search

tseemann / prokka

:zap: :aquarius: Rapid prokaryotic genome annotation
822 stars 224 forks source link

prokka issues. Please how do I fix this? #667

Open chimaobi2000 opened 1 year ago

chimaobi2000 commented 1 year ago

Argument "1.7.8" isn't numeric in numeric lt (<) at /usr/bin/prokka line 259. [19:31:53] System has 8 cores. [19:31:53] Will use maximum of 8 cores. [19:31:53] Annotating as >>> Bacteria <<< [19:31:53] The sequence databases have not been indexed. Please run 'prokka --setupdb' first.

please what do i do?

abhijeetsingh1704 commented 1 year ago

This is probably due ot newer installation. If you have installed it on ubuntu, for example, by apt, there will be other errors if you try to setup db. This problem and database setup can be solved by downloading prokka from github as shown in instructions. If you face problem with libidn.so.11 try installing sudo apt install libidn12 and copy libidn.so.12 as libidn.so.11 for my system it was sudo cp /usr/lib/x86_64-linux-gnu/libidn.so.12 /usr/lib/x86_64-linux-gnu/libidn.so.11

after this fix your path or use prokka from your prokka directory them try running prokka --setupdb

devilfrute commented 7 months ago

@abhijeetsingh1704 this is what showing after running > prokka --setupdb any help please? (prokka) vamsi@HP:~$ prokka --setupdb Appending to PATH: /usr/bin Cleaning databases in /home/vamsi/.local/lib/prokka/db Cleaning complete. Looking for 'makeblastdb' - found /usr/bin/makeblastdb Determined makeblastdb version is 002012 from 'makeblastdb: 2.12.0+' Looking for 'hmmpress' - found /usr/bin/hmmpress Determined hmmpress version is 003003 from '# HMMER 3.3.2 (Nov 2020); http://hmmer.org/' Looking for 'cmpress' - found /usr/bin/cmpress Determined cmpress version is 001001 from '# INFERNAL 1.1.4 (Dec 2020)' Pressing CM database: /home/vamsi/.local/lib/prokka/db/cm/Viruses Running: cmpress \/home\/vamsi\/.local\/lib\/prokka\/db\/cm\/Viruses

Error: File existence/permissions problem in trying to open CM file /home/vamsi/.local/lib/prokka/db/cm/Viruses. CM file /home/vamsi/.local/lib/prokka/db/cm/Viruses not found (nor an .i1m binary of it)

Could not run command: cmpress \/home\/vamsi\/.local\/lib\/prokka\/db\/cm\/Viruses

devilfrute commented 7 months ago

@chimaobi2000 is your problem resolved ? , I know its long back. this tool is very important to me ,i want suggestions, thank you.

chimaobi2000 commented 7 months ago

yes its been resolved. had to create an env for prokka On Thursday, February 8, 2024 at 08:31:27 AM GMT+1, devilfrute @.***> wrote:

@chimaobi2000 is your problem resolved ? , I know its long back. this tool is very important to me ,i want suggestions, thank you.

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: @.***>

devilfrute commented 7 months ago

@chimaobi2000 thanks for the reply ☺️, can you please ellobrate cause iam new to linux, thanks!

abhijeetsingh1704 commented 7 months ago

@devilfrute The error is due to permission issue. Try running command with sudo and see what happens.