Deconseq running error -cannot find db's in config file- but the're there!

[thijmen.b...@wur.nl]

Dear all,

Sorry, I have sent this question just a minute ago to the personal e-mail address mentioned in the manual just found this google group. Looks like I've found a bug, or am I doing something wrong?

I am currently running the stand-alone Deconseq on my computer and I constantly bump into the same error:
ERROR: database "Bacterial_genomes" does not exist in config file.

Off course I made sure the database does exist in the config file:

use constant DB_DIR => 'deconseq_DB/All/';
use constant TMP_DIR => 'Deconseq/temp';
use constant OUTPUT_DIR => 'Deconseq/output';

use constant PROG_NAME => 'bwa64'; # should be either bwa64 or bwaMAC (based on your system architecture)
use constant PROG_DIR => 'Programs/deconseq-standalone-0.4.3'; # should be the location of the PROG_NAME file (use './' if in the same location at the perl script)

use constant DBS => {hsref => {name => 'Human_Reference_GRCh38',
db => 'DB_HS_GRCh38'},
bact => {name => 'Bacterial_genomes',
db => 'DB_BG_bacteria1,DB_BG_bacteria2'},
Drosophila => {name => 'Drosophila',
db => 'DB_DM_drosophila6.21'},
Apisum => {name => 'Apisum',
db => 'DB_AP_2.1b'},
Bombyx => {name => 'Bombyx',
db => 'DB_BM_ASM15162v1'}};
use constant DB_DEFAULT => 'hsref';

I get the same error if I change the order of -dbs. The command I am using:

nohup perl deconseq.pl -i 98 -c 90 -f file.fasta -dbs Bacterial_genomes,Human_Reference_GRCh38 -dbs_retain Drosophila,Apisum,Bombyx > nohupdeconseq.out &

Could this be some kind of bug, how can I solve this?

[thijmen.b...@wur.nl]

SOLVED

It took some time and MANY attempts but for thoe of you interested. The is solved by a combination of:

Changing the config file, and simply kept the names for the DB's and the names to call the names in the command identical like:

Apisum => {name => 'Apisum',

db => 'Apisum'},

And to index the databases I used "bwa" (following the webpage on the manual. But had to change this into bwa64 (initially only 5 files are created, but this needs to be 8) like here: https://groups.google.com/forum/#!topic/edwardslabtools/r-VMLVqWTSU

[loren...@gmail.com]

Quick question. I am having the same error

What is exactly on your 'file.fasta' file? Is that a generic name or what kind of organisms fasta is that. 

Also, what exactly do you do when you chop the files into n-10? 

This is my first time trying this out and I've been having the hardest time to understand the instructions.

Any help is appreciated.