Entering edit mode
11 weeks ago
Martina
•
0
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
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
Error reporting 101: if the error mentions memory, you tell us about your computer's memory. Chances are your system falls short there.
I have checked my computer's memory and it seems to have 88GB available.
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).
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?
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.