Question: Issue with version of makeblastdb during Prokka installation
0
gravatar for dongyun.jung
13 months ago by
dongyun.jung0 wrote:

Hello,

First of all, it's the very first time for me to use any bioinformatics tools so this could be a dumb question.

Can you explain how to update makeblastdb, one of the binaries for Prokka?

I've been attempting to install Prokka using Ubuntu on Windows 10. I've tried to install it so many times but always stuck in this part:

[16:53:07] Appending to PATH: /home/djung0928/prokka/bin/../binaries/linux
[16:53:07] Appending to PATH: /home/djung0928/prokka/bin/../binaries/linux/../common
[16:53:07] Appending to PATH: /home/djung0928/prokka/bin
[16:53:07] Cleaning databases in /home/djung0928/prokka/db
[16:53:07] Cleaning complete.
[16:53:07] Looking for 'makeblastdb' - found /usr/bin/makeblastdb
**[16:53:11] Determined makeblastdb version is 2.6
[16:53:11] Prokka needs makeblastdb 2.8 or higher. Please upgrade and try again.**

I also tried to get up to date version of it from ncbi multiple times but it still doesn't work.

Anyone can help please?

Thanks very much

prokka makeblastdb • 1.8k views
ADD COMMENTlink modified 11 months ago by pehenriquejp0 • written 13 months ago by dongyun.jung0

I also tried to get up to date version of it from ncbi multiple

How did you try? Which file did you download? How did you install the NCBI-downloaded Blast?

You have to be more detailed, show the commands used.

ADD REPLYlink written 13 months ago by h.mon30k

It the new version in PATH?

ADD REPLYlink written 13 months ago by ATpoint36k

How have you been installing it?

I would strongly advise you do it with conda.

ADD REPLYlink written 13 months ago by Joe17k

I had the same problem. I just changed makeblastdb of bin for another directory to solve the problem.

ADD REPLYlink written 11 months ago by pehenriquejp0
1

Your answer is the same as Mensur's; there is no need to add a new answer in that case.

ADD REPLYlink written 11 months ago by RamRS28k
2
gravatar for Mensur Dlakic
13 months ago by
Mensur Dlakic6.0k
USA
Mensur Dlakic6.0k wrote:

I also tried to get up to date version of it from ncbi multiple times but it still doesn't work.

How exactly did you update blast? NCBI's numbering scheme is very clear, so it should be very easy to select a version higher than 2.6. Just in case, here is a link to version 2.9.

I think it is more likely that your old version is taking precedence even after you re-install. If that's the case, it may help if you install in the same location as old executables. I know, one should not be over-writing programs, but BLAST is free and you can always re-download if something goes wrong.

It seems that you have 2.6, but type this just in case:

makeblastdb -version

On my Linux box it says makeblastdb: 2.2.26+. Next, find where this executable is installed:

which makeblastdb

For me it says /home/bin/makeblastdb. If I were to upgrade to version 2.9, I would download the appropriate file from the link above, unpack it, and move all the executables into /home/bin. If you are not sure how to do this, go to the directory with executables and type:

find . -executable -type f | xargs -i mv {} /home/bin

You should change /home/bin to the location appropriate for your system. Keep in mind that for you this may require sudo privileges.

ADD COMMENTlink written 13 months ago by Mensur Dlakic6.0k
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