Question: blast+ 2.10.1+ Failed to create a database
0
gravatar for ievainis
5 months ago by
ievainis0
ievainis0 wrote:

I am very new to blast+. I tried to create a database from my own sequences (not downloading existing databases). The sequences are genomes. I tried to look at manuals how to do it but could not find the answer. This is what I got:

C:\Program Files\NCBI\blast-2.10.1+\bin>makeblastdb -in 1genome.fasta -dbtype nucl -out 1genome


Building a new DB, current time: 06/22/2020 12:40:54
New DB name:   C:\Program Files\NCBI\blast-2.10.1+\bin\1genome
New DB title:  1genome.fasta
Sequence type: Nucleotide
Keep MBits: T
Maximum file size: 1000000000B

No volumes were created.

Error: mdb_env_open: Input/output error

Are there any mistakes? Also I'm wondering, is it possible to create a database from a singe sequence?

blast sequence • 461 views
ADD COMMENTlink modified 5 months ago by scholastic_grade_descent0 • written 5 months ago by ievainis0

Is 1genome.fasta a simple multi-fasta format nucleotide sequence file? What size?

ADD REPLYlink written 5 months ago by genomax92k

Yes, it is multifasta (has 7 sequences inside) and the size is 5,61MB.

ADD REPLYlink written 5 months ago by ievainis0

Is it plain text? i.e. it has not been edited with MSFT Word etc? Have you tried to make a small fasta format sequence file and made sure you are able to make the blast database as a test with that?

ADD REPLYlink written 5 months ago by genomax92k

During yesterday and today, I did: 1) opened the file through text editor and made sure that the sequences are separated (everything was great) 2) downloaded 2.9.0 version just to make sure it is not a bug: this version was able to read the sequences (command prompt told there were 7 sequences which is right) however, no database files were made

Can you tell or give a link on what exact requirements should be met to make a multifasta file to work as database?

ADD REPLYlink written 5 months ago by ievainis0

Hi,

I had this same problem a short while ago. There seems to be a problem with makeblastdb in 2.10.1

To fix it, I downloaded BLAST+ 2.2.30. Finding the distribution appropriate for your OS & the command above on it should work.

ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/

ADD REPLYlink written 5 months ago by scholastic_grade_descent0
1

That is not a valid answer. You are referring to a legacy version of blast that has not been used for years.

ADD REPLYlink written 5 months ago by genomax92k

I also tried 2.9.0 version (I removed 1 longer sequence from the file). this version was able to read the sequences, but no database files were made.

C:\Program Files\NCBI\blast-2.9.0+\bin>makeblastdb -in db.fasta -dbtype nucl -out db

Building a new DB, current time: 06/23/2020 12:37:06 New DB name: C:\Program Files\NCBI\blast-2.9.0+\bin\db New DB title: db.fasta Sequence type: Nucleotide Keep MBits: T Maximum file size: 1000000000B Adding sequences from FASTA; added 6 sequences in 0.0208748 seconds.

ADD REPLYlink written 5 months ago by ievainis0
0
gravatar for genomax
5 months ago by
genomax92k
United States
genomax92k wrote:

Did you try using one simple sequence (take top few lines of the file you have) to make sure that works? How about this minimal variation:

makeblastdb -in 1genome.fasta -dbtype nucl

Since this is Windows not sure if this will apply but does the account you are using blast from have write permissions to C:\Program Files\NCBI\blast-2.9.0+\bin directory? If not you should try to write the database files out to some other directory where you do with -out c:\other_location.

ADD COMMENTlink modified 5 months ago • written 5 months ago by genomax92k

Finally found the problem: command promt was opened on administrator account but not using administrator rights, hence in Windows there was no output. Thank you for your help.

ADD REPLYlink written 5 months ago by ievainis0

I am also facing the same problem..could you please brief what has to be done. I have BLAST 2.10.1+ version and I wanted to do blast against transcriptome data. After writing command, it is showing no volumes created and file do not exist. could you please help me...

ADD REPLYlink written 4 months ago by porko97veeru0
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