Question: DECONSEQ error: cannot find all database files
2
gravatar for marongiu.luigi
3.7 years ago by
Germany, Mannheim, UMM
marongiu.luigi420 wrote:

Dear all, I created a database of human chromosomes using the ftp.ncbi.nlm.nih.gov/genomes repository. The database was created in the folder refChr and contained the files:

hs_ref_GRCh38_p2.amb  hs_ref_GRCh38_p2.pac   hs_ref_GRCh38_p2.sa
hs_ref_GRCh38_p2.ann  hs_ref_GRCh38_p2.rbwt  hs_ref_GRCh38_p2_split.fa
hs_ref_GRCh38_p2.bwt  hs_ref_GRCh38_p2.rpac  hs_ref_GRCh38_p2_split.fa.log
hs_ref_GRCh38_p2.fa   hs_ref_GRCh38_p2.rsa   hs_ref_GRCh38_p2_split_PS.fa.fasta

I then modified the DECONSEQ config file DeconSeqConfig.pm in order to point to the right database with the lines:

use constant DBS => {hs_ref_GRCh38_p2 => {name => 'Human Reference GRCh38',  
db => 'hs_ref_GRCh38_p2'}, ...
use constant DB_DEFAULT => 'refChr';

and then I ran DECONSEQ as follows:

perl /usr/local/lib/Deconseq/deconseq.pl -f fu_1.fq -dbs ./refChr/hs_ref_GRCh38_p2 -i 90 -c 90 -out_dir DECONSEQ

where fu_1.fq is the file to be analyzed but I obtained:

ERROR: database "./refChr/hs_ref_GRCh38_p2" does not exist in config file.

When running:

perl /usr/local/lib/Deconseq/deconseq.pl -f fu_1.fq -dbs hs_ref_GRCh38_p2 -i 90 -c 90 -out_dir DECONSEQ

the result was:

ERROR: cannot find all database files for database "hs_ref_GRCh38_p2" in dir "db/".

Could you please tell what I am getting wrong?
Thanks
Luigi

sequence • 1.7k views
ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by marongiu.luigi420
2
gravatar for marongiu.luigi
3.7 years ago by
Germany, Mannheim, UMM
marongiu.luigi420 wrote:

I was told by Dr Frost (Cambridge) that the issue was simply in the relative paths to use, therefore the DeconSeqConfig.pm should be modified as follows (on my machine):

...
use constant DB_DIR => '/usr/local/lib/Deconseq/refChr/';
...
use constant PROG_DIR => '/usr/local/lib/Deconseq/';      
use constant DBS => {hs_ref_GRCh38_p2 => {name => 'Human Reference GRCh38',  
                               db => 'hs_ref_GRCh38_p2'},           
...

Query solved
L

ADD COMMENTlink written 3.7 years ago by marongiu.luigi420
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