Difference between revisions of "Prokka"

From wiki
Jump to: navigation, search
(Created page with "= Introduction = genome annotator for bacterial circular genomes.")
 
Line 2: Line 2:
  
 
genome annotator for bacterial circular genomes.
 
genome annotator for bacterial circular genomes.
 +
 +
 +
= Installation issues (sysadmins only) =
 +
 +
> ./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

Revision as of 15:57, 7 June 2016

Introduction

genome annotator for bacterial circular genomes.


Installation issues (sysadmins only)

> ./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
Retrieved from "http://stab.st-andrews.ac.uk/wiki/index.php?title=Prokka&oldid=349"