Difference between revisions of "Prokka"

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

Revision as of 16:57, 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
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