Question: BLAST Database creation error
0
gravatar for sahilbioinf0
12 months ago by
sahilbioinf00 wrote:

I managed to download a nr ref sequence from ncbi ftp using the command..

wget 'ftp://ftp.ncbi.nlm.nih.gov/blast/db/nr.*.tar.gz'
cat nr.*.tar.gz | tar -zxvi -f - -C .

I have also created database using this command:

makeblastdb -dbtype prot -out /home/ska/Downloads/Nr/nr -in /home/namita/Downloads/Nr/nr -parse_seqids

When I used this command:

blastp -db /home/namita/Downloads/Nr/nr  -word_size 7 -query /home/ska/Downloads/sequence.fasta -out /home/namita/Downloads/analysis/MF.txt  -outfmt 6 -max_target_seqs 2

I am getting this error:

BLAST Database error: No alias or index file found for nucleotide database [/home/namita/Downloads/Nr/nr] in search path [/home/ska/Downloads/ncbi-blast-2.6.0+/bin:$/home/ska/Downloads/Nr/nr:]

Please help ??

sequence • 284 views
ADD COMMENTlink modified 12 months ago by _r_am32k • written 12 months ago by sahilbioinf00

When you download preformatted databases you don't need to do makeblastdb. Just unarchive all nr* files and keep them in the same directory. Use the basename of the index when you search.

ADD REPLYlink modified 12 months ago • written 12 months ago by GenoMax95k

But when I unarchived it I only get single file of 143.2 gb.

enter image description here

ADD REPLYlink written 12 months ago by sahilbioinf00

You should not do this cat nr..tar.gz. Just get the files and unarchive.

ADD REPLYlink written 12 months ago by GenoMax95k

Drag+drop pictures to the website does not equal uploading them. See instructions on how to upload images here: How to add images to a Biostars post

ADD REPLYlink written 12 months ago by _r_am32k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2321 users visited in the last hour
_