Hi,
I'm writing this post because the AutoAug.pl README file is a little bit out of date. An exactly that part which advises to delete -S option from process_gmap_alignments.pl . Because of that, new PASA+GMAP starts complaining on duplicate entry, and asks to rerun pipline at index 4.
The exact error message is:
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DBD::mysql::db do failed: Duplicate entry 'gmap-comp0_c0_seq1_Sample1' for key 2 at /home/user/species/PASA_r2012-06-25/PerlLib//Mysql_connect.pm line 155, <BTAB> line 3.
Undefined subroutine &Scalar::Util::blessed called at /usr/lib/perl5/5.8.8/overload.pm line 89, <BTAB> line 3.
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contig642325 gmap comp0_c0_seq1_Sample1 294 546
1 253 99 1 1
contig642325 gmap comp0_c0_seq1_Sample1 421 540
254 373 99 1 2
scaffold25491 gmap comp100019_c0_seq1_Sample1 8575
6355 62 2284 99 12 2
scaffold25491 gmap comp100019_c0_seq1_Sample1 3901
3815 2285 2371 100 12 3
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my $cmd = "gmap_setup -S -D gmap_db_dir -d $genome_db $genome_db";
I used PASA_r2012-06-25 and GMAP-2012-04-07 (Don't use GMAP beta ver. because it causes segmentation fault).
And one more thing, when using MySQL without root priveleges, use should first create database for pasa (for example:dbname-PASA , user priv> read and write), and write it into conf.txt (as said in PASA readme) and then create a new DB with read and write priveleges with name PASAspeciesname, where species name is the same name you use in --species=speciesname. Then there would be no poblems.
Hope this information would be somehow useful.
Vickie