DECONSEQ error: cannot find all database files

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marongi...@gmail.com

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Mar 20, 2016, 12:20:29 PM3/20/16

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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/".