For annotation, I am using PASA pipeline while I am running the following error occurred . Please suggest what is this error ? and how to solve it.
./Launch_PASA_pipeline.pl -c alignAssembly.config -C -R -g ATCC.fasta -t transcript.fasta --ALIGNERS blat,gmap
I followed all the steps given in PASA website. Here I used non-strand specific RNA seq ,while running above command I got error like
enter CMD: /home/abc1/Videos/PASApipeline-2.0.2/sample_data/..//scripts/create_mysql_cdnaassembly_db.dbi -c alignAssembly.config -S /home/abc1/Videos/PASApipeline-2.0.2/sample_data/..//schema/cdna_alignment_mysqlschema
Can't exec "/home/abc1/Videos/PASApipeline-2.0.2/sample_data/..//scripts/create_mysql_cdnaassembly_db.dbi": Permission denied at ./Launch_PASA_pipeline.pl line 978. Use of uninitialized value $index in concatenation (.) or string at ./Launch_PASA_pipeline.pl line 981. Use of uninitialized value $index in concatenation (.) or string at ./Launch_PASA_pipeline.pl line 981.
ERROR: The following command died with exit code (-1):
/home/abc1/Videos/PASApipeline-2.0.2/sample_data/..//scripts/create_mysql_cdnaassembly_db.dbi -c alignAssembly.config -S /home/abc1/Videos/PASApipeline-2.0.2/sample_data/..//schema/cdna_alignment_mysqlschema
Thank you
