Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
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
#66 - Error: Invalid alphabet type in target for nhmmer.
Issue -
State: open - Opened by theo-allnutt-bioinformatics about 1 year ago
#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
#58 - please add option to force overwrite .fai index during, or automatically delete fai file after barrnap run
Issue -
State: open - Opened by jvollme about 3 years ago
#57 - calling two overlapping sequences separate partial 16S sequences
Issue -
State: open - Opened by ileleiwi about 3 years ago
#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
#54 - nhmmer failed to run - Error: Invalid alphabet type in target for nhmmer. Expect DNA or RNA
Issue -
State: open - Opened by minjinhan over 3 years ago
- 6 comments
#53 - GFF output and Fasta-headers give different start-coordinates of rRNA-genes
Issue -
State: open - Opened by jvollme over 3 years ago
#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
#46 - possible option for "prokaryotic" search (archaeal + procaryotic)?
Issue -
State: open - Opened by jvollme over 3 years ago
#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