For eukaryotic genome annotation , I used PASA pipeline for annotation while running I got the following error How to solve this mysql connection error.
root@abc1-desktop:/home/abc1/Desktop/PASApipeline-2.0.2/sample_data# perl Launch_PASA_pipeline.pl -c alignAssembly.config -R -g genome_sample.fasta -t all_transcripts.fasta.clean -T -u all_transcripts.fasta -f FL_accs.txt --ALIGNERS blat,gmap --CPU 4
## Processing CMD: 1/32
14:20:31 CMD: /home/abc1/Desktop/PASApipeline-2.0.2/sample_data/..//scripts/upload_transcript_data.dbi -M sample_mydb_pasa -t all_transcripts.fasta.clean -f FL_accs.txt
DBI connect('sample_mydb_pasa:localhost # or server.com','user',...) failed: Unknown MySQL server host 'localhost # or server.com' (0) at /home/abc1/Desktop/PASApipeline-2.0.2/sample_data/..//PerlLib/Mysql_connect.pm line 31.
Cannot connect to localhost # or server.com: Unknown MySQL server host 'localhost # or server.com' (0) at /home/abc1/Desktop/PASApipeline-2.0.2/sample_data/..//scripts/upload_transcript_data.dbi line 54.
ERROR: The following command died with exit code (65280):
/home/abc1/Desktop/PASApipeline-2.0.2/sample_data/..//scripts/upload_transcript_data.dbi -M sample_mydb_pasa -t all_transcripts.fasta.clean -f FL_accs.txt
Must re-run pipeline starting at index [1] via running Launch_PASA_pipeline with parameter '-s 1' (exclude param '-C' since db already created)
I used lastest versions but get the same error information.could u help me?:)
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It looks like you need a database server running on your computer with the
sample_mydb_pasadatabase or you need to provide the credentials to access a server hosting that database.