sanger-pathogens/Roary issues and pull requests

#600 - Cant open file: _clustered.clstr

Issue - State: open - Opened by albbaous over 1 year ago - 1 comment

#599 - change the labels of the roary plots

Issue - State: open - Opened by saras224 over 1 year ago

#598 - GFF3 file by Bakta

Issue - State: open - Opened by ryu1013 over 1 year ago

#597 - Tutorial problem "'GCA_000008285.1_ASM828v1_genomic.fna' is not a readable non-empty FASTA file"

Issue - State: closed - Opened by Turnerathopedotedu almost 2 years ago

#596 - Gene subset from table

Issue - State: open - Opened by canarioviana almost 2 years ago

#595 - kraken

Issue - State: open - Opened by zzzapperant almost 2 years ago - 1 comment

#594 - MCL clustering

Issue - State: open - Opened by mweberr almost 2 years ago

#593 - Compilation Failed

Issue - State: open - Opened by jhill4796 almost 2 years ago

#592 - Roary needs Rscript 3 or higher Please upgrade and try again

Issue - State: open - Opened by jhcuarta almost 2 years ago - 1 comment

#591 - Problem with windows wsl and prokka

Issue - State: open - Opened by Bjiornone about 2 years ago

#590 - Parameters for Nanopore (ONT) long-reads sequence data

Issue - State: open - Opened by m-ocejo about 2 years ago

#589 - Roary won't install in Conda/Mamba python 3.10 environment, does work in python 3.7

Issue - State: open - Opened by dutchscientist about 2 years ago

#588 - Use of uninitialized value in require at /Users/.....darwin-thread-multi-2level/Encode.pm line 61

Issue - State: open - Opened by peflanag about 2 years ago - 1 comment

#587 - Roary using large dataset

Issue - State: open - Opened by MenusGarg about 2 years ago

#586 - MSG: Got a sequence without letters. Could not guess alphabet

Issue - State: closed - Opened by augustkx about 2 years ago

#585 - installation seem to be stuck

Issue - State: open - Opened by azat-badretdin about 2 years ago - 3 comments

#584 - Get a wrong core_gene_alignment.aln

Issue - State: closed - Opened by augustkx about 2 years ago - 1 comment

#583 - Roary not working

Issue - State: closed - Opened by KFWins2022 about 2 years ago - 2 comments

#582 - core_gene_alignment file only seems to have 2 of 21 samples

Issue - State: closed - Opened by Barrington-wustl over 2 years ago - 1 comment

#581 - Question about the fasta cluster iteratively

Issue - State: closed - Opened by bucongfan over 2 years ago - 1 comment

#580 - Should assemblies be removed if core gene alignment shows redundancies?

Issue - State: closed - Opened by chahatupreti over 2 years ago - 1 comment

#579 - Error: Cant access the groups file: clustered_proteins

Issue - State: open - Opened by ryu1013 over 2 years ago - 2 comments

#578 - wrong indentation output file "gene_presence_absence.csv"

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

#577 - Use of uninitialized value in require at /usr/lib/x86_64-linux-gnu/perl5/5.34/Encode.pm line 70.

Issue - State: open - Opened by RightCake1 over 2 years ago - 8 comments

#576 - core gene alignment timeout

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

#575 - roary_plots.py - PDF heatmap blurs edges where png does not

Issue - State: open - Opened by alanbeavan over 2 years ago - 1 comment

#574 - I couldn't find specific predicted coding regions in gene_presence_absence.csv.

Issue - State: open - Opened by huminfo8 over 2 years ago

#573 - What configuration do I need for the server?

Issue - State: open - Opened by chen202101 over 2 years ago

#572 - Problem with running Roary/Blast error

Issue - State: open - Opened by GM110Z over 2 years ago

#571 - Annotation of protein clusters in roary?

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

#570 - core_gene_alignment.newick

Issue - State: closed - Opened by valery-shap over 2 years ago - 1 comment

#569 - roary : Depends: r-cran-ggplot2 but it is not going to be installed E: Unable to correct problems, you have held broken packages.

Issue - State: open - Opened by neelam19051 over 2 years ago - 4 comments

#568 - MSG: Got a sequence without letters. Could not guess alphabet

Issue - State: open - Opened by dhiru16 almost 3 years ago - 2 comments

#567 - Using Galaxy for Roary

Issue - State: closed - Opened by Jennifer-1991 almost 3 years ago - 1 comment

#566 - Fix create_pan_genome_plots.R script

Pull Request - State: closed - Opened by gallardoalba almost 3 years ago - 3 comments

#565 - how to extract the sequence of core gene or accessory gene after running roary

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

#564 - _clustered.clstr file does not exist, cannot be read

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

#563 - Can't open file: IS12-12674_pk.gff.proteome.faa(roary).

Issue - State: open - Opened by angeladelvalle almost 3 years ago

#562 - roary and cd-hit

Issue - State: open - Opened by zhichusun almost 3 years ago - 1 comment

#561 - Bio::Roary::CommandLine::Roary module not installed

Issue - State: open - Opened by cylcheyanlin almost 3 years ago - 1 comment

#560 - Creating gene presence/absence of novel query against existing dataset

Issue - State: open - Opened by annabelledamerum almost 3 years ago

#559 - How to calculate Heaps Alpha value from the roary pangenome analysis ?

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

#558 - Roary Unable to Install on Remote Linux Server with SLURM manager

Issue - State: closed - Opened by callaband almost 3 years ago - 4 comments

#557 - Roary plot takes a long time to run

Issue - State: open - Opened by matnguyen almost 3 years ago

#556 - Roary running error

Issue - State: open - Opened by sekhwal almost 3 years ago - 1 comment

#555 - Install macOS Monterey (M1, arm64)

Issue - State: open - Opened by ONeillMB1 almost 3 years ago

#554 - Why no core-genes?

Issue - State: open - Opened by jpinus almost 3 years ago - 1 comment

#553 - When I am using query_pan_genome -a difference --input_set_one Sample1.gff, Sample2.gff--input_set_two Sample3.gff, Sample4.gff some genes in the set_difference_unique_set_one_statistics file are not really unique. I found genes supposedly Unique for Sample1 in Sample4 too. Is there something I am missing.

Issue - State: open - Opened by pkokate18 almost 3 years ago

#552 - number_of_conserved_genes_r.tab

Issue - State: open - Opened by aparajuli12 almost 3 years ago

#551 - How to choose right blastp minimum precent indentity and mcl inflation value?

Issue - State: open - Opened by AmayAgrawal almost 3 years ago - 1 comment

#550 - Install hanging

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

#549 - Running Roary in rootless docker - Roary can't access files

Issue - State: open - Opened by Mike1359 almost 3 years ago

#548 - Gene present in Prokka but absent in Roary

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

#547 - docker run command

Issue - State: open - Opened by ryao-mdanderson about 3 years ago - 1 comment

#546 - Roary analysis - core/pan genome

Issue - State: open - Opened by nanzhen102 about 3 years ago

#545 - NCBI annotated sequence use as input of Roary

Issue - State: open - Opened by manoj044 about 3 years ago - 1 comment

#544 - Installation error, cd-hit version, cant open file while Combine proteins into a single file

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

#543 - Blast percentage identity

Issue - State: closed - Opened by Virome1 over 3 years ago

#542 - Core genome alignment failure

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

#541 - Core genome command not running

Issue - State: open - Opened by Ujjwal-Madaan over 3 years ago

#540 - Why 100 identity sequence are different groups?

Issue - State: open - Opened by zckoo007 over 3 years ago

#539 - Cant open file: _clustered.clstr

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

#538 - SyntaxError: invalid syntax

Issue - State: open - Opened by TC-2021 over 3 years ago - 1 comment

#537 - Distance accessory binary genes

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

#536 - Error: Cant access file -a

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

#535 - Output Data Without Annotation

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

#534 - missing results in the roary outputs

Issue - State: open - Opened by shafi-OZ almost 4 years ago - 2 comments

#533 - Interpreting of roary output (pangenome frequence)

Issue - State: open - Opened by vappiah almost 4 years ago

#532 - Geneious generated .gff files not compatible with Roary !!

Issue - State: open - Opened by Diksharma almost 4 years ago

#531 - roary_plots.py download/clone

Issue - State: closed - Opened by sharbie88 almost 4 years ago

#530 - can't open roary_plots

Issue - State: closed - Opened by sharbie88 almost 4 years ago

#529 - cd-hit version not being recognised

Issue - State: open - Opened by sharbie88 almost 4 years ago

#528 - Analysis using refseq complete genome sequence

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

#527 - Unable to run roary.plots

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

#526 - No sequence data in core_gene_alignment.aln

Issue - State: closed - Opened by haruosuz almost 4 years ago - 1 comment

#525 - how to load roary data into panx

Issue - State: open - Opened by taffners about 4 years ago - 1 comment

#523 - Unique genes issue

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

#519 - Can´t open file: proteome.faa

Issue - State: closed - Opened by mdiricks over 4 years ago - 1 comment

#517 - Illegal division by zero error

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

#505 - Is there any way to compare core genes from two different pan genome results on Roary?

Issue - State: open - Opened by djung0928 almost 5 years ago - 1 comment

#501 - Error for Roary Installation

Issue - State: open - Opened by beherrm almost 5 years ago - 3 comments

#500 - Error when running mafft in roary

Issue - State: open - Opened by igarrom almost 5 years ago - 4 comments

#495 - Interpretation of Blastp percentage identity

Issue - State: open - Opened by mweberr almost 5 years ago - 1 comment

#490 - Understanding Roary outputs to get core genes(common genes)amongst the species.

Issue - State: open - Opened by sarvanivadali almost 5 years ago - 2 comments

#489 - Define Output Options for roary_plots.py

Issue - State: open - Opened by Nilad almost 5 years ago - 3 comments

#487 - MSG: '' is not a valid frame

Issue - State: open - Opened by Bleed242 about 5 years ago - 1 comment

#479 - "roary" running time benchmark

Issue - State: closed - Opened by npavlovikj about 5 years ago - 8 comments

#478 - Roary grouping nearby dissimilar genes into the same group

Issue - State: open - Opened by cwbcm about 5 years ago - 1 comment

#441 - Can't locate Bio/Roary/CommandLine/Roary.pm in @INC

Issue - State: open - Opened by beudes almost 6 years ago - 15 comments

#438 - Group Naming Convention | Question

Issue - State: open - Opened by JDHarlingLee almost 6 years ago - 2 comments

#436 - roary_plots output matrix

Issue - State: open - Opened by StephanieRodrigues almost 6 years ago - 3 comments

#426 - Could not obtain pan_genome_sequences

Issue - State: closed - Opened by pedrorvc over 6 years ago - 14 comments

#425 - Pan genome for fungal genomes

Issue - State: closed - Opened by bhanusakhamuri over 6 years ago - 5 comments

#423 - roary_plots.py KeyError: "X" not in index

Issue - State: closed - Opened by PhilPalmer over 6 years ago - 5 comments
Labels: data

#403 - Tutorial data: extract_proteome_from_gff

Issue - State: closed - Opened by tylerarice over 6 years ago - 3 comments

#368 - unexpected output folder

Issue - State: closed - Opened by thkuo about 7 years ago - 4 comments
Labels: question

#353 - -s and split groups with paralogs!

Issue - State: closed - Opened by maesaar over 7 years ago - 1 comment
Labels: bug

#349 - number of clusters(51652) exceeds limit 5000 Multifastas not created. please check the spread for cintamination from differert species of increase the --group_limit parameter.

Issue - State: closed - Opened by cccsnd over 7 years ago - 9 comments
Labels: enhancement, question

#284 - core_gene_alignment.aln missing

Issue - State: closed - Opened by nikolay12 over 8 years ago - 3 comments

#221 - roary_plots.py generating flawed plots

Issue - State: closed - Opened by swlong about 9 years ago - 21 comments
Labels: bug

GitHub / sanger-pathogens/Roary issues and pull requests