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