Issues

• Issue with singularity and trainGlimmerHMM

  nextgenusfs/funannotate2#98 · Filter by author aldendirks opened on Sep 17, 2026
  1

• Problem with funannote2 annotate parsing from funannotate-addons results

  nextgenusfs/funannotate2#96 · Filter by author OceaneMion opened on Aug 26, 2026
  2

• predictions with RNA evidence

  nextgenusfs/funannotate2#92 · Filter by author xvazquezc opened on Aug 11, 2026
  3

• prothint.py:503: SyntaxWarning: invalid escape sequence '\.'

  nextgenusfs/funannotate2#88 · Filter by author peterjc opened on Aug 3, 2026
  3

• No "funannotate2 check" command?

  enhancement
  nextgenusfs/funannotate2#87 · Filter by author peterjc opened on Aug 3, 2026
  1

• Why can't install funannotate2 Databases

  nextgenusfs/funannotate2#78 · Filter by author zut0may0 opened on Jul 15, 2026
  6

• Genemark run failed: '_io.TextIOWrapper' object has no attribute 'splitlines'

  nextgenusfs/funannotate2#61 · Filter by author user0380 opened on May 18, 2026
  1

• Problem on finding best augustus species

  nextgenusfs/funannotate2#60 · Filter by author 444thLiao opened on May 7, 2026

• Bug with pyfastx in f2 train [with solution]

  nextgenusfs/funannotate2#59 · Filter by author edwhisnant opened on Apr 28, 2026
  3

• Augustus CMD ERROR during f2 predict

  nextgenusfs/funannotate2#54 · Filter by author edwhisnant opened on Apr 21, 2026
  3

• Potential bug in tmp directory cleanup

  nextgenusfs/funannotate2#49 · Filter by author edwhisnant opened on Apr 2, 2026
  3

• diploid assemblies, how do we annotate?

  enhancementquestion
  nextgenusfs/funannotate2#47 · Filter by author nextgenusfs opened on Mar 19, 2026
  2

• ERROR in parsing gene gapmm2_4

  nextgenusfs/funannotate2#44 · Filter by author Iruj-04 opened on Mar 3, 2026
  5

• Separate genes are merging as single gene with long intron

  nextgenusfs/funannotate2#43 · Filter by author drew-olson-tmru opened on Feb 22, 2026
  15

• problem installing funannotate 26.02.12

  nextgenusfs/funannotate2#42 · Filter by author patmsim opened on Feb 19, 2026
  5

• ERROR in train module :

  nextgenusfs/funannotate2#41 · Filter by author patmsim opened on Feb 13, 2026
  2

• IndexError: list index out of range

  nextgenusfs/funannotate2#38 · Filter by author labpro1-commits opened on Feb 11, 2026
  2

• Request for feature

  nextgenusfs/funannotate2#36 · Filter by author rohitlb-1999 opened on Dec 17, 2025
  1

• Question regarding funannotate annotation of UTR

  nextgenusfs/funannotate2#34 · Filter by author OceaneMion opened on Nov 17, 2025

• TypeError funannotate2 train Choosing best augustus species based on taxonomy

  nextgenusfs/funannotate2#33 · Filter by author termithorbor opened on Nov 5, 2025
  2

• Failure in annotate.py with lookup_taxonomy

  nextgenusfs/funannotate2#32 · Filter by author edwhisnant opened on Oct 16, 2025
  3

• [ERROR] failed to open file 'funannotate2-db/mito.refseq.fasta': No such file or directory

  nextgenusfs/funannotate2#18 · Filter by author marcinschmidt opened on Jul 9, 2025
  3

• Busco completeness missing genes

  nextgenusfs/funannotate2#15 · Filter by author termithorbor opened on Jul 1, 2025
  1

• Illegal instruction

  nextgenusfs/funannotate2#9 · Filter by author FKazuki0801 opened on May 29, 2025
  6

• Issues with inputting unmasked sequences

  nextgenusfs/funannotate2#6 · Filter by author edwhisnant opened on Apr 30, 2025
  11