Ecosyste.ms: Issues

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GitHub / tseemann/barrnap issues and pull requests

#68 - Bug getfasta with --outseq

Issue - State: open - Opened by johanzi 5 months ago

#67 - update DBs using RFAM 15.9 & SILVA 138.1

Pull Request - State: open - Opened by mr-c 10 months ago - 1 comment

#65 - SILVA version?

Issue - State: open - Opened by Unaimend about 1 year ago - 1 comment

#64 - Barrnap (nhmmer) takes an eternity to run

Issue - State: closed - Opened by erzakiev over 1 year ago - 1 comment

#63 - Building eukaryotic rrna operon database

Issue - State: open - Opened by DeniRibicic over 2 years ago

#62 - barrnap

Issue - State: open - Opened by 473021677 over 2 years ago

#61 - barrnap doesn't create any output

Issue - State: open - Opened by neelam19051 over 2 years ago

#60 - Fail if Bedtools issues a fasta normalization error

Issue - State: open - Opened by jdwinkler-lanzatech almost 3 years ago

#59 - barrnap-v0.9 debian package has incomplete database

Issue - State: open - Opened by thackl almost 3 years ago - 2 comments

#56 - issue with rrna.fa writing and bed tools

Issue - State: closed - Opened by anbazhagan6 over 3 years ago - 2 comments

#55 - [barrnap] ERROR: nhmmer failed to run

Issue - State: open - Opened by nick-youngblut over 3 years ago - 3 comments

#52 - Cannot specify a file on cmdline?

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

#51 - updates to silva 138 (with license info)

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

#50 - silva switched to cc4

Pull Request - State: closed - Opened by bwlang over 3 years ago

#49 - tweak for new license

Pull Request - State: closed - Opened by bwlang over 3 years ago

#48 - Adding fungal HMM

Issue - State: open - Opened by danwiththeplan over 3 years ago - 4 comments

#47 - Overlapping 5.8S and 28S annotations in Eukaryotic rDNAs

Issue - State: open - Opened by BartvdVossenberg over 3 years ago - 4 comments

#45 - Could the barrnap be used to predict the rrna of *.fna.gz file?

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

#44 - Can not find required 'nhmmer'

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

#43 - What does column 8 stand for?

Issue - State: open - Opened by roey-angel almost 4 years ago

#42 - [Syntax error] Outseq argument

Issue - State: closed - Opened by mirajaonison about 4 years ago

#41 - can barrnap-0.9 use hmmer/3.3

Issue - State: closed - Opened by EricDeveaud over 4 years ago - 2 comments
Labels: enhancement

#40 - Question about using barrnap on reads

Issue - State: closed - Opened by jolespin over 4 years ago - 4 comments
Labels: question

#39 - Add --slow/--accurate mode that uses RFAM/Infernal

Issue - State: open - Opened by tseemann over 4 years ago
Labels: enhancement

#38 - Error: Cannot write foo.fa.fai index

Issue - State: open - Opened by tseemann over 4 years ago
Labels: bug

#37 - Fasta file and GFF have shifted start of 16S

Issue - State: closed - Opened by sleyn over 4 years ago - 2 comments
Labels: question

#36 - Mycobacteria & 5S rRNA

Issue - State: open - Opened by ppgardne about 5 years ago

#35 - archaea and bacteria 16S duplicate

Issue - State: open - Opened by chloelulu over 5 years ago - 1 comment

#34 - Check versions of bedtools is >= 2.27

Issue - State: open - Opened by tseemann over 5 years ago - 1 comment
Labels: enhancement

#33 - Uncorrect bedtools flag name fixed

Pull Request - State: closed - Opened by mariafiruleva over 5 years ago - 3 comments
Labels: invalid

#32 - minor doc typo on main README.md

Issue - State: closed - Opened by jfass almost 6 years ago - 1 comment
Labels: bug

#31 - fix bedtools call so --outseq works

Pull Request - State: open - Opened by JamesRH about 6 years ago

#30 - -outseq parameter

Issue - State: closed - Opened by FabyanoLopes about 6 years ago - 1 comment
Labels: no_response

#29 - Typo in bedtools command breaks 0.9

Issue - State: closed - Opened by kes1smmn about 6 years ago - 4 comments
Labels: wontfix

#28 - ECCN for BARRNAP version 0

Issue - State: closed - Opened by kbhatna1 about 6 years ago - 1 comment
Labels: question

#27 - Line 170 "+" after -name flag

Pull Request - State: closed - Opened by kkapuria3 about 6 years ago - 1 comment

#26 - Please create new release

Issue - State: closed - Opened by snayfach over 6 years ago - 1 comment
Labels: question

#25 - Add TRAVIS-CI support

Issue - State: closed - Opened by tseemann almost 7 years ago
Labels: enhancement

#24 - --help returns 1

Issue - State: closed - Opened by tseemann almost 7 years ago
Labels: bug

#23 - Concatenating all .hmm for a "meta" search?

Issue - State: closed - Opened by bachev almost 7 years ago - 2 comments
Labels: duplicate, enhancement

#22 - Identical results with --kingdom bac arc and euk

Issue - State: closed - Opened by snayfach almost 7 years ago - 1 comment
Labels: question, no_response

#21 - Default # of cores leads to OOM reaping on Linux

Issue - State: closed - Opened by taltman almost 7 years ago - 1 comment
Labels: bug

#20 - Barrnap 0.8 issues with 18S sequences

Issue - State: closed - Opened by tseemann about 7 years ago - 2 comments
Labels: bug

#19 - Get rid of Time::Piece

Issue - State: closed - Opened by tseemann about 7 years ago
Labels: enhancement

#18 - Add RnaseP and SRP genes

Pull Request - State: closed - Opened by michaelbarton over 7 years ago - 2 comments

#17 - enhancement: add option to slice input contigs

Issue - State: open - Opened by jbadomics almost 8 years ago - 1 comment
Labels: enhancement

#16 - Silva 123 up to date !!!

Issue - State: closed - Opened by davidvilanova over 8 years ago - 2 comments
Labels: bug

#15 - Feature request: allow input from stdin

Issue - State: closed - Opened by mdehollander over 8 years ago - 3 comments
Labels: enhancement

#14 - Clarify that Barrnap handles metazoan mitochondria

Pull Request - State: open - Opened by sjackman almost 9 years ago

#13 - Replace SILVA databases with unencumbered-licence source

Issue - State: open - Opened by tseemann almost 9 years ago - 8 comments
Labels: enhancement

#12 - Clarify --kingdom mito documentation

Issue - State: closed - Opened by sjackman almost 9 years ago - 1 comment
Labels: enhancement

#11 - /nhmmer: Syntax error: ")" unexpected in barranp-0.7

Issue - State: closed - Opened by MaggieLoT almost 9 years ago - 1 comment
Labels: question

#10 - How do I rebuild the files 12S.mito.aln and 16S.mito.aln?

Issue - State: closed - Opened by sjackman almost 9 years ago - 3 comments
Labels: question

#9 - build_HMMs.sh: 404 for LSURef_115_tax_silva_full_align_trunc.fasta.tgz

Issue - State: closed - Opened by sjackman almost 9 years ago - 1 comment
Labels: bug

#8 - Output rRNA features to a fasta file

Pull Request - State: closed - Opened by ctSkennerton about 9 years ago - 4 comments
Labels: enhancement

#7 - Source .bashrc to reload the PATH var

Pull Request - State: closed - Opened by mberacochea about 9 years ago - 2 comments

#6 - added -gene switch

Pull Request - State: open - Opened by HRGV over 9 years ago - 2 comments

#5 - Barrnap manual with typo

Issue - State: closed - Opened by dutchscientist over 9 years ago - 1 comment

#4 - Metagenome mode with ALL kingdoms

Issue - State: open - Opened by tseemann over 9 years ago - 3 comments
Labels: enhancement

#3 - barrnap 0.4.2 HMM profile EUK 18S missing

Issue - State: closed - Opened by tseemann almost 10 years ago - 1 comment
Labels: bug

#2 - Support plant mitochondrion

Issue - State: open - Opened by sjackman about 10 years ago - 5 comments
Labels: enhancement

#1 - Annotate rRNA genes containing gaps of Ns

Issue - State: open - Opened by sjackman about 10 years ago - 2 comments
Labels: enhancement