Question: makeblastdb; it says 'Adding sequences from FASTA; added 27200239 sequences in 55053 seconds.'
0
gravatar for junghyunjulie
3.9 years ago by
United States
junghyunjulie0 wrote:

I am trying to index nt database. I have used makeblastdb so far and it has worked perfectly. But now when I tried to index my NT database, I got this message - "Adding sequences from FASTA; added 27200239 sequences in 55053 seconds." I did specify output file path, but the result is not there.

./makeblastdb -in <nt path here> -title nt3.2_new -dbtype nucl -out <output path here>/nt3.2New/ -parse_seqids

Above is the command I used(<nt path here> and <output path here> I have the right path but just abbreiviated). I found the similar issue posted here. But the op found where the result file is without any explanation. I am using grep to see if I can find where it is but no luck. Any ideas or suggestions would be highly appreciated. Thanks!

makeblastdb • 1.3k views
ADD COMMENTlink modified 3.9 years ago by SES8.2k • written 3.9 years ago by junghyunjulie0
1

Is there a reason you are making your own when NCBI makes pre-made indexes for NT available? ftp://ftp.ncbi.nih.gov/blast/db/

ADD REPLYlink written 3.9 years ago by genomax72k

Yes, I am using filtered NT which means I filter out environmental samples. So I have to index it on my own. 

ADD REPLYlink written 3.9 years ago by junghyunjulie0
1

If you have a list of GI's for the env samples you could use the blastdb_aliastool to create the subset blast database.

Not sure if it would be any faster since you already have the filtered NT files available.

ADD REPLYlink written 3.9 years ago by genomax72k
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