA_pipeline.pl line 981.

ERROR: The following command died with exit code (256):

/home/bio_soft/1-test/PASApipeline-2.0.2/scripts/..//scripts/create_mysql_cdnaassembly_db.dbi -c alignAssembly.config -S /home/bio_soft/1-test/PASApipeline-2.0.2/scripts/..//schema/cdna_alignment_mysqlschema

Must re-run pipeline starting at index [] via running Launch_PASA_pipeline with parameter '-s ' (exclude param '-C' since db already created)

       How could I do to solve this problem? Thank you!

 

                                                                                                                                                                                                                                                                   wang

[Stefania Bertazzoni]

Hi there, I'm having the very same issue as this guy.
Looking forward for a reply.

I also feel like adding:
1 blat/gmap/fasta correctly in the path
2 connecting to mysql through command line works fine but I assumed that was the issue anyway
3 PASAlite was my next attempt as you sugested to another user having troubles with installation but it seems to me the software is still in his embryo phase and has less capabilities (no BLAT2gff3 converter, no LongOrf extraction etc) so at some stage I'll have to sort this issue out

Any help greatly welcomed

[Brian Haas]

Hi all,

The error:

   '/home/bio_soft/1-test/PASApipeline-2.0.2/schema/cdna_alignment_mysqlschema': Invalid default value for 'date

suggests that either the mysql version is new and has broken some compatibilities.    The version I've been using is:

  mysql  Ver 14.14 Distrib 5.6.25, for osx10.8 (x86_64) using  EditLine wrapper

and PASA has been in use for over a decade now, so my guess is that the newer mysql is causing some trouble.   Try using an earlier mysql version and see if that helps, or you can tweak the schema file:

     PASApipeline-2.0.2/scripts/..//schema/cdna_alignment_mysqlschema

so that it complies with what the new version expects.

I'm hoping to finish PASA-Lite later this year and drop the mysql dependency altogether, but it still requires a lot of work to get there.

best,

~brian

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

 

[Stefania Bertazzoni]

Good Afternoon,

Following up on this. I'm able to confirm the problem disappeard downgrading to :

mysql  Ver 14.14 Distrib 5.6.30, for debian-linux-gnu (x86_64) using  EditLine wrapper


Thanks for the prompt response and for all your work.


Stefania

[Brian Haas]

Great!  Thanks for the update!

~brian

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