Issues

• Main README and docs do not mention funannotate2

  nextgenusfs/funannotate#1187 · Filter by author peterjc opened on Jul 31, 2026
  4

• Support Python 3.12 onwards

  nextgenusfs/funannotate#1184 · Filter by author peterjc opened on Jul 29, 2026

• Genes are misassigned to "Envelope glycoprotein gp160" by eggnog

  nextgenusfs/funannotate#1159 · Filter by author alexcritschristoph opened on May 11, 2026

• CMD ERROR: gmes_petap.pl

  nextgenusfs/funannotate#1154 · Filter by author Tassadaar opened on Mar 19, 2026
  3

• Query Regtarding Funannotate/MySQL

  nextgenusfs/funannotate#1151 · Filter by author ufaroooq opened on Feb 9, 2026
  3

• smcluster.proteins.fasta from antismash output is empty. funannotate annotate fails at MIBiG cross-reference stage

  nextgenusfs/funannotate#1147 · Filter by author eggrandio opened on Jan 7, 2026
  1

• Problem setting PASA MySQL

  nextgenusfs/funannotate#1136 · Filter by author eggrandio opened on Dec 14, 2025
  2

• CMD ERROR in Singularity container: GeneMark fails with "Can't locate FindBin.pm in @INC

  nextgenusfs/funannotate#1135 · Filter by author Jaabbey2005 opened on Dec 12, 2025
  2

• Tips for visualisation

  nextgenusfs/funannotate#1127 · Filter by author pwkooij opened on Sep 26, 2025

• error when running funannotate predict

  nextgenusfs/funannotate#1126 · Filter by author xiaorongsmile opened on Sep 22, 2025

• funannotate test fails at signalp step

  nextgenusfs/funannotate#1120 · Filter by author vkkodali opened on Jul 28, 2025
  2

• Suggestion: option to specify evidence type to '--other_gff'

  nextgenusfs/funannotate#1119 · Filter by author jamesord opened on Jul 17, 2025

• what data and files are needed for train step

  nextgenusfs/funannotate#1118 · Filter by author ds-gene104 opened on Jul 15, 2025

• CMD ERROR: stringtie

  nextgenusfs/funannotate#1117 · Filter by author shanmugavadivelps opened on Jul 9, 2025
  2

• tmp files after predict run

  nextgenusfs/funannotate#1112 · Filter by author keroguynes opened on Jun 25, 2025

• Can funanotate use strand-specific RNA-seq data to annotate overlapped gene?

  nextgenusfs/funannotate#1111 · Filter by author sysu-cxz opened on May 30, 2025
  1

• SignalP results not ending up in final annotation

  nextgenusfs/funannotate#1110 · Filter by author JWDebler opened on May 24, 2025
  10

• funannotate annotate fails at the BUSCO annotation step

  nextgenusfs/funannotate#1108 · Filter by author SM-2797 opened on May 20, 2025
  2

• funannotate iprscan local producing empty XML file

  nextgenusfs/funannotate#1106 · Filter by author EEscuderoL opened on May 9, 2025
  2

• Issue with PASA

  nextgenusfs/funannotate#1104 · Filter by author lalalagartija opened on May 6, 2025
  2

• trainGlimmerHMM ERROR 30: creating acceptor sites. Not enough data or check input files for wrong format.

  nextgenusfs/funannotate#1102 · Filter by author dicesaref opened on Apr 24, 2025

• Query Regarding Optimal --cpus Setting for Funannotate

  nextgenusfs/funannotate#1101 · Filter by author Nitin123-4 opened on Apr 19, 2025

• Unreasonably large introns

  nextgenusfs/funannotate#1098 · Filter by author drdna opened on Apr 10, 2025
  2

• Question on --augustus_species, --busco_db, and --busco_seed_species

  nextgenusfs/funannotate#1097 · Filter by author cizydorczyk opened on Mar 28, 2025
  4

• Automatic cleanup of tar.gz files after setup

  nextgenusfs/funannotate#1094 · Filter by author bernt-matthias opened on Feb 19, 2025
  1