Question: Use of Deconseq chromosome libraries
0
gravatar for luigi.marongiu
3.9 years ago by
United Kingdom
luigi.marongiu0 wrote:

Dear all,

I created a database with the human sequences using the following command:

bwa64 index -p hs_ref_GRCh38_p2 -a bwtsw hs_ref_GRCh38_p2_split_PS.fa.fasta > bwa.log 2 >&1

 

This created a series of files that I placed in a subfolder named refChr. The list of files is:

 

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 ran the following command for Deconseq:

 

~$ perl /usr/bin/deconseq.pl -f fu_1.fq -dbs ./refChr/hs_ref_GRCh38_p2 -i 90 -c 90 -out_dir DECONSEQ


But I got the following error:

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

Try 'deconseq -h' for more information.
Exit program.


I tried with '/refChr/...' and 'refChr/...' and also with '...hs_ref_GRCh38_p2.fa' and '...hs_ref_GRCh38_p2.sa' but same error. And I fear to try all possible combinations.
What would be the correct use of Deconseq with the human library to remove the human contaminants?
Thank you

ADD COMMENTlink modified 12 months ago by Biostar ♦♦ 20 • written 3.9 years ago by luigi.marongiu0
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