Prokka
Introduction
genome annotator for bacterial circular genomes.
Installation issues (sysadmins only)
Prokka can be cloned from github and its first step is of setting up databases, like so:
> ./prokka --setupdb [16:54:57] Appending to PATH: /home/nutria/gitrepos/prokka/bin/../binaries/linux [16:54:57] Appending to PATH: /home/nutria/gitrepos/prokka/bin/../binaries/linux/../common [16:54:57] Appending to PATH: /home/nutria/gitrepos/prokka/bin [16:54:57] Cleaning databases in /home/nutria/gitrepos/prokka/bin/../db [16:54:57] Cleaning complete. [16:54:57] Looking for 'makeblastdb' - found /usr/bin/makeblastdb [16:54:57] Determined makeblastdb version is 2.2 [16:54:57] Making kingdom BLASTP database: /home/nutria/gitrepos/prokka/bin/../db/kingdom/Archaea/sprot [16:54:57] Running: makeblastdb -hash_index -dbtype prot -in \/home\/nutria\/gitrepos\/prokka\/bin\/\.\.\/db\/kingdom\/Archaea\/sprot -logfile /dev/null [16:54:58] Making kingdom BLASTP database: /home/nutria/gitrepos/prokka/bin/../db/kingdom/Bacteria/sprot [16:54:58] Running: makeblastdb -hash_index -dbtype prot -in \/home\/nutria\/gitrepos\/prokka\/bin\/\.\.\/db\/kingdom\/Bacteria\/sprot -logfile /dev/null [16:54:59] Making kingdom BLASTP database: /home/nutria/gitrepos/prokka/bin/../db/kingdom/Mitochondria/sprot [16:54:59] Running: makeblastdb -hash_index -dbtype prot -in \/home\/nutria\/gitrepos\/prokka\/bin\/\.\.\/db\/kingdom\/Mitochondria\/sprot -logfile /dev/null [16:54:59] Making kingdom BLASTP database: /home/nutria/gitrepos/prokka/bin/../db/kingdom/Viruses/sprot [16:54:59] Running: makeblastdb -hash_index -dbtype prot -in \/home\/nutria\/gitrepos\/prokka\/bin\/\.\.\/db\/kingdom\/Viruses\/sprot -logfile /dev/null [16:54:59] Making genus BLASTP database: /home/nutria/gitrepos/prokka/bin/../db/genus/Enterococcus [16:54:59] Running: makeblastdb -hash_index -dbtype prot -in \/home\/nutria\/gitrepos\/prokka\/bin\/\.\.\/db\/genus\/Enterococcus -logfile /dev/null [16:54:59] Making genus BLASTP database: /home/nutria/gitrepos/prokka/bin/../db/genus/Escherichia [16:54:59] Running: makeblastdb -hash_index -dbtype prot -in \/home\/nutria\/gitrepos\/prokka\/bin\/\.\.\/db\/genus\/Escherichia -logfile /dev/null [16:55:00] Making genus BLASTP database: /home/nutria/gitrepos/prokka/bin/../db/genus/Staphylococcus [16:55:00] Running: makeblastdb -hash_index -dbtype prot -in \/home\/nutria\/gitrepos\/prokka\/bin\/\.\.\/db\/genus\/Staphylococcus -logfile /dev/null [16:55:00] Looking for 'hmmpress' - found /usr/bin/hmmpress [16:55:00] Determined hmmpress version is 3.1 [16:55:00] Pressing HMM database: /home/nutria/gitrepos/prokka/bin/../db/hmm/HAMAP.hmm [16:55:00] Running: hmmpress \/home\/nutria\/gitrepos\/prokka\/bin\/\.\.\/db\/hmm\/HAMAP\.hmm Working... done. Pressed and indexed 1463 HMMs (1463 names). Models pressed into binary file: /home/nutria/gitrepos/prokka/bin/../db/hmm/HAMAP.hmm.h3m SSI index for binary model file: /home/nutria/gitrepos/prokka/bin/../db/hmm/HAMAP.hmm.h3i Profiles (MSV part) pressed into: /home/nutria/gitrepos/prokka/bin/../db/hmm/HAMAP.hmm.h3f Profiles (remainder) pressed into: /home/nutria/gitrepos/prokka/bin/../db/hmm/HAMAP.hmm.h3p [16:55:01] Looking for 'cmpress' - found /usr/bin/cmpress [16:55:01] Determined cmpress version is 1.1 [16:55:01] Pressing CM database: /home/nutria/gitrepos/prokka/bin/../db/cm/Viruses [16:55:01] Running: cmpress \/home\/nutria\/gitrepos\/prokka\/bin\/\.\.\/db\/cm\/Viruses Working... done. Pressed and indexed 142 CMs and p7 HMM filters (142 names and 142 accessions). Covariance models and p7 filters pressed into binary file: /home/nutria/gitrepos/prokka/bin/../db/cm/Viruses.i1m SSI index for binary covariance model file: /home/nutria/gitrepos/prokka/bin/../db/cm/Viruses.i1i Optimized p7 filter profiles (MSV part) pressed into: /home/nutria/gitrepos/prokka/bin/../db/cm/Viruses.i1f Optimized p7 filter profiles (remainder) pressed into: /home/nutria/gitrepos/prokka/bin/../db/cm/Viruses.i1p [16:55:01] Pressing CM database: /home/nutria/gitrepos/prokka/bin/../db/cm/Bacteria [16:55:01] Running: cmpress \/home\/nutria\/gitrepos\/prokka\/bin\/\.\.\/db\/cm\/Bacteria Working... done. Pressed and indexed 564 CMs and p7 HMM filters (564 names and 564 accessions). Covariance models and p7 filters pressed into binary file: /home/nutria/gitrepos/prokka/bin/../db/cm/Bacteria.i1m SSI index for binary covariance model file: /home/nutria/gitrepos/prokka/bin/../db/cm/Bacteria.i1i Optimized p7 filter profiles (MSV part) pressed into: /home/nutria/gitrepos/prokka/bin/../db/cm/Bacteria.i1f Optimized p7 filter profiles (remainder) pressed into: /home/nutria/gitrepos/prokka/bin/../db/cm/Bacteria.i1p [16:55:01] Looking for databases in: /home/nutria/gitrepos/prokka/bin/../db [16:55:01] * Kingdoms: Archaea Bacteria Mitochondria Viruses [16:55:01] * Genera: Enterococcus Escherichia Staphylococcus [16:55:01] * HMMs: HAMAP [16:55:01] * CMs: Bacteria Viruses
