bactopia/bactopia issues and pull requests

#437 - [bug] Bactopia running LisSero on Enterococci?

Issue - State: open - Opened by incoherentian over 1 year ago - 1 comment
Labels: bug

#436 - [question] main bactopia pipeline with both Merlin and abricate possible?

Issue - State: closed - Opened by incoherentian over 1 year ago - 2 comments
Labels: question

#435 - [question]

Issue - State: open - Opened by Kokejuli over 1 year ago - 1 comment
Labels: question

#434 - Fix amrfinderdb dataset name

Pull Request - State: closed - Opened by mehalter over 1 year ago - 4 comments

#433 - Fatal Error: not enough memory, please set -M option greater than 2330

Issue - State: open - Opened by haruosuz over 1 year ago - 4 comments
Labels: question

#432 - [question] Equivalent Polypolish parameters Dragonflye-->Bactopia?

Issue - State: open - Opened by incoherentian over 1 year ago - 17 comments
Labels: question

#431 - [bug] Corrupted read inputs silently fail in BACTOPIA:GATHER:GATHER_MODULE

Issue - State: open - Opened by rwilliams over 1 year ago - 2 comments
Labels: bug, fixed-in-v3

#430 - [bug] WARN: There's no process matching config selector:

Issue - State: open - Opened by rwilliams over 1 year ago - 1 comment
Labels: bug

#429 - Failing perl due to locale (conda) [bug]

Issue - State: open - Opened by iferres over 1 year ago - 2 comments
Labels: bug, fixed-in-v3

#428 - [bug] datasets fails when setting up amrfinder database

Issue - State: open - Opened by nbel15 over 1 year ago - 1 comment
Labels: bug, fixed-in-v3

#427 - Error running minmer sketch using -profile singularity

Issue - State: closed - Opened by azmigueldario over 1 year ago - 8 comments
Labels: question

#426 - [bug] STECFINDER does not work

Issue - State: open - Opened by PHemarajata over 1 year ago - 6 comments
Labels: bug, fixed-in-v3

#425 - [question] AWS Batch/NF Tower Queue Size

Issue - State: closed - Opened by rwilliams over 1 year ago - 3 comments
Labels: question

#424 - [question] Usage of modules

Issue - State: open - Opened by Kokejuli over 1 year ago - 3 comments
Labels: question, fixed-in-v3

#423 - new version of bactopia sif file[question]

Issue - State: open - Opened by mtswanson2017 over 1 year ago - 20 comments
Labels: question

#422 - [bug] ncbi-genome-download

Issue - State: open - Opened by steven-bioinfo over 1 year ago - 3 comments
Labels: bug, fixed-in-v3

#421 - [bactopia-tool] Phispy

Issue - State: open - Opened by Kiratrea over 1 year ago - 3 comments
Labels: add-bactopia-tool, fixed-in-v3

#420 - multiple ont reads for one sample-how to prepare --sample file[question]

Issue - State: open - Opened by kusandeep over 1 year ago - 4 comments
Labels: question

#419 - BACTOPIA STOPS AT GATHER SAMPLE STEP

Issue - State: open - Opened by Michaelijesse over 1 year ago - 12 comments
Labels: question, fixed-in-v3

#417 - summary path not consistant with the tool suggest argument [bug]

Issue - State: open - Opened by alarawms over 1 year ago - 1 comment
Labels: bug

#416 - [feature] Adding support for medaka_model r1041_e82_400bps_sup_g615 in assembly for Nanopore reads

Issue - State: open - Opened by llk578496 over 1 year ago - 4 comments
Labels: enhancement, fixed-in-v3

#415 - Quick Start failed at "bactopia datasets"

Issue - State: open - Opened by xykb86 over 1 year ago - 1 comment
Labels: fixed-in-v3

#414 - [question] Can I run ariba tool with all databases in one go?

Issue - State: open - Opened by shigdon over 1 year ago - 1 comment
Labels: question

#413 - Hybrid assembly with adapter removal and filtering [question]

Issue - State: closed - Opened by lenorakepler over 1 year ago - 4 comments
Labels: question

#412 - [feature] Add masking support to snippy workflow

Issue - State: open - Opened by embatty over 1 year ago - 2 comments
Labels: enhancement, fixed-in-v3

#411 - AMR Finder update

Issue - State: open - Opened by veganm almost 2 years ago - 1 comment
Labels: fixed-in-v3

#410 - [bug] bactopia search using "Invalid fieldName(s)"

Issue - State: open - Opened by lenorakepler almost 2 years ago - 1 comment
Labels: bug, fixed-in-v3

#409 - Bactopia fails to set up AMRFinder+ database

Issue - State: open - Opened by qi-shen almost 2 years ago - 2 comments
Labels: bug, fixed-in-v3

#408 - [question] manually download datasets in v3?

Issue - State: closed - Opened by incoherentian almost 2 years ago - 9 comments
Labels: question

#407 - [question] using Bactopia Tools on non-bactopia output?

Issue - State: open - Opened by Svnipni almost 2 years ago - 1 comment
Labels: question, fixed-in-v3

#406 - pneumoCat added to strep pneumo merlin workflow

Issue - State: open - Opened by flashton2003 almost 2 years ago - 7 comments
Labels: enhancement, fixed-in-v3

#405 - conda keyerror

Issue - State: open - Opened by gagi19993 almost 2 years ago - 2 comments
Labels: fixed-in-v3

#404 - Erro: unable to open summary.json

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

#403 - [bug] Unknown option

Issue - State: open - Opened by KhadimGueyeKGY almost 2 years ago - 1 comment
Labels: bug

#402 - [bug] Unable to install on SLURM cluster through Singularity

Issue - State: closed - Opened by Svnipni almost 2 years ago - 3 comments
Labels: bug

#401 - Could not solve for environment specs for dragonflye-1.0.13

Issue - State: closed - Opened by lskatz almost 2 years ago - 3 comments
Labels: bug

#400 - [question]post-link.sh was unable to download /opt/conda/envs/bactopia/share/bactopia-2.2.x/conda/envs/assembly_qc-2.2.x/staging/checkm_data_2015_01_16.tar.gz

Issue - State: open - Opened by chengweiwu2002 almost 2 years ago - 5 comments
Labels: question, fixed-in-v3

#399 - error on running bactopia datasets

Issue - State: open - Opened by arsp-dev almost 2 years ago - 2 comments
Labels: question, fixed-in-v3

#398 - Error for Mac

Issue - State: open - Opened by lingbingzeng1985 almost 2 years ago - 1 comment

#397 - [bug] Roary error: .aln.gz Unknown sequence type?

Issue - State: open - Opened by Svnipni almost 2 years ago - 4 comments
Labels: bug

#396 - [bug] Sequence_type

Issue - State: open - Opened by MartinVad almost 2 years ago - 1 comment
Labels: bug, fixed-in-v3

#395 - [question] Continuing with GenBank .gbk and .gff files

Issue - State: closed - Opened by Svnipni almost 2 years ago - 3 comments
Labels: question

#394 - Bactopia v3 - Help Wanted

Issue - State: open - Opened by rpetit3 almost 2 years ago - 88 comments
Labels: enhancement, help wanted

#393 - [bug] Singularity container link not reachable?

Issue - State: open - Opened by uloeber almost 2 years ago - 3 comments
Labels: bug

#392 - [question] ariba can't find samples

Issue - State: closed - Opened by Svnipni almost 2 years ago - 6 comments
Labels: question

#391 - [question] genome size = 1bp?

Issue - State: closed - Opened by Svnipni almost 2 years ago - 3 comments
Labels: question

#390 - [Solved] Bactopia stucks or hangs [Because .nextflow directory accumulates]

Issue - State: closed - Opened by llk578496 about 2 years ago - 24 comments
Labels: bug

#389 - [question] Defining .bactopia / .cache env variables with conda install

Issue - State: closed - Opened by aforestsomewhere about 2 years ago - 9 comments
Labels: question

#388 - [bug] art_illumina: error while loading shared libraries: libgsl.so.25

Issue - State: open - Opened by lfenske-93 about 2 years ago - 4 comments
Labels: bug, fixed-in-v3

#387 - How to just download everything in the beginning?

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

#386 - A bug in install of bactopia：assembly_qc-2.2.x and checkm_data_2015_01_16.tar.gz

Issue - State: open - Opened by plasminogene about 2 years ago - 2 comments
Labels: bug, fixed-in-v3

#385 - error while running Snippy

Issue - State: open - Opened by Farhad63 about 2 years ago - 16 comments
Labels: fixed-in-v3

#384 - Update annotate_genome.yml

Pull Request - State: closed - Opened by idolawoye about 2 years ago - 1 comment

#383 - Update call_variants.yml

Pull Request - State: closed - Opened by idolawoye about 2 years ago - 1 comment

#382 - [bug] error in updata datasets

Issue - State: open - Opened by plasminogene about 2 years ago - 3 comments
Labels: bug, fixed-in-v3

#381 - SnpEff version incompatibility [bug]

Issue - State: closed - Opened by idolawoye about 2 years ago - 5 comments
Labels: bug

#380 - Species 'Staphylococcus aureus' not available

Issue - State: open - Opened by AroobAlhumaidy about 2 years ago - 3 comments
Labels: fixed-in-v3

#379 - [question] Command Error: cp: cannot create regular file

Issue - State: open - Opened by erin-thei about 2 years ago - 22 comments
Labels: question, fixed-in-v3

#378 - libgsl.so.25: cannot open shared object file: No such file or directory

Issue - State: open - Opened by MalcolmorianVII about 2 years ago - 1 comment
Labels: fixed-in-v3

#377 - [bug] bactopia datasets AMRFinder+

Issue - State: open - Opened by MRMHmdeleeuw about 2 years ago - 15 comments
Labels: bug, fixed, fixed-in-v3

#376 - [question] Issue running Bactopia script in updated version

Issue - State: closed - Opened by jjhill4796 about 2 years ago - 13 comments
Labels: question

#375 - [question] Errors running bactopia singularity container in slurm cluster (ComputeCanada)

Issue - State: open - Opened by azmigueldario about 2 years ago - 5 comments
Labels: question

#374 - sync to master

Pull Request - State: closed - Opened by rpetit3 about 2 years ago

#373 - bactopia datasets not running because mv command failing during amrfinder db setup [bug]

Issue - State: closed - Opened by flashton2003 about 2 years ago - 2 comments
Labels: bug, fixed

#372 - bump to v2.2.0

Pull Request - State: closed - Opened by rpetit3 about 2 years ago

#371 - Unable to run Bactopia 2.1.x: downloaded and set up through conda [question]

Issue - State: open - Opened by UpalabdhaD about 2 years ago - 16 comments
Labels: question

#370 - [question] Polishing steps.

Issue - State: open - Opened by lfenske-93 about 2 years ago - 3 comments
Labels: question

#369 - sync with master

Pull Request - State: closed - Opened by rpetit3 about 2 years ago

#368 - [bactopia-tool] Add RagTag for scaffolding

Issue - State: open - Opened by steven-bioinfo over 2 years ago - 2 comments
Labels: add-bactopia-tool

#367 - Problems with MLST schema retrieval [bug]

Issue - State: closed - Opened by mtruglio over 2 years ago - 4 comments
Labels: bug

#366 - Sorry another perl problem!

Issue - State: closed - Opened by zephykoh over 2 years ago - 6 comments

#365 - error - fastq-scan not found

Issue - State: closed - Opened by Oelsakha over 2 years ago - 48 comments

#364 - Tool Suggestion: Piggy

Issue - State: open - Opened by gracehm over 2 years ago - 1 comment
Labels: enhancement, add-bactopia-tool

#363 - [bactopia-tool] Replace CheckM1 with CheckM2

Issue - State: open - Opened by g1ronn1mo over 2 years ago - 1 comment
Labels: add-bactopia-tool

#362 - [bug] docker Invalid maximum heap size

Issue - State: closed - Opened by ShawnHawken over 2 years ago - 4 comments
Labels: bug

#361 - Hi! I'm trying to use Bactopia Datasets but get this error:

Issue - State: closed - Opened by zephykoh over 2 years ago - 10 comments
Labels: question

#360 - [bug] Issue with Mash / Minimers workflow

Issue - State: open - Opened by dankein over 2 years ago - 1 comment
Labels: bug, fixed-in-v3

#359 - [bug]

Issue - State: closed - Opened by egenomics over 2 years ago - 4 comments
Labels: bug

#358 - [bug] Process failed: execution is retried

Issue - State: closed - Opened by baileybowcutt over 2 years ago - 10 comments
Labels: bug

#357 - Conda create argument runs for hours

Issue - State: closed - Opened by mbyott over 2 years ago - 3 comments
Labels: bug

#356 - Bactopia Roadmap and TODOs

Issue - State: open - Opened by rpetit3 over 2 years ago - 1 comment

#355 - [bug] Unable to download bactopia

Issue - State: closed - Opened by baileybowcutt over 2 years ago - 17 comments
Labels: bug, fixed

#354 - Bactopia tool summary and Kraken2

Issue - State: open - Opened by Clr27 over 2 years ago - 14 comments
Labels: question

#353 - [question] How to set up a copy of Bactopia for development

Issue - State: open - Opened by zachary-foster over 2 years ago - 2 comments
Labels: question

#352 - [bug] ability to run without internet

Issue - State: open - Opened by rpetit3 over 2 years ago
Labels: bug

#351 - Installing bactopia

Issue - State: open - Opened by tbazilegith over 2 years ago - 14 comments
Labels: bug

#350 - [question] Bactopia Assembly Failing

Issue - State: open - Opened by erin-thei over 2 years ago - 34 comments
Labels: question

#349 - [question]

Issue - State: closed - Opened by sekhwal over 2 years ago - 33 comments
Labels: question

#348 - [bactopia-tool] Panaroo

Issue - State: closed - Opened by themudo over 2 years ago - 4 comments
Labels: done, add-bactopia-tool

#347 - [feature] Add option --nanohq in assembly when using bactopia with ONT reads

Issue - State: closed - Opened by llk578496 over 2 years ago - 7 comments
Labels: enhancement, fixed

#346 - [question] SPAdes version in Bactopia v2.1.1.

Issue - State: closed - Opened by ingridvanw over 2 years ago - 3 comments
Labels: question

#345 - add missing citations

Pull Request - State: closed - Opened by rpetit3 over 2 years ago

#344 - Bump to v2.1.0

Pull Request - State: closed - Opened by rpetit3 over 2 years ago

#343 - [question] Setting Up Latest AMRFinder+ Database failed...

Issue - State: closed - Opened by erin-thei over 2 years ago - 17 comments
Labels: question

#342 - tmpdir error during BACTOPIA:CALL_VARIANTS

Issue - State: closed - Opened by anwarMZ over 2 years ago - 19 comments
Labels: bug

#341 - Bactopia-tools ariba: ariba-summary error

Issue - State: closed - Opened by alienzj over 2 years ago - 12 comments
Labels: bug, fixed

#340 - [feature] Call variant without network accessing

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

#339 - [bug] Pipeline failing when supplied adapter file

Issue - State: closed - Opened by alienzj over 2 years ago - 6 comments
Labels: bug, fixed

#338 - [bug] pipeline failing when supplied ONT reads

Issue - State: closed - Opened by bernadettecy over 2 years ago - 7 comments
Labels: bug

#337 - [question] How to get available_datasets ?

Issue - State: closed - Opened by alienzj over 2 years ago - 6 comments
Labels: bug, question, fixed

GitHub / bactopia/bactopia issues and pull requests