Question: BLAST Database creation error
0
gravatar for sahilbioinf0
8 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 • 241 views
ADD COMMENTlink modified 8 months ago by RamRS30k • written 8 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 8 months ago • written 8 months ago by genomax91k

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

enter image description here

ADD REPLYlink written 8 months ago by sahilbioinf00

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

ADD REPLYlink written 8 months ago by genomax91k

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 8 months ago by RamRS30k
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