broadinstitute/StrainGE

Issues

• Running StrainGR call with refs_concat.fasta results TypeError: 'NoneType' object is not subscriptable

  #40 opened 4 months ago by sjmiller-sahmri
  0

• cannot convert float NaN to integer

  #31 opened 2 years ago by nick-youngblut
  2

• 'VariantCallData' object has no attribute 'bad_read'

  #39 opened 10 months ago by sconlan
  0

• Error in customising database through straingst

  #37 opened 10 months ago by sahilrishav2
  4

• StrainGR identifies SNVs in samples where StrainGST did not detect a strain

  #36 opened a year ago by kebow
  0

• straingr prepare-ref gives warning about missing metadata each time it is run

  #35 opened a year ago by joelewis101
  1

• KeyError when running straingst cluster

  #12 opened a year ago by samnooij
  16

• Installation error with incompatible scipy version

  #34 opened a year ago by parul-sharma
  1

• Error due to five indices for possible alleles, rather than six

  #33 opened a year ago by gavinmdouglas
  2

• ValueError: cannot set null allele

  #32 opened 2 years ago by wwood
  0

• ncbi-genome-download-The download content is empty!

  #23 opened 2 years ago by qkqk-hub
  2

• ZeroDivisionError: division by zero when setting up DB for acinetobacter genus

  #30 opened 2 years ago by AdrianLimaG
  1

• Preparing a DB for StrainGR

  #29 opened 2 years ago by wwood
  0

• How do you define the unique reads

  #28 opened 2 years ago by StickHu
  0

• Can we run on non complete genomes

  #26 opened 2 years ago by SilasK
  1

• straingr compare all vs all deon't create output file.

  #21 opened 2 years ago by SilasK
  1

• Installation instructions do not work with micromamba

  #25 opened 2 years ago by tstraub89
  1

• 'utf-8' codec can't decode byte 0x89 in position 0

  #24 opened 2 years ago by nick-youngblut
  1

• mummer is not part of the conda env.

  #20 opened 2 years ago by SilasK
  1

• Division by Zero Error during Database Creation Step (straingst kmersim)

  #17 opened 2 years ago by autpereira
  2

• prepare-ref looks for metadata file inside fasta file repository, with no option to parametrise this

  #19 opened 2 years ago by SilasK
  1

• Change path template

  #16 opened 3 years ago by Ahmedbargheet
  0

• Prepare a concatenated reference

  #15 opened 3 years ago by Ahmedbargheet
  1

• "straginst kmerize --filter ..." crashing

  #13 opened 3 years ago by w1bw
  2

• Stopiteration

  #11 opened 3 years ago by Ahmedbargheet
  3

• issues with straingr view: --vcf and --verbose-vcf arguments produced no or unexpected output

  #10 opened 3 years ago by biolene
  3

• straingst run => non-standard tsv

  #7 opened 3 years ago by nick-youngblut
  2

• straingr prepare-ref => .fa.gz.fa.gz does not exist!

  #8 opened 3 years ago by nick-youngblut
  3

• prepare_strainge_db.py

  #4 opened 3 years ago by nick-youngblut
  3

• Use of BWA-MEM2 or BWA-MEME

  #9 opened 3 years ago by nick-youngblut
  1

• straingst kmerize => parallel

  #6 opened 3 years ago by nick-youngblut
  1

• Can I use my own genomes/data and skip the ncbi-download phase?

  #3 opened 4 years ago by drelo
  5

• ncbi-genome-download `ERROR: No entry for file ending in '_rm.out.gz'`

  #2 opened 4 years ago by drelo
  2

• Python packaging improvements

  #1 opened 6 years ago by lrvdijk
  0