search

tseemann / prokka

:zap: :aquarius: Rapid prokaryotic genome annotation
843 stars 226 forks source link

Prokka does not recognize blast 2.10 as >= blast 2.8 #449

Closed natachacouto closed 4 years ago

natachacouto commented 4 years ago

Hey Torsten,

Just upgraded Blast to version 2.10 and I get the following message when I try to run prokka --setupdb [13:34:45] Appending to PATH: /usr/local/Cellar/prokka/1.14.0/bin [13:34:45] Cleaning databases in /usr/local/Cellar/prokka/1.14.0/db [13:34:45] Cleaning complete. [13:34:45] Looking for 'makeblastdb' - found /usr/local/bin/makeblastdb [13:34:45] Determined makeblastdb version is 2.10 [13:34:45] Prokka needs makeblastdb 2.8 or higher. Please upgrade and try again.

Can you help me with this?

turpinpl commented 4 years ago

natachacouto, I just ran into the same problem. Were you able to come up with a solution?

gaboentropy commented 4 years ago

Apparently this was fixed in prokka 1.14.5, but homebrew continues installing 1.14.0 If I knew anyting about homebrew I'd change it, but I don't have the time to learn right now.

tseemann commented 4 years ago

Thanks for reminding me I fixed it before I went on long holidays/vacation.

I see i never got the brew recipe accepted due to weird errors: https://github.com/brewsci/homebrew-bio/pull/831

gaboentropy commented 4 years ago

Hum. In my mac, when I install. by hand, the newest prokka, it fails because macs use an older perl version. In the meantime I changed the line in prokka referring to the minimum blastp and makeblastdb versions to 2.0 (I know that can bring trouble, but I did not have time to try more stuff). Maybe make perl a requirement so that a newer perl is installed by homebrew when prokka is installed as well?

Possible solution: Catalina has two versions of perl. With: export VERSIONER_PERL_VERSION=5.28 The newest installed version, 5.28, is used. That one should be compatible with the latest prokka.

SabSN commented 4 years ago

Hi, I have updated Prokka to version 1.14.5, but it still won't accept my blastp version 2.9, giving me the same error described here:

[13:24:38] Looking for 'blastp' - found /home/kma/miniconda3/bin/blastp [13:24:38] Determined blastp version is 002002 from 'blastp: 2.2.31+' [13:24:38] Prokka needs blastp 2.8 or higher. Please upgrade and try again.

Any solutions?

gaboentropy commented 4 years ago

SasSN, That sounds like you truly have a very old blastp version, and that it is such that your prokka is seeing. I installed prokka 1.14.15, finally, and it does accept either of 2.9.0+ and 2.10.0+

mostueve commented 4 years ago

Hi, I am having the same problem with a conda install of Prokka. My blastp version is definitely 2.10.0, prokka version is 1.13 (??).

So I guess I should use another way of installation in order to get the newest version of Prokka?

Edit: I tried installing on Ubuntu 16.04 with the commands supplied, this fails at the cpan BIO::Perl part. I am abandoning prokka for the time being.

tseemann commented 4 years ago

I believe this was fixed a while back in Prokka 1.14. Please upgrade. Try conda update --all --yes or create a new env conda create -n prokka_env prokka>=1.14 ?

jdwinkler-lanzatech commented 4 years ago

Hi,

I'm having the same problem using prokka v. 1.14.6 (from conda) and ncbi-blast+ v. 2.8.1-1+deb10u1. This is in a docker container base on miniconda3, so there shouldn;t be any issues with a broken miniconda installation. I've tried including both blast system-wide and as another conda package included in the environment.

Error message: Could not determine version of blastp - please install version 2.8 or higher

minna-miha commented 3 years ago

Hi, I have updated Prokka to version 1.14.5, but it still won't accept my blastp version 2.9, giving me the same error described here:

[13:24:38] Looking for 'blastp' - found /home/kma/miniconda3/bin/blastp [13:24:38] Determined blastp version is 002002 from 'blastp: 2.2.31+' [13:24:38] Prokka needs blastp 2.8 or higher. Please upgrade and try again.

Any solutions?

How did you update to prokka v 1.14.6? I tried this using a few methods (ex: conda update prokka) but it stays at 1.13.

minna-miha commented 3 years ago

Thanks for reminding me I fixed it before I went on long holidays/vacation.

I see i never got the brew recipe accepted due to weird errors: brewsci/homebrew-bio#831

Is this supposed to be resolved? Because I am having the same issues: prokka won't update beyond 1.13, and when I try to run my script it says I need blastp >2.2, even though I have v 2.10.

I also tried your two suggestions from above: 1) conda update --all --yes (this did not update it, I also tried conda update prokka, which also didn't work) 2) create a new env conda create -n prokka_env prokka>=1.14, this just throws:

PackagesNotFoundError: The following packages are not available from current channels:

  - prokka

Current channels:

  - https://repo.anaconda.com/pkgs/main/linux-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/r/linux-64
  - https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.
971202 commented 3 years ago

Just run on the node

tianrenmaogithub commented 3 years ago

I solved it by changing the script prokka. I changed the MINVERSION of blastp and makeblastdb to 2.1 so my blastp version 2.13 will be higher than 2.1. Try it.

mmcguffi commented 3 years ago

I solved it by changing the script prokka. I changed the MINVERSION of blastp and makeblastdb to 2.1 so my blastp version 2.13 will be higher than 2.1. Try it.

I also had troubles getting prokka updated (using conda installation). Simply changing the script to 2.1 did indeed solve the issue

yangm9 commented 2 years ago

I have tried many methods above to solve this issue, but it did nothing. Finally, I changed MINVER => "2.2" to MINVER => "2.10" in the line 159 and 165 of prokka code file (~/miniconda3/envs/metawrap/bin/prokka in MetaWRAP v1.2.1), respectively. Then, it worked well very much!!!

TristansCloud commented 2 years ago

I solved it by changing the script prokka. I changed the MINVERSION of blastp and makeblastdb to 2.1 so my blastp version 2.13 will be higher than 2.1. Try it.

Just for the noobs like me who took a while to find where the prokka script is:

cd $CONDA_PREFIX/bin
nano prokka
# now within nano
^W # search for this text GETVER  => "blastp -version",
# Change MINVER  => "2.2" to MINVER  => "2.1"
# A few lines down is the option for makeblastdb, do the same change you did for blastp:
# Change MINVER  => "2.2" to MINVER  => "2.1"
YuLanSky commented 2 years ago

This is work! Even you never known about perl, you can DO it if you try!

cd $CONDA_PREFIX/bin nano prokka

now within nano

^W # search for this text GETVER => "blastp -version",

Change MINVER => "2.2" to MINVER => "2.1"

A few lines down is the option for makeblastdb, do the same change you did for blastp:

Change MINVER => "2.2" to MINVER => "2.1"

romaro-gomes commented 2 years ago

I solved it by changing the script prokka. I changed the MINVERSION of blastp and makeblastdb to 2.1 so my blastp version 2.13 will be higher than 2.1. Try it.

Just for the noobs like me who took a while to find where the prokka script is:

cd $CONDA_PREFIX/bin
nano prokka
# now within nano
^W # search for this text GETVER  => "blastp -version",
# Change MINVER  => "2.2" to MINVER  => "2.1"
# A few lines down is the option for makeblastdb, do the same change you did for blastp:
# Change MINVER  => "2.2" to MINVER  => "2.1"

Thanks so much!

jdwinkler-lanzatech commented 1 year ago

Just FYI for everyone: this is not fixed in the latest version of prokka.