tseemann/prokka issues and pull requests

#622 - Improve lists of Rfam domain-specific models

Issue - State: open - Opened by AntonPetrov over 3 years ago

#621 - Problem of Output Files

Issue - State: open - Opened by Chauncy-Fang over 3 years ago

#620 - Unable to locate some packages

Issue - State: open - Opened by unnatiaggarwalsmile over 3 years ago - 1 comment

#619 - Use the version module to parse Bioperl version strings

Pull Request - State: open - Opened by prehensilecode over 3 years ago

#618 - Error Prokka and Roary

Issue - State: open - Opened by sekhwal over 3 years ago

#617 - Prokka error

Issue - State: open - Opened by sekhwal over 3 years ago - 11 comments

#616 - Prokka running error

Issue - State: open - Opened by sekhwal over 3 years ago - 2 comments

#615 - Conda install work around

Issue - State: open - Opened by samche42 over 3 years ago - 5 comments

#614 - Issue calling Hmmer when running Prokka

Issue - State: open - Opened by skbrimer over 3 years ago - 2 comments

#613 - Problem with databas

Issue - State: open - Opened by H440775h over 3 years ago

#612 - Plasmid Annotations

Issue - State: open - Opened by Javaria-Ashraf over 3 years ago - 1 comment

#611 - Link `--proteins` section of manual to `fasta-db-format` section

Pull Request - State: open - Opened by 0xaf1f over 3 years ago - 1 comment

#610 - How to create a local (custom) database with a multifasta DNA sequence file in Prokka?

Issue - State: open - Opened by Felipedb02 over 3 years ago

#609 - Unnamed/uncharacterized genes are not annotated as expected

Issue - State: open - Opened by ReganDM over 3 years ago

#608 - prokka install issue with M1 mac processor using homebrew - miniforge

Issue - State: open - Opened by beherrm over 3 years ago - 7 comments

#607 - Running prokka-genbank_to_fasta_db on new genbank format

Issue - State: open - Opened by emmannaemeka over 3 years ago - 1 comment

#606 - Where to obtain gene length from reference sequences?

Issue - State: closed - Opened by miguelsemedobb over 3 years ago

#605 - usegenus but no genus

Issue - State: open - Opened by EllistonV over 3 years ago

#604 - prokka signalp

Issue - State: open - Opened by Gao-Lei-Xinjiang over 3 years ago

#603 - strange characters in intermediate files lead to failure in generating gbf output

Issue - State: open - Opened by Yasana1990 over 3 years ago

#602 - Manual installation of database

Issue - State: open - Opened by Bibi888 over 3 years ago

#599 - prokka setup db

Issue - State: open - Opened by annavet over 3 years ago - 2 comments

#598 - Bio::SearchIO: hmmer3 cannot be found

Issue - State: open - Opened by yzhzu over 3 years ago - 6 comments

#593 - bioperl v1.7.8 kills the prokka 🐿🔫

Issue - State: open - Opened by lskatz almost 4 years ago - 1 comment

#589 - [question] Can I train prodigals on several good quality genomes instead of just one?

Issue - State: closed - Opened by avilaHugo almost 4 years ago

#582 - Four extra unexpected output files with prefix 'protein.XXX'....

Issue - State: closed - Opened by RunJiaJi about 4 years ago - 2 comments
Labels: bug

#577 - error of minced to run prokka

Issue - State: open - Opened by huiluocao about 4 years ago - 3 comments

#576 - prokka output files for gene quantification

Issue - State: closed - Opened by khemlalnirmalkar about 4 years ago - 6 comments
Labels: question, assume_resolved, metagenome

#566 - Can't locate Bio/Root/Version.pm in @INC (you may need to install the Bio::Root::Version module)

Issue - State: open - Opened by ramnageena11 over 4 years ago - 19 comments

#564 - Could not run command: cat prokka

Issue - State: open - Opened by AlonsoFelipeRuiz over 4 years ago - 2 comments

#558 - Incorrect annotations from custom database

Issue - State: open - Opened by jellila over 4 years ago - 1 comment

#557 - initialization of Vm error

Issue - State: open - Opened by nanzhen102 over 4 years ago - 1 comment

#554 - ncRNA prediction does not work

Issue - State: open - Opened by Ekie22 over 4 years ago - 2 comments

#549 - blastp version issue

Issue - State: closed - Opened by Ankita-1211 over 4 years ago - 4 comments

#544 - check blast version fails due to v2.10 which is recognized as <2.2

Issue - State: open - Opened by uloeber over 4 years ago - 8 comments

#542 - date format in gbk file

Issue - State: closed - Opened by fetyj over 4 years ago - 9 comments

#540 - Databases not indexed; after indexing they still aren't indexed? Or are they missing?

Issue - State: open - Opened by wolfgangrumpf over 4 years ago - 13 comments

#532 - blastp version number comparison error

Issue - State: closed - Opened by CuriousTim over 4 years ago - 3 comments

#528 - Prokka is not generating all the files while invoking prokka using shell script but working fine while running directly from commandline, why?

Issue - State: open - Opened by Unlock-ViV almost 5 years ago - 14 comments

#520 - Can prokka annotate only from --protein file?

Issue - State: open - Opened by Zazgah almost 5 years ago - 6 comments

#519 - Issue after conda install: Can't locate Bio/Root/Version.pm in @INC (you may need to install the Bio::Root::Version module)

Issue - State: open - Opened by c-leber almost 5 years ago - 23 comments

#508 - Argument "1.7.7" isn't numeric in numeric

Issue - State: open - Opened by tseemann about 5 years ago - 19 comments
Labels: bug

#506 - mRNA created for misc_RNA or tRNA or RNA and reported as duplicated by the ENA validator

Issue - State: open - Opened by Jeepee8820 about 5 years ago - 3 comments
Labels: bug

#500 - --proteins option

Issue - State: closed - Opened by Vers4L about 5 years ago - 2 comments
Labels: question

#494 - prokka-genbank_to_fasta_db error

Issue - State: open - Opened by ramadatta about 5 years ago - 10 comments
Labels: bug

#485 - rRNA not well annotated with Barrnap

Issue - State: open - Opened by ireneortega over 5 years ago - 6 comments

#482 - Adding The Virulence Factor Database to Prokka?

Issue - State: open - Opened by djung0928 over 5 years ago - 2 comments

#474 - Proposing a few changes

Issue - State: open - Opened by fluhus over 5 years ago - 3 comments
Labels: enhancement

#449 - Prokka does not recognize blast 2.10 as >= blast 2.8

Issue - State: closed - Opened by natachacouto over 5 years ago - 19 comments
Labels: conda/brew/docker

#446 - Prokka issue :Can't locate Bio/Root/Version.pm in @INC

Issue - State: closed - Opened by RamaSravanimeduri over 5 years ago - 14 comments
Labels: user_env, conda/brew/docker

#420 - prokka getting stuck on tbl2asn

Issue - State: closed - Opened by nixon444 almost 6 years ago - 3 comments
Labels: question, tbl2asn, assume_resolved, metagenome

#419 - Ubuntu issues loading fasta file "not a readable non-empty FASTA"

Issue - State: closed - Opened by beherrm almost 6 years ago - 19 comments
Labels: question

#402 - Could not run command: cat prokka\/IS\.faa

Issue - State: closed - Opened by lucaspompeun almost 6 years ago - 18 comments
Labels: user_env

#397 - Mitochondrial genome annotation - strange behaviour

Issue - State: closed - Opened by apredeus about 6 years ago - 7 comments
Labels: bug

#396 - Minced version issue

Issue - State: closed - Opened by emmadoughty about 6 years ago - 9 comments
Labels: conda/brew/docker

#390 - Problem with the version of makeblastdb

Issue - State: closed - Opened by djung0928 about 6 years ago - 10 comments
Labels: user_env

#349 - Can't locate XML/Simple.pm in @INC

Issue - State: closed - Opened by letunglam1991 almost 7 years ago - 9 comments
Labels: user_env

#327 - Could not determine version of blastp - please install version 2.2 or higher

Issue - State: closed - Opened by nailabc almost 7 years ago - 5 comments
Labels: conda/brew/docker

#319 - Add information about plasmid annotation

Issue - State: open - Opened by tseemann about 7 years ago - 9 comments
Labels: enhancement

#314 - Could not run command: cmpress

Issue - State: closed - Opened by zhibaosuo about 7 years ago - 5 comments
Labels: question

#297 - XML :: simple cannot locate

Issue - State: closed - Opened by jasonbhn over 7 years ago - 10 comments
Labels: user_env, conda/brew/docker

#283 - Partial v Complete Genes for Metagenomic Analysis

Issue - State: open - Opened by JChristopherEllis over 7 years ago - 8 comments
Labels: question, metagenome

#266 - cmpress install

Issue - State: closed - Opened by JibrinLab over 7 years ago - 10 comments
Labels: question

#259 - non-specific Could not run command:

Issue - State: closed - Opened by GeoMicroSoares almost 8 years ago - 7 comments
Labels: user_env, assume_resolved

#258 - Mobile elements annotation with prokka

Issue - State: closed - Opened by MostafaYA almost 8 years ago - 8 comments
Labels: bug

#253 - Pseudogene detection?

Issue - State: closed - Opened by rbeinart almost 8 years ago - 4 comments
Labels: question

#238 - Why exclude CDS's that are being overlapped by RNA?

Issue - State: closed - Opened by alexblex1 about 8 years ago - 2 comments
Labels: question

#237 - Bulk annotation in prokka?

Issue - State: closed - Opened by maesaar about 8 years ago - 10 comments

#203 - MSG: Seq [contigxxxx]: Terminator codon inside CDS!

Issue - State: closed - Opened by blancaverag almost 9 years ago - 20 comments
Labels: bug, mystery

#187 - Multiple genome analysis

Issue - State: closed - Opened by lucaz88 almost 9 years ago - 4 comments
Labels: question

#176 - For loop and 'filename' is not a readable non-empty FASTA file

Issue - State: closed - Opened by TreeT2 about 9 years ago - 1 comment

#153 - GenBank file: Contig name and length collision

Issue - State: open - Opened by VGalata over 9 years ago - 11 comments
Labels: question, genbank

#139 - Could not run command: tbl2asn

Issue - State: closed - Opened by tallnuttcsiro over 9 years ago - 7 comments
Labels: question

#135 - Please rename your contigs or use --centre XXX to generate clean contig names

Issue - State: open - Opened by xapple almost 10 years ago - 9 comments

#86 - not a readable FASTA file error

Issue - State: closed - Opened by Biomicrogen over 10 years ago - 15 comments
Labels: bug, invalid, question, wontfix

#55 - Could not run command: makeblastdb -dbtype prot

Issue - State: closed - Opened by oisky over 10 years ago - 3 comments

#14 - Missing short genes

Issue - State: open - Opened by sjackman about 11 years ago - 6 comments
Labels: enhancement

GitHub / tseemann/prokka issues and pull requests