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Blast database built error
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
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written by Ap1438 • 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.

• 0 views • link
written by Ap1438 • Ap1438

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.

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written by GenoMax GenoMax

Thanks for your valuable time and information.

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written by Ap1438 • 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.

• 0 views • link
written by Ap1438 • Ap1438

1 answer

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)

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written by Yannick Wurm Yannick Wurm

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.

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written by Ap1438 • Ap1438

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