PASA pipeline running error

Question

[Bioblazer]

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)

[Ram]

It looks like you need a database server running on your computer with the sample_mydb_pasa database or you need to provide the credentials to access a server hosting that database.

Answer 1

[h.mon]

The current version (version 2.3.3) of PASA defaults to using SQLITE, so should solve your issue with MySQL. However, the reason I am writing an answer to this old post is to warn you to never run analysis software as root, as you are doing here.

[yanyueyang]

I used lastest versions but get the same error information.could u help me?:)