bowmanjeffs/paprica

Issues

• The “fake” database seems to be incomplete

  #96 opened 2 years ago by masikol
  2

• notify user about existing files

  #95 opened 2 years ago by RJ333
  2

• gRodon improvements

  #93 opened 2 years ago by bowmanjeffs
  0

• unambigously specify user for the linux install script

  #94 opened 2 years ago by RJ333
  1

• Error: HMM banded truncated alignment mxes need 1392.25 Mb > 1028.00 Mb limit

  #92 opened 3 years ago by Ql-cy
  9

• OTUs missing in edge_data file

  #91 opened 3 years ago by cwatt
  5

• removal of chloroplasts and mitochondria

  #90 opened 3 years ago by bowmanjeffs
  0

• Docker/Singularity support

  #88 opened 3 years ago by gasperpetelin
  6

• better selection of random reps

  #84 opened 4 years ago by bowmanjeffs
  0

• FileNotFoundError: [Errno 2] No such file or directory: 'test.bacteria.phylum_reps.edpllist.csv'

  #87 opened 4 years ago by lee-s17
  6

• Proper citation forwarding

  #85 opened 4 years ago by lczech
  6

• Potential problem with test.bacteria.phylum_reps

  #86 opened 4 years ago by PaulTillich
  3

• new workflow

  #83 opened 4 years ago by bowmanjeffs
  0

• poor read placement to master tree

  #82 opened 4 years ago by bowmanjeffs
  1

• Error running paprica

  #78 opened 4 years ago by eperezv
  20

• duplicate unique reads

  #81 opened 4 years ago by bowmanjeffs
  1

• branch_length should be be parsed from jplace

  #80 opened 4 years ago by bowmanjeffs
  0

• placements to phylum_ref don't appear in taxon map

  #79 opened 4 years ago by bowmanjeffs
  0

• placements to phylum ref with n = 1

  #77 opened 4 years ago by bowmanjeffs
  0

• integrate orthoMCL to define meaningful groups of CDS

  #57 opened 4 years ago by bowmanjeffs
  0

• taxid for draft genomes in paprica-place_it

  #46 opened 4 years ago by bowmanjeffs
  0

• add a setup.py and upload to pypi

  #59 opened 4 years ago by nick-youngblut
  3

• euk draft genomes

  #65 opened 4 years ago by bowmanjeffs
  0

• ptools v24 issues

  #75 opened 4 years ago by bowmanjeffs
  0

• Error running test

  #76 opened 4 years ago by lee-s17
  1

• Implementation of epa-ng doesn't allow for multiple threads

  #73 opened 4 years ago by elijthomas
  5

• Error running ./paprica-run.sh

  #71 opened 4 years ago by chongchunwie
  5

• problem with infernal when running ./paprica-run.sh test bacteria

  #72 opened 4 years ago by lottedemaeyer
  2

• Single edn reads preprocessing

  #70 opened 4 years ago by roman-spanek
  2

• error when running ./paprica-mg_run.py

  #68 opened 4 years ago by ajiwahyu
  9

• analyzing edge_data

  #69 opened 5 years ago by GucciBawler
  1

• HMM banded truncated alignment

  #50 opened 6 years ago by lucaz88
  6

• SettingWithCopyWarning: harmless or a bigger problem?

  #67 opened 6 years ago by Gustius
  1

• Wrong argument in make_edge_fasta.py?

  #66 opened 6 years ago by Gustius
  1

• look for most recent PGDB version

  #53 opened 6 years ago by bowmanjeffs
  0

• parallelize cmscan

  #63 opened 6 years ago by bowmanjeffs
  0

• use STAR for alignment

  #55 opened 6 years ago by bowmanjeffs
  0

• How to obtain parent taxonomy level for metabolic pathways?

  #61 opened 6 years ago by roman-spanek
  1

• "[Name].combined_16S.bacteria.tax.clean.align.csv does not exist" error

  #60 opened 6 years ago by sturne29
  11

• fasta for unannotated reads

  #58 opened 7 years ago by bowmanjeffs
  0

• paprica did not work

  #56 opened 7 years ago
  1

• error when identical draft and final 16S sequence

  #54 opened 7 years ago by bowmanjeffs
  0

• assigning enzyme names to E.C numbers

  #52 opened 7 years ago by garimaraj
  4

• Benchmarking against PICRUst/Tax4fun?

  #51 opened 7 years ago by GeoMicroSoares
  1

• Virtual box

  #49 opened 7 years ago by AnweshaGhosh
  1

• test flag

  #48 opened 8 years ago by bowmanjeffs
  0

• Speed up PAPRICA by only using unique sequences?

  #47 opened 8 years ago by chassenr
  1

• paprica-mt ouput needs taxid and taxa name

  #45 opened 8 years ago by bowmanjeffs
  0

• include proteins without EC numbers (e.g. KO)

  #44 opened 8 years ago by bowmanjeffs
  0

• MAP data in tally_pathways

  #42 opened 8 years ago by bowmanjeffs
  0