merenlab/anvio

Issues

• [BUG] anvi-setup-kegg-data encountered an error

  #2372 opened 14 days ago by Zerong0513
  0

• [FEATURE REQUEST] Profiling of secondary mapping and read with no sequence in bam files

  #2369 opened 20 days ago by FlorianTrigodet
  17

• [BUG] manual curation import binning to profile.db not working

  #2370 opened 16 days ago by emily-ap
  5

• [FEATURE REQUEST] Simplify the anvi'o conda installation command

  #2368 opened 21 days ago by ahenoch
  4

• [BUG] Colors in the legend not matching the figure

  #2367 opened 24 days ago by FlorianTrigodet
  2

• [BUG] `anvio-summarize` : `popper.min.js` is missing.

  #2365 opened 21 days ago by Louis-MG
  10

• [FEATURE REQUEST] Using external gene clusters for anvi-pan-genome

  #2317 opened 24 days ago by FlorianTrigodet
  1

• [BUG] Anvio-8 installation

  #2359 opened a month ago by DMarques99
  1

• KeyError: 'modelseed_reaction_id'

  #2363 opened a month ago by ranjanmanishblue
  3

• [BUG] KeyError: 'pop from an empty set'

  #2360 opened a month ago by Louis-MG
  1

• [BUG] anvi-setup-scg-taxonomy not working - v8

  #2358 opened a month ago by FlorianTrigodet
  1

• [BUG] `anvi-script-gen-function-matrix-across-genomes` does not know option `--skip-checking-genome-hashes`

  #2343 opened a month ago by Louis-MG
  7

• [BUG] Error in rule megahit

  #2352 opened 2 months ago by PeymanDerik
  8

• [BUG] Error when writing output files with anvi-dereplicate-genomes and pyANI

  #2339 opened 2 months ago by uguyet
  4

• [FEATURE REQUEST] adding contigs database names to deflines of exported genes/proteins fasta

  #2329 opened 2 months ago by dspeth
  3

• anvi-draw-kegg-pathways: command not found

  #2348 opened 2 months ago by marlaux
  4

• [BUG] Python version is incompatible with Anvi'o

  #2347 opened 2 months ago by okcoskun
  3

• [BUG] Error in anvi-setup-ncbi-cogs: makeblastdb

  #2346 opened 2 months ago by PeymanDerik
  5

• [BUG] Insert a short but descriptive title (leave the '[BUG]' part)

  #2345 opened 2 months ago by PeymanDerik
  1

• [BUG] cannot import vbgmm in concoct

  #2330 opened 2 months ago by NebulaSL
  2

• [BUG] `anvi-run-hmms` does not accurately detect 5S rRNA

  #2344 opened 2 months ago by philipwoods
  3

• [BUG] `anvi-dereplicate-genomes` does not accept float in `--min-fraction`

  #2342 opened 2 months ago by u-xixi
  0

• Adding binning step to workflow

  #2340 opened 2 months ago by UniAlberta
  1

• Anvi'o workflow ends prematurely

  #2338 opened 3 months ago by UniAlberta
  12

• [FEATURE REQUEST] Genome redundancy estimations compatible with introns

  #2337 opened 3 months ago by tdelmont
  8

• phylogenetic tree build fails

  #2335 opened 3 months ago by jsalas0798
  2

• [FEATURE REQUEST] Adding a program to annotate viral PHROGs via their HMMs

  #2300 opened 5 months ago by ivagljiva
  3

• [FEATURE REQUEST] A conda package for anvi'o with a minimal installation option

  #2304 opened 5 months ago by ivagljiva
  2

• Running anvio through snakemake, no errors but the job submission stops running

  #2333 opened 3 months ago by UniAlberta
  12

• [BUG] anvi-pan-genome - diamond BUG

  #2331 opened 3 months ago by pcampiteli
  0

• [BUG] Pandas dataframe has no attribute 'append'

  #2313 opened 4 months ago by philipwoods
  4

• [BUG] The CONTIGS.db file is 0kb and slurm job is still running

  #2324 opened 4 months ago by itpcas-zcb
  2

• Interactive interface, TypeError: Cannot read properties of undefined (reading 'angle') when trying to organize by length

  #2325 opened 4 months ago by jwilliams648
  5

• [FEATURE REQUEST] Case-sensitive search in `anvi-export-locus`

  #2319 opened 4 months ago by philipwoods
  6

• [BUG] ERROR in running anvi-script-gen_stats_for_single_copy_genes.R

  #2316 opened 4 months ago by AlenaYoung
  1

• [BUG] contigs.db has issues when inputing aa_sequence in the external-gene-call file

  #2310 opened 4 months ago by pcampiteli
  9

• [BUG] Pandas error in `anvi-get-codon-frequencies`

  #2314 opened 4 months ago by philipwoods
  6

• [BUG] anvio installation

  #2312 opened 4 months ago by UniAlberta
  15

• [BUG] MaxBin2 failing due to one missing coverage

  #2311 opened 4 months ago by lmrodriguezr
  2

• [BUG] Missing USearch in installation instruction and workflow DAG declarations

  #2309 opened 4 months ago by lmrodriguezr
  1

• [BUG] `--prodigal-single-mode` breaks metagenomic workflow

  #2305 opened 4 months ago by lmrodriguezr
  5

• [BUG] anvi-meta-pan-genome does not allow me to use gene calls not from prodigal

  #2308 opened 4 months ago by Louis-MG
  10

• [BUG] anvio-cluster-contigs fails with Generate input data

  #2307 opened 4 months ago by AlenaYoung
  0

• [FEATURE REQUEST] Different gene caller option(s) for `anvi-gen-contigs-database`

  #2298 opened 5 months ago by ivagljiva
  5

• [FEATURE REQUEST] add parameter --temp for temporary files path

  #2296 opened 5 months ago by Louis-MG
  5

• [FEATURE REQUEST] See external/third-party dependencies on program documentation pages

  #2299 opened 5 months ago by ivagljiva
  1

• [FEATURE REQUEST] Annotate which KOfams were added by our bitscore relaxation heuristic

  #2303 opened 5 months ago by ivagljiva
  0

• [FEATURE REQUEST] Environment variables for KEGG, Pfam, and other data directories so sys admins can set a global --xxxx-data-dir value

  #2302 opened 5 months ago by ivagljiva
  0

• [FEATURE REQUEST] A shortcut for importing layer orders that doesn't go through `anvi-import-misc-data`

  #2301 opened 5 months ago by ivagljiva
  0

• [FEATURE REQUEST] Refactoring Anvio to be more eukaryote friendly/account for different genetic architectures

  #2297 opened 5 months ago by bcoltman
  0