BLAST Database error: Database memory map file error

Question

[Martina]

when running the command on MacOS: "makeblastdb -in protein.fa -dbtype prot -parse_seqids" it results in the following error: BLAST Database error: Database memory map file error. I need help to create the database

[peacecreed]

add title when making db. On v2.16, I had the same issue with downloaded db from NCBI ftp. Worked after adding db alias so worth a try

[Mensur Dlakic]

Error reporting 101: if the error mentions memory, you tell us about your computer's memory. Chances are your system falls short there.

[Martina]

I have checked my computer's memory and it seems to have 88GB available.

[Michael]

So this is a Mac Pro (they can be fitted with 64,128, or 196GB RAM, 88GB I haven't seen)? What is the output of "About this Mac"?

And can you please run makeblastdb with only a small single protein sequence to see if the problem is related to DB size or a problem of the binary?

Which version of the binaries did you install? This may have to do with processor type. Try to re-install the MacOS universal binaries from https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ or the ones compiled for your chip (M1,M2: aarch64; Intel: x64).

[Martina]

I am working with a MacBook Air with 8GB, M1 chip. I tried with another small sequence and it gives me the same error. And regarding the version of the binaries, I am not very familiar with these terms so I don't really know what to do with the link you provided. I followed my professor's instructions to install everything. When I run makeblastdb -version it says that is the 2.16.0+ version. Do you think you could give me a hand? Do you need any more information?

[Michael]

If the smaller sequence yields the same error it doesn't have anything to do with the memory. Try to reinstall using this package: https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.16.0+-universal.dmg The universal image should work on both intel and M1 macs. Unfortunately, I am still on intel mac, so unfortunately I cannot reproduce any M-chip related problems.

[Tim]

Did you find the answer to this please?

I find the same on a decent spec Intel mac, using both the correct binaries and the universal one. This is a test of 10 records:

tim@iMac ncbi-blast-2.16.0+ % bin/makeblastdb -in ~/dev/data/sequence/sample.fasta -dbtype prot -out /tmp/delme/blast -title Tim


Building a new DB, current time: 01/20/2025 17:32:27
New DB name:   /tmp/delme/blast
New DB title:  Tim
Sequence type: Protein
Keep MBits: T
Maximum file size: 3000000000B
Adding sequences from FASTA; added 10 sequences in 0.00264096 seconds.


tim@iMac ncbi-blast-2.16.0+ % sudo bin/blastn -query ~/dev/data/sequence/sample.fasta -db /tmp/delme/blast.pdb                  
BLAST Database error: Database memory map file error

[GenoMax]

BLAST Database error: Database memory map file error

You made a protein database but are trying to use blastn (with nucleotide or protein data) against it.

If you have nucleotide data as query then you need to use blastx. If you have protein queries then use blastp.

[Tim]

Thank you for taking the time to help this newbie @genomax. What I should have been using is this, which does work:

bin/makeblastdb -in ~/dev/data/sequence/sample.fasta -dbtype nucl -out /tmp/delme/blast 
blastn -query ~/dev/data/sequence/sample.fasta -db /tmp/delme/blast

[GenoMax]

That makes sense. Thanks for confirming.

[vernisara]

Goodrmorning everyone, I have the same problem, I am trying to built a local BLAST for nucleotide and I downloaded all the .nt file with this command: for i in $(seq -w 0 225); do wget "https://ftp.ncbi.nlm.nih.gov/blast/db/nt.${i}.tar.gz"; done then decompressed them: for f in nt.*.tar.gz; do tar -xvzf "$f"; done an then when I run this : blastdbcmd -db nt -info and I obtain this error: BLAST Database error: Database memory map file error.

The files seems fine and decompressed with all the correct extensions: .nog, .nni, .nnd, .nin, .nhr. I also should have enough memory. Anyone has some ideas to fix this issue? Thank you!!

[Michael]

First, please don't do this, use the update_blastdb.pl command.

Second, as to why this doesn't work this time: Because as of 2025-02-19, the NT database has 228 archives and counting. Another reason to use the update script.

[vernisara]

Thank you! I used this pipeline and it is working right now! I used update_blastdb.pl --decompress nt and now it seems to recognize the database

[lieven.sterck]

on a side note: if you download it directly from NCBI do also download the md5 checksum keys and use them to check the sanity of your downloaded files (they are provided for a reason ;) )

more on topic, can you confirm you also have a file with extension .pal ? (that's the one that ties all those others together to a single DB )

[vernisara]

I downloaded also the md5 checksum, I still don't have the file with the extension .pal but it seems to work at the moment, do you thin it's a problem if I don't have it? Thank you!

[lieven.sterck]

also not a .nal (since you're using the nucleotide DB) ? maybe it's not needed anymore ...

[Mensur Dlakic]

I also should have enough memory. Anyone has some ideas to fix this issue?

The only idea I have is that you don't have enough memory. What exactly does it mean that you should have enough memory? 256+ GB? I don't know what the current memory requirement is for a local BLAST run, but it wouldn't surprise me if it is inching towards half a TB.

Assuming that you have enough memory, how long does it take from the moment you hit Enter on your command line until the error shows up?

[vernisara]

I am working from a remote university server and I have 17 tera so I think is enough to run a local blast, before the error it was immediate, now it seems to work! thank you!

Answer 1

[Albert]

I had the same problem. The path to the fasta file contained a space. After moving the fasta file to a folder without spaces in the path I was able to run the makeblastdb command.

Answer 2

[tony_s]

I also had this error. The fasta source file was on an external drive but when I moved it to my internal drive in my home folder the makeblastdb command worked just fine. I suspect it's a permissions error for using external drives (Sequoia, Mac mini M4, 24 GB RAM) but I'm not certain. I set the external drive's permissions to "Ignore ownership on this volume" using "Get Info" in the finder, but that did not resolve the problem.