Prokka ChangeLog ---------------- v1.12 - 14 Mar 2017 * Lots of bug fixes. * Improved documentation, especially installation * Newer static binaries for Linux and MacOS * Updated protein and ncRNA databases * Better default unique locus_tag based on contig MD5 * Option --cdsrnaolap to allow tRNA/rRNA overlapping CDS * Option --addmrna to add mRNA features for each CDS * Option --noanno to just predict CDS coordinates but not /product * Option --fast to just BLAST sprot and ignore slower HMMs * Better log file * New .tsv output of annotated features v1.11 - 15 Feb 2015 * Option --proteins now supports .GBK/.EMBL files directly! * Support for user supplied HMM via --hmms [Connor Driscoll] * Add Prodigal -c option when in metagenome mode [Daan Speth] * Wierd coordinate errors with long Spades contig names [Stephan Pabinger] * Replaced dodgy OSX aragorn binary [Yevgeny Nikolaichik] * Handle translation table 25 [Mads Albertsen] * Fix semantically incorrect GFF3 output [Marc Hoeppner] * Fix contigs with pipe characters from Quiver [Vaughn Cooper] * Keep original contig ordering [Jane Hawkey] * Fix protein translation with alternate --gcode [Andreas Leimbach] * Various bug fixes in prokka-* support scripts [Andreas Leimbach] * Workaround tbl2asn bug with COORDINATES:profile [Wiep Smits] * Provide MD5 checksum for website download [Willem VA Viljoen] * Hopefully slightly improved cleanup_product() function * Ensure released are tagged on github for Linux Brew [Shaun Jackman] * Check databases exist before searching against them * Updated bundled binaries v1.10 - 28 July 2014 * Support for barrnap 0.4 with Archaea and Mito support [Lionel Guy] * New legal assembly_gap feature in gbk, sqn, tbl files [Connor Skennerton] * Bug fix: for hypos with /gene and /EC [Connor Skennerton] * Improved cleanup_product [Connor Skennerton] * Bug fix: aragorn tmRNA parsing [Connor Skennerton] * New --depends option to list all dependencies * Check for exes needed for --setupdb before attemping it [nsoranzo] * Bug fix: missing ID on 'gene' feature tytpes [Chris Fields] * Upgraded minced to 0.1.6 to avoid out-by-1 bug * Bug fix: Bio::RootI file handle issues in latest BioPerl [Chris Fields] * Bug fix: --setupdb doesn't have bundled binaries in PATH [Connor Skennerton] * Command line and other improvements [Shaun Jackman] * Added --rnammer switch to prefer RNAmmer over Barrnap * Added --rawproduct to turn off /product cleaning * Typo in help for --compliant [Haruo Suzuki] v1.9 - 8 May 2014 * MAJOR: Bug in prokka-uniprot_to_fasta_db: was allowing Altname instead of Recname This affected the /product names that were used in the core protein database! * Updated kingdom databases (sprot) * Updated 'cmscan' binaries from 1.1rc to 1.1 (linux + darwin) * Fixed bug when input fasta has duplicate sequence IDs [James Doonan] * Removed linux/nhmmer binary as it is not used by Prokka * Experimental --kingdom Mitochondria * prokka-uniprot_to_fasta_db now has --term empty as default * More prokka-XXXX_to_fasta_db scripts (not for general use just yet) * New --setupdb function to press/index databases ready for Prokka to use * New --cleandb function to remove all redundant indices (useful for making tarball) * Introduction of 'HAMAP' HMM before CLUSTERS as smaller, faster, reliable * Removal of 'Cdd' HMM as no longer maintained * Removal of 'TIGRFAMs' HMM as doesn't add much * New dependencies of hmmpress and cmpress to support --setupdb * Fixed bug with parsing "X.Yb" version format with signalp [Peter Cock] * Put unique prefix on contig names in --compliant mode [Peter Cock] v1.8 - Nov 2013 * Added support for 'minced' CRISPR finder [Connor Skennerton] * If --cpus > no. cores in system, reduce it down * Improved message explaining CDS overlapping existing RNAs * Defend against Bio::SearchIO bug for parsing hmmscan [Andrew Page] v1.7.2 - 2 Nov 2013 * Fixed serious++ memory leak if --genes/--compliant used [Geoff Winsor] v1.7.1 - 10 Oct 2013 * bug when --cpu 0 set [Lionel Guy] * added two more entries to FAQ * check for BioPerl >= 1.6.2 (not 1.6) for hmmer3 parsing [Bastien Chevreux] * typo: "againt" => "against" [Dieter Bulach] * cleanup product exception for 'rep' phage protein [Dieter Bulach] * check for Parallel >= 20130422 bug https://savannah.gnu.org/bugs/?34241 [Nicola Soranzo] * BUG: rnammer used -S bac no matter what --kingdom was [Harald Gruber-Vodicka] v1.7 - 3 Sep 2013 * complete overhaul of method of using GNU parallel, twice as fast now! * add support for my BARRNAP rRNA predictor software, will use before RNAmmer * added --norrna flag to disable rRNA searching * added --notrna flaf to disable tRNA searching * add --plasmid option to enable /plasmid in 'source' tag * add .txt output file summarising feature counts * added name/version/author to --help output * bugfix: parallel *.seq command line too long with >10^5 contigs [Jon Graf] * updated kingdom uniprot databases * filtered hypothetical/UPF/DUF proteins from all HMMs * put TIGRFAMs before Cdd as COG names showing their age now * bug: didn't check if was a readable, non-empty file * option --moncontig renamed to --moncontiglen (backward compatible) * default value for --mincontig set to 1 rather than 0 * exit if input fasta file doesn't contain any valid sequences * added new binaries/{linux,darwin}, only used if not already installed v1.6 - 7 Aug 2013 * fixed bug: 'infernal' exe doesn't exist, look for 'cmscan' * added custom trusted E.coli --proteins file derived from EcoCyc * added prokka-biocyc_to_fasta to make Prokka databases from Biocyc downloads * leave contig names alone if --centre is NOT set * make --centre '' the default * fixed bug where --centre '' caused faulty /protein_id and no CDS in .gbk * new --metagenome for working with fragmented genomes (sets prodigal --meta) * new --compliant option to auto-set options for NCBI submission * dont remove CDS overlapping ncRNA found via --rfam * document the "tbl2asn" out of date problem! * add --gnu option to parallel and require version XXX * fixed problem where .gbk had no CDS features (added "-a s" to tbl2asn) * added parallel and blastp to version checking * enforcing minimum version of software to ensure compatibility * signalp(--gram),makeblastdb(--proteins),cmscan(--rfam) are now optional installs * added support to add platform binaries to binaries/{linux,darwin}/ * added prokka-build_kingdom_dbs to enable user updating of uniprot BLAST dbs * added prokka-build_genus_dbs to enable user to generate new ones ??? * added support for binaries/linux and binaries/darwin to be included * fixed bug: wrong detection of rfam index file v1.5.2 - 14 Sep 2012 * fixed bug to handle -ve strand ncRNAs [Adam Caldwell] v1.5.1 - 13 Sep 2012 * fixed bug parsing cmscan output [Adam Caldwell] * added Infernal to documentation requirements * record $USER in .log file v1.5 - 9 Sep 2012 * fixed .faa output not honouring --gctable [Adam Caldwell] * option --addgenes causes duplicate entries in the .ffn output * removed --coverage option which wasn't being used/honoured * changed /usr/bin/perl to /usr/bin/env perl * added support for tmRNA (ssrA/10S) features from Aragorn * added support for Infernal/cmscan 1.1 against Rfam * added a "Bug" to docs * consisified some warning messages * added LICENSE for Rfam and Pfam * removed redundant sprot fasta files: prokka/db/kingdom/*/sprot v1.4.1 - 14 Aug 2012 * fixed bug which rejected --increment 1 default! [Simon Gladman] v1.4 - 13 Aug 2012 * improved cleaning up of product names to (help) satisfy NCBI tests * added LICENCE information for Swissprot, TIGRFams in doc/ [Emailed Uniprot] * option to change locus_tag numbering increment [Roderick Felsheim] * fixed bug where setting --gcode was over-ridden by --kingdom v1.3 - 17 Jun 2012 * removed 'sprot' fasta files, can recover from indices with fastacmd/blastdbcmd * removed Time::Seconds->walltime() as it is too new [Heikki Lehvaslaiho] * checked for GNU parallel VS "parallel" from Debian moreutils pkg [Heikki Lehvaslaiho] * fixed 'ribsomnal' / 'Ecoli.faa' typo in manual * added citations for GNU Parallel and all other tools [Ole Tange] * add /protein_id tags to CDS [NCBI] * added --citation option to show publication reference * improved manual w/ details on how to get RNAmmer working with old HMMER * added "Installation" section to manual * changed NCBI error suggestion file from *.val to *.err * added prokka-make_tarball script to automate new releases v1.2 - 28 Apr 2012 * fixed changelog 1.01 to 1.1 as released * fixed bug so only newly created files are listed at end when --outdir='.' * work-around for bug in Aragorn reporting 27000bp long tRNAs at contig ends * wrote blog post about it at http://thegenomefactory.blogspot.com/ * announced on Google+, Twitter v1.1 - 25 Apr 2012 * fixed accidental forcing lower case for strain instead of species * use of genus-specific DBs is now default off, use --usegenus to enable it * changed $URL * altered COMMENT about prokka in .gbk file * features weren't sorted by location before locus tag assignment * identified bug in tbl2asn introducing space in /inference="COORDINATES: profile" * added support to "un-collide" duplicate /gene names by adding _1 _2 etc * added more documentation in doc/prokka-manual.html * added --listdb option to show what databases are configured * removed .gz versions of raw HMM databases, as not needed v1.00 - 23 Apr 2012 * first public version