noisrevni
commented
2 years ago BTW, When I install prokka v14.5 via "prokka-1.14.5.tar.gz", it can't continue with makeblastdb v2.12, showed "Prokka needs makeblastdb 2.2 or higher.":
(torsten) cyl@cyl-TravelMate-P249-MG:~/prokka/prokka-1.14.5/bin$ prokka --setupdb [15:24:48] Appending to PATH: /home/cyl/anaconda3/envs/torsten/bin [15:24:48] Cleaning databases in /home/cyl/anaconda3/envs/torsten/bin/../db [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/kingdom/Archaea/sprot.phd [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/kingdom/Archaea/sprot.phi [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/kingdom/Archaea/sprot.phr [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/kingdom/Archaea/sprot.pin [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/kingdom/Archaea/sprot.pog [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/kingdom/Archaea/sprot.psd [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/kingdom/Archaea/sprot.psi [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/kingdom/Archaea/sprot.psq [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/kingdom/Bacteria/sprot.phd [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/kingdom/Bacteria/sprot.phi [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/kingdom/Bacteria/sprot.phr [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/kingdom/Bacteria/sprot.pin [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/kingdom/Bacteria/sprot.pog [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/kingdom/Bacteria/sprot.psd [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/kingdom/Bacteria/sprot.psi [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/kingdom/Bacteria/sprot.psq [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/kingdom/Mitochondria/sprot.phd [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/kingdom/Mitochondria/sprot.phi [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/kingdom/Mitochondria/sprot.phr [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/kingdom/Mitochondria/sprot.pin [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/kingdom/Mitochondria/sprot.pog [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/kingdom/Mitochondria/sprot.psd [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/kingdom/Mitochondria/sprot.psi [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/kingdom/Mitochondria/sprot.psq [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/kingdom/Viruses/sprot.phd [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/kingdom/Viruses/sprot.phi [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/kingdom/Viruses/sprot.phr [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/kingdom/Viruses/sprot.pin [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/kingdom/Viruses/sprot.pog [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/kingdom/Viruses/sprot.psd [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/kingdom/Viruses/sprot.psi [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/kingdom/Viruses/sprot.psq [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/genus/Enterococcus.phd [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/genus/Enterococcus.phi [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/genus/Enterococcus.phr [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/genus/Enterococcus.pin [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/genus/Enterococcus.pog [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/genus/Enterococcus.psd [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/genus/Enterococcus.psi [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/genus/Enterococcus.psq [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/genus/Escherichia.phd [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/genus/Escherichia.phi [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/genus/Escherichia.phr [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/genus/Escherichia.pin [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/genus/Escherichia.pog [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/genus/Escherichia.psd [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/genus/Escherichia.psi [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/genus/Escherichia.psq [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/genus/Staphylococcus.phd [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/genus/Staphylococcus.phi [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/genus/Staphylococcus.phr [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/genus/Staphylococcus.pin [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/genus/Staphylococcus.pog [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/genus/Staphylococcus.psd [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/genus/Staphylococcus.psi [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/genus/Staphylococcus.psq [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/hmm/HAMAP.hmm.h3f [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/hmm/HAMAP.hmm.h3i [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/hmm/HAMAP.hmm.h3m [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/hmm/HAMAP.hmm.h3p [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/cm/Bacteria.i1f [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/cm/Bacteria.i1i [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/cm/Bacteria.i1m [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/cm/Bacteria.i1p [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/cm/Viruses.i1f [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/cm/Viruses.i1i [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/cm/Viruses.i1m [15:24:48] Deleting unwanted file: /home/cyl/anaconda3/envs/torsten/bin/../db/cm/Viruses.i1p [15:24:48] Cleaning complete. [15:24:48] Looking for 'makeblastdb' - found /home/cyl/anaconda3/envs/torsten/bin/makeblastdb [15:24:48] Determined makeblastdb version is 2.12 [15:24:48] Prokka needs makeblastdb 2.2 or higher. Please upgrade and try again.
Hello Tessmann,
I installed prokka via anaconda (only version 1.13 available), it showed:
(torsten) cyl@cyl-TravelMate-P249-MG:~/batch1/spades/fasta$ prokka --proteins TIGR4_sequence.gb --outdir /home/cyl/batch1/prokka/HX001 --prefix HX001 HX001.fasta [10:11:39] This is prokka 1.13 [10:11:39] Written by Torsten Seemann <torsten.seemann@gmail.com> [10:11:39] Homepage is https://github.com/tseemann/prokka [10:11:39] Local time is Sat May 7 10:11:39 2022 [10:11:39] You are cyl [10:11:39] Operating system is linux [10:11:39] You have BioPerl 1.006924 [10:11:39] System has 4 cores. [10:11:39] Option --cpu asked for 8 cores, but system only has 4 [10:11:39] Will use maximum of 4 cores. [10:11:39] Annotating as >>> Bacteria <<< [10:11:39] Generating locus_tag from 'HX001.fasta' contents. [10:11:39] Setting --locustag PMLOIHBL from MD5 965821b5097e171e830a4d95d3c3b9d5 [10:11:39] Creating new output folder: /home/cyl/batch1/prokka/HX001 [10:11:39] Running: mkdir -p \/home\/cyl\/batch1\/prokka\/HX001 [10:11:39] Using filename prefix: HX001.XXX [10:11:39] Setting HMMER_NCPU=1 [10:11:39] Writing log to: /home/cyl/batch1/prokka/HX001/HX001.log [10:11:39] Command: /home/cyl/anaconda3/envs/torsten/bin/prokka --proteins TIGR4_sequence.gb --outdir /home/cyl/batch1/prokka/HX001 --prefix HX001 HX001.fasta [10:11:39] Appending to PATH: /home/cyl/anaconda3/envs/torsten/bin [10:11:39] Looking for 'aragorn' - found /home/cyl/anaconda3/envs/torsten/bin/aragorn [10:11:39] Determined aragorn version is 1.2 [10:11:39] Looking for 'barrnap' - found /home/cyl/anaconda3/envs/torsten/bin/barrnap [10:11:39] Determined barrnap version is 0.9 [10:11:39] Looking for 'blastp' - found /home/cyl/anaconda3/envs/torsten/bin/blastp [10:11:40] Determined blastp version is 2.12 [10:11:40] Prokka needs blastp 2.2 or higher. Please upgrade and try again.