Prokka - Revision history

Rf at 16:11, 10 August 2016

2016-08-10T16:11:32Z

Rf at 16:10, 10 August 2016

2016-08-10T16:10:12Z

Rf at 15:00, 10 August 2016

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Rf at 14:09, 10 August 2016

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Rf at 14:06, 10 August 2016

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Rf at 13:30, 10 August 2016

2016-08-10T13:30:55Z

Rf at 13:20, 10 August 2016

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Rf at 13:02, 10 August 2016

2016-08-10T13:02:03Z

Rf at 12:57, 10 August 2016

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Rf at 15:58, 7 June 2016

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@@ Line 105: / Line 105: @@
 * <name>.'''.tbl''': Feature Table file, used by "tbl2asn" to create the .sqn file.
 * <name>'''.err''': Unacceptable annotations - the NCBI discrepancy report.
-* <name>'''.log''': Contains all the output that Prokka produced during its run. This is a record of what settings you used, even if the --quiet option was enabled.
+* <name>'''.log''': Contains all the output that Prokka produced during its run. This is a record of what settings you used, even if the --quiet option was enabled. This file will be almst the same as the qsub jobscript output file.
 * <name>'''.txt''': Statistics relating to the annotated features found

← Older revision		Revision as of 16:10, 10 August 2016
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	* If given a fragmented scaffold file (typically from a de-novo assembler), prokka will refer to each scaffold / contigs as "nodes".		* If given a fragmented scaffold file (typically from a de-novo assembler), prokka will refer to each scaffold / contigs as "nodes".
		+	* prokka's putput files will be given a standard name based on the date, so it is quite important to store prokka output in a subdirectory using the '''-outdir''' command so as to avoid overwriting results from other prokka runs.

		+	Here is a list of output files which should be found in the subdirectory defined by the '''--outdir''' option:
		+
		+	* <name>'''.gff''': the master annotation in GFF3 format, containing both sequences and annotations. It can be viewed directly in Artemis or IGV.
		+	* <name>'''.gbk''': the standard Genbank file derived from the master .gff. If the input to prokka was a multi-FASTA, then this will be a multi-Genbank, with one record for each sequence.
		+	* <name>.'''.fna''': Nucleotide FASTA file of the input contig sequences.
		+	* <name>.'''.faa''': Protein FASTA file of the translated CDS sequences.
		+	* <name>.'''ffn''': Nucleotide FASTA file of all the annotated sequences, not just CDS.
		+	* <name>.'''.sqn''': ASN1 format "Sequin" file for submission to Genbank. It needs to be edited to set the correct taxonomy, authors, related publication etc.
		+	* <name>.'''fsa''': Nucleotide FASTA file of the input contig sequences, used by "tbl2asn" to create the .sqn file. It is mostly the same as the .fna file, but with extra Sequin tags in the sequence description lines.
		+	* <name>.'''.tbl''': Feature Table file, used by "tbl2asn" to create the .sqn file.
		+	* <name>'''.err''': Unacceptable annotations - the NCBI discrepancy report.
		+	* <name>'''.log''': Contains all the output that Prokka produced during its run. This is a record of what settings you used, even if the --quiet option was enabled.
		+	* <name>'''.txt''': Statistics relating to the annotated features found

	= Installation issues (sysadmins only) =		= Installation issues (sysadmins only) =

@@ Line 10: / Line 10: @@
 == Example jobscript for prokka ==
   #!/bin/bash
   #$ -cwd
@@ Line 17: / Line 19: @@
   #$ -q marvin.q
   #$ -pe multi 16
   DIR=$
-  prokka --fast --cpus $NSLOTS --outdir
+ # some quick "argument accounting"
 == prokka's standard help file ==

@@ Line 7: / Line 7: @@
 Prokka's manual is [http://bioinformatics.net.au/prokka-manual.html here]
 == Example jobscript for prokka ==
@@ Line 77: / Line 76: @@
     --notrna          Don't run tRNA search (default OFF)
     --rnammer         Prefer RNAmmer over Barrnap for rRNA prediction (default OFF)

@@ Line 11: / Line 11: @@
 == Example jobscript for prokka ==
-#!/bin/bash
+ #!/bin/bash
-#$ -cwd
+ #$ -cwd
-#$ -j y
+ #$ -j y
-#$ -S /bin/bash
+ #$ -S /bin/bash
-#$ -V
+ #$ -V
-#$ -q marvin.q
+ #$ -q marvin.q
-#$ -pe multi 16
+ #$ -pe multi 16
-DIR=$
+ DIR=$
-prokka --fast --cpus $NSLOTS --outdir
+ prokka --fast --cpus $NSLOTS --outdir
 == prokka's standard help file ==

← Older revision		Revision as of 13:30, 10 August 2016
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	Prokka's manual is [http://bioinformatics.net.au/prokka-manual.html here]		Prokka's manual is [http://bioinformatics.net.au/prokka-manual.html here]
		+
		+
		+	== Example jobscript for prokka ==
		+
		+	#!/bin/bash
		+	#$ -cwd
		+	#$ -j y
		+	#$ -S /bin/bash
		+	#$ -V
		+	#$ -q marvin.q
		+	#$ -pe multi 16
		+	DIR=$
		+	prokka --fast --cpus $NSLOTS --outdir

	== prokka's standard help file ==		== prokka's standard help file ==

← Older revision		Revision as of 13:20, 10 August 2016
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−	= prokka's standard help file =	+	= Usage =
		+
		+	Prokka's manual is [http://bioinformatics.net.au/prokka-manual.html here]
		+
		+	== prokka's standard help file ==

	Name:		Name:

@@ Line 6: / Line 6: @@
 = prokka's standard help file =
   Name:
     Prokka 1.12-beta by Torsten Seemann <torsten.seemann@gmail.com>
@@ Line 125: / Line 121: @@
   [16:55:01] * HMMs: HAMAP
   [16:55:01] * CMs: Bacteria Viruses

← Older revision		Revision as of 12:57, 10 August 2016
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	genome annotator for bacterial circular genomes.		genome annotator for bacterial circular genomes.
		+
		+
		+	= prokka's standard help file =
		+
		+	[ramon@marvin ~]$ prokka
		+	[13:52:03] Appending to PATH: /usr/local/Modules/modulefiles/tools/prokka/gitv1_8f07048/bin/../binaries/linux
		+	[13:52:03] Appending to PATH: /usr/local/Modules/modulefiles/tools/prokka/gitv1_8f07048/bin/../binaries/linux/../common
		+	[13:52:03] Appending to PATH: /usr/local/Modules/modulefiles/tools/prokka/gitv1_8f07048/bin
		+	Name:
		+	Prokka 1.12-beta by Torsten Seemann <torsten.seemann@gmail.com>
		+	Synopsis:
		+	rapid bacterial genome annotation
		+	Usage:
		+	prokka [options] <contigs.fasta>
		+	General:
		+	--help This help
		+	--version Print version and exit
		+	--docs Show full manual/documentation
		+	--citation Print citation for referencing Prokka
		+	--quiet No screen output (default OFF)
		+	--debug Debug mode: keep all temporary files (default OFF)
		+	Setup:
		+	--listdb List all configured databases
		+	--setupdb Index all installed databases
		+	--cleandb Remove all database indices
		+	--depends List all software dependencies
		+	Outputs:
		+	--outdir [X] Output folder [auto] (default '')
		+	--force Force overwriting existing output folder (default OFF)
		+	--prefix [X] Filename output prefix [auto] (default '')
		+	--addgenes Add 'gene' features for each 'CDS' feature (default OFF)
		+	--addmrna Add 'mRNA' features for each 'CDS' feature (default OFF)
		+	--locustag [X] Locus tag prefix (default 'PROKKA')
		+	--increment [N] Locus tag counter increment (default '1')
		+	--gffver [N] GFF version (default '3')
		+	--compliant Force Genbank/ENA/DDJB compliance: --addgenes --mincontiglen 200 --centre XXX (default OFF)
		+	--centre [X] Sequencing centre ID. (default '')
		+	Organism details:
		+	--genus [X] Genus name (default 'Genus')
		+	--species [X] Species name (default 'species')
		+	--strain [X] Strain name (default 'strain')
		+	--plasmid [X] Plasmid name or identifier (default '')
		+	Annotations:
		+	--kingdom [X] Annotation mode: Archaea\|Bacteria\|Mitochondria\|Viruses (default 'Bacteria')
		+	--gcode [N] Genetic code / Translation table (set if --kingdom is set) (default '0')
		+	--gram [X] Gram: -/neg +/pos (default '')
		+	--usegenus Use genus-specific BLAST databases (needs --genus) (default OFF)
		+	--proteins [X] FASTA or GBK file to use as 1st priority (default '')
		+	--hmms [X] Trusted HMM to first annotate from (default '')
		+	--metagenome Improve gene predictions for highly fragmented genomes (default OFF)
		+	--rawproduct Do not clean up /product annotation (default OFF)
		+	--cdsrnaolap Allow [tr]RNA to overlap CDS (default OFF)
		+	Computation:
		+	--cpus [N] Number of CPUs to use [0=all] (default '8')
		+	--fast Fast mode - only use basic BLASTP databases (default OFF)
		+	--noanno For CDS just set /product="unannotated protein" (default OFF)
		+	--mincontiglen [N] Minimum contig size [NCBI needs 200] (default '1')
		+	--evalue [n.n] Similarity e-value cut-off (default '1e-06')
		+	--rfam Enable searching for ncRNAs with Infernal+Rfam (SLOW!) (default '0')
		+	--norrna Don't run rRNA search (default OFF)
		+	--notrna Don't run tRNA search (default OFF)
		+	--rnammer Prefer RNAmmer over Barrnap for rRNA prediction (default OFF)

← Older revision		Revision as of 15:58, 7 June 2016
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	= Installation issues (sysadmins only) =		= Installation issues (sysadmins only) =
		+
		+	Prokka can be cloned from github and its first step is of setting up databases, like so:

	> ./prokka --setupdb		> ./prokka --setupdb