Question: Appending sequences to downloaded NCBI nt database
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gravatar for Biogeek
11 weeks ago by
Biogeek400
Biogeek400 wrote:

I have an issue.

I already have the entire ncbi nt database downloaded which I perform my nulceotide searches on.

I am wishing to add sequences from a .fasta file.

My file format is as follows:

>Allobacillus_halotolerans
GTAATCCGTGAAAGAGAAATCGGCGTTAATTAATTGACAATTGAGAGGAGGTCAACCTCAAATGAGTGAACGCAATAACCGTAAAGTTTACAGTGGTCGTGTTGTTTCTGACAAAGCAGACAAAACAATCACTGTTGTGGTAGAAACGTATAAATTCCATC

I run the command:

$ makeblastdb -in Allobacillus.halotolerans.genome.fasta -dbtype nucl -out allobac_halo-parse_seqids

I get: .nsq, .nsi, .nsd, .nog, .nin, .nhr files out

I compare to the files which exist for the ncbi nt files. Im missing an .nhd, .nhi, .nnd and .nni file. Any idea how to generate those? Contrary, I've produced an .nsd and .nsi file which don't exist for the NCBI nt database. I've looked for information on these formats and there is none. Great.

My main problem is when I try and combine the nt database with my new sequence database with the alias tool

$ blastdb_aliastool -dblist nt allobac_halo -dbtype nucl -title "ntbh" -out ntandbh

I get the following error 'Too many positional arguments (1), the offending value: allobac_halo'. The command is written out and not copied from anywhere, so it can't possibly be a problem with the hyphenation. I've looked at previous answers on the forum which imply my command is correct.

If anyone can share some knowledge, that would be appreciated. Thanking you.

ADD COMMENTlink written 11 weeks ago by Biogeek400

I've worked out I can generate .nhd and .nhi by using the additional option '-hash_index'. Still need to generate .nnd and .nni.

ADD REPLYlink written 11 weeks ago by Biogeek400

Also tried

$ blastdb_aliastool -dblist_file dblistfile -dbtype nucl -title "ntandalh" -out ntandalh

Still failing with error message:

BLAST Database error: BLASTDB alias file creation failed. Some referenced files may be missing

ADD REPLYlink modified 11 weeks ago • written 11 weeks ago by Biogeek400

Enclose the database name in quotes. See example below.

blastdb_aliastool -dblist "nt allobac_halo" -dbtype nucl -title "ntbh" -out ntandbh
ADD REPLYlink modified 11 weeks ago • written 11 weeks ago by GenoMax96k

May I ask, why you want to append this to nt?

ADD REPLYlink written 11 weeks ago by 5heikki9.3k
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