KwanLab/Autometa

Issues

• Error in AUTOMETA:TAXON_ASSIGNMENT:LCA:PREP_DBS

  #363 opened 7 months ago by bindiyabajracharya
  5

• NA ambiguous in recursive_dbscan

  #349 opened 7 months ago by hyphaltip
  12

• ncbi rsync error when downloading markers

  #347 opened 7 months ago by hyphaltip
  4

• "TypeError: boolean value of NA is ambiguous" came back

  #360 opened 7 months ago by imonteroo
  1

• module 'Bio.SeqUtils' has no attribute 'GC' in autometa-length-filter

  #357 opened 7 months ago by imonteroo
  4

• Fix Biopython deprecation warning

  #326 opened 7 months ago by evanroyrees
  1

• line_terminator not lineterminator use in .to_csv from pandas throws error with pandas > 1.5

  #350 opened 7 months ago by hyphaltip
  2

• The number of contigs after autometa-taxonomy is not consistent to the original contig fasta

  #296 opened a year ago by chtsai0105
  5

• 💚 Fix pytest error

  #327 opened a year ago by evanroyrees
  0

• Add "remove unused imports" hook to pre-commit hooks

  #330 opened a year ago by evanroyrees
  0

• Propagate contigs not recovered in blastp search to `unclassified.fna`

  #305 opened a year ago by evanroyrees
  0

• :bug: in `autometa-binning-ldm`: Missing/incorrect `binning_checkpoints` variable init/assignment

  #324 opened a year ago by evanroyrees
  0

• Replace `conda` commands with `mamba` and add `-c conda-forge` channel to `mamba install autometa`

  #331 opened a year ago by evanroyrees
  0

• autometa-update-databases, error building GTDB diamond database

  #328 opened a year ago by Kohtzanth
  2

• Missing example data causes gdown script to fail

  #308 opened 2 years ago by chasemc
  4

• kingdoms does not need to be defined multiple times in workflows/autometa_flagged.sh

  #332 opened a year ago by jason-c-kwan
  0

• Change arg name `--norm-output` for `autometa-kmers` entrypoint

  #310 opened 2 years ago by chasemc
  2

• :bug:💚 :memo: Autometa modules in documentation are empty

  #311 opened 2 years ago by evanroyrees
  0

• Look into using taxon result limited blastp instead of top-n limited

  #322 opened 2 years ago by chasemc
  1

• Fix BLAST results protein to taxonomic accession assignment

  #317 opened 2 years ago by chasemc
  1

• Migrate documentation from reStructuredText to MyST Markdown

  #240 opened 3 years ago by evanroyrees
  4

• Documentation needs edit

  #304 opened 2 years ago by chasemc
  0

• Move unrelated files out of Nextflow pipeline directory

  #309 opened 2 years ago by chasemc
  1

• Add helpful error message

  #306 opened 2 years ago by chasemc
  1

• error: archaea.markers.tsv not found

  #298 opened 2 years ago by Valentin-Bio-zz
  2

• :snake: Replace `attrs` with `dataclasses`

  #303 opened 2 years ago by evanroyrees
  0

• Replace prodigal subprocess with pyrodigal

  #301 opened 2 years ago by evanroyrees
  0

• Add `average_method` argument to `compute_clustering_metrics` function

  #289 opened 2 years ago by evanroyrees
  0

• Problem when running Autometa using bash script

  #297 opened 2 years ago by Valentin-Bio-zz
  6

• Error occurred on running autometa-binning

  #295 opened 2 years ago by chtsai0105
  2

• Running the test profile fails, unable to find docker image

  #291 opened 2 years ago by chasemc
  0

• No clusters can be found in the dataset

  #288 opened 2 years ago by ReneKat
  4

• 🐌 ➡️ 🐎 Optimize DBSCAN clustering method for genome binning

  #287 opened 2 years ago by evanroyrees
  0

• Pin scipy release to `1.8.*` until scikit-bio uses scipy 1.9

  #285 opened 2 years ago by evanroyrees
  0

• FileNotFoundError: [Errno 2] No such file or directory: '/databases/autometa/ncbi/delnodes.dmp'

  #282 opened 2 years ago by JoshuaTCooper
  1

• Print commands run in context in autometa.sh script

  #274 opened 3 years ago by kirstengott
  2

• General Query on improvising Metagenome binning

  #268 opened 3 years ago by srisvs33
  6

• :bug::snake: Add `n_jobs` argument to `kmers.embed(...)` function and replace `**method_args`

  #266 opened 3 years ago by evanroyrees
  0

• Add threads for for bowtie2-build

  #263 opened 3 years ago by chasemc
  0

• internet_is_connected() function

  #257 opened 3 years ago by paulineauffret
  4

• Missing step in documentation (Bash workflow)

  #261 opened 3 years ago by jason-c-kwan
  0

• :bug:🪲 Prevent edge case where MAG completeness is incorrectly computed

  #255 opened 3 years ago by evanroyrees
  0

• 🔥🍏 Remove duplicate nextflow runtime defaults

  #251 opened 3 years ago by evanroyrees
  0

• in check_samplesheet.py, incorporate more flexible encoding when reading

  #249 opened 3 years ago by shaneroesemann
  0

• You can add a CITATION file to your repository to help users correctly cite your software.

  #241 opened 3 years ago by chasemc
  0

• autometa-taxonomy-lca return TypeError without specifying --cache

  #246 opened 3 years ago by chtsai0105
  3

• README should have link to contribution guidelines in the documentation

  #245 opened 3 years ago by jason-c-kwan
  0

• Calculation of coverage

  #239 opened 3 years ago by chtsai0105
  1

• No markers found - attempts made to find/count kmers

  #237 opened 3 years ago by samche42
  2

• 🍏 Add fail safe for `--resume` flag

  #230 opened 3 years ago by evanroyrees
  1