Is prokka could run in blast v2.10 ?

[TianZonglin]

It seems NOT! but unfortunately, my previous work used blast v2.10. I installed prokka several months ago, I didn't see there is a big update recently. Anyway, hope you can give me some advice.

[16:23:06] This is prokka 1.13
[16:23:06] Written by Torsten Seemann <[email protected]>
[16:23:06] Homepage is https://github.com/tseemann/prokka
[16:23:06] Local time is Fri Jun 11 16:23:06 2021
[16:23:06] You are yao
[16:23:06] Operating system is linux
[16:23:06] You have BioPerl 1.7.8
Argument "1.7.8" isn't numeric in numeric lt (<) at /home/yao/miniconda3/bin/prokka line 253.
[16:23:06] System has 4 cores.
[16:23:06] Option --cpu asked for 8 cores, but system only has 4
[16:23:06] Will use maximum of 4 cores.
[16:23:06] Annotating as >>> Bacteria <<<
[16:23:06] Generating locus_tag from '/home/yao/Documents/S_uberis/1349.30.fna' contents.
[16:23:06] Setting --locustag DMHLBFEL from MD5 d615bfe5deb7e3631c43a7b5e3d354e5
[16:23:06] Creating new output folder: /home/yao/Documents/S_uberis/22902
[16:23:06] Running: mkdir -p \/home\/yao\/Documents\/S_uberis\/22902
[16:23:06] Using filename prefix: test2.XXX
[16:23:06] Setting HMMER_NCPU=1
[16:23:06] Writing log to: /home/yao/Documents/S_uberis/22902/test2.log
[16:23:06] Command: /home/yao/miniconda3/bin/prokka --proteins /home/yao/Documents/S_uberis/Suberis0140JGenBanFull.gb --outdir /home/yao/Documents/S_uberis/22902 --prefix test2 /home/yao/Documents/S_uberis/1349.30.fna
[16:23:06] Appending to PATH: /home/yao/miniconda3/bin
[16:23:06] Looking for 'aragorn' - found /home/yao/miniconda3/bin/aragorn
[16:23:06] Determined aragorn version is 1.2
[16:23:06] Looking for 'barrnap' - found /home/yao/miniconda3/bin/barrnap
[16:23:06] Determined barrnap version is 0.9
[16:23:06] Looking for 'blastp' - found /home/yao/ncbi-blast-2.10.1+/bin/blastp
[16:23:07] Determined blastp version is 2.10
[16:23:07] Prokka needs blastp 2.2 or higher. Please upgrade and try again.

[wanyuac]

It seems to be an issue of v1.13-3 or inappropriate configuration of the conda package. I installed this version from conda using command conda install -c bioconda prokka and then ran into the same problem of blastp version. However, following the README page of this GitHub repository, I reinstalled Prokka using command conda install -c conda-forge -c bioconda -c defaults prokka, which gave me prokka v1.14.6. Now everything works well.

[TianZonglin]

It seems to be an issue of v1.13-3 or inappropriate configuration of the conda package. I installed this version from conda using command conda install -c bioconda prokka and then ran into the same problem of blastp version. However, following the README page of this GitHub repository, I reinstalled Prokka using command conda install -c conda-forge -c bioconda -c defaults prokka, which gave me prokka v1.14.6. Now everything works well.

Yes, it's clear that pokka v1.13 cannot - run with blast v2.11, and you are right if change to use pokka v1.14 then everything will be fine.