Blast database built error

Question

[Ap1438]

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

[GenoMax]

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

[Ap1438]

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.

[GenoMax]

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.

[Ap1438]

Thanks for your valuable time and information.

[Ap1438]

$ 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.

Answer 1

[Yannick Wurm]

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)

[Ap1438]

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.