Blast database built error
1
0
Entering edit mode
6 weeks ago
makeblastdb -in nt -dbtype nucl -out nt


Building a new DB, current time: 12/09/2021 15:55:27
New DB name:   /home/internal/Databases/NT/NT_Jul2021/nt
New DB title:  nt
Sequence type: Nucleotide
Deleted existing Nucleotide BLAST database named /home/internal/Databases/NT/NT_Jul2021/nt
Keep MBits: T
Maximum file size: 1000000000B

No volumes were created.

Error: mdb_env_open: Function not implemented

this is the command and error. Please help me resolve and create database

blast makeblastdb • 456 views
ADD COMMENT
0
Entering edit mode

Please don't try to create nt databases locally. It is easier to simply download pre-built ones from NCBI as noted below.

There is a solution in this thread that may be applicable (it does not seem like you are using Windows so ignore that solution): makeblastdb Fasta file with 25 sequences gives Error: mdb_env_open: There is not enough space on the disk

ADD REPLY
0
Entering edit mode

its a .fasta file. i tried with
makeblastdb -in nt.fasta -dbtype nucl -blastdb_version 4

It worked.But i am still wondering what is the difference between -blastdb version 4 and other versions.

ADD REPLY
0
Entering edit mode

blastdb version 4 works with older blast+ executables. They will not work with new blast. If you are ok with older blast versions that that will work. If you need to use any taxonomic information then you will need to use a new version of blast and thus a new version (v 5) of the database as well.

ADD REPLY
0
Entering edit mode

Thanks for your valuable time and information.

ADD REPLY
0
Entering edit mode

$ makeblastdb -in nt.fasta -dbtype nucl -blastdb_version 5

Building a new DB, current time: 12/11/2021 15:18:39
New DB name: /home/internal/Databases/NT/NT_July2021_v5_db/nt.fasta
New DB title: nt.fasta
Sequence type: Nucleotide
Keep MBits: T
Maximum file size: 1000000000B

No volumes were created.

Error: mdb_env_open: Function not implemented

I tried with -blastdb version 5 but it shows the same error.

ADD REPLY
2
Entering edit mode
6 weeks ago
Yannick Wurm ★ 2.4k

I suspect there may be some problem with your input file.

Does it exist? Is it FASTA? If it is FASTA, perhaps it has some weird stuff in it - you could try cleaning it through seqtk seq nt > out.fa Are you able to write to the directory you're trying to write in? (test that through touch asdf)

(but if your database name NT refers to NCBI's nt, you should also simply be able to download the formatted blast database)

ADD COMMENT
0
Entering edit mode

Thanks for your valuable time and information .Input file is correct. Its with -builtdb_version.
if i give 4 its working but with 5 its showing error.

ADD REPLY

Login before adding your answer.

Traffic: 1849 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6