Issues

• Bug: Clustering disparity between the same gene in query and target genomes

  soedinglab/spacedust#23 · Filter by author atsh00001 opened on Jun 26, 2026
  3

• Bug Report: Can not allocate entries memory in IndexTable::initMemory persists regardless of available memory and --split settings

  soedinglab/spacedust#22 · Filter by author Xiewentao17 opened on Feb 27, 2026

• step-by-step scripts for the example data

  soedinglab/spacedust#20 · Filter by author BinhongLiu opened on Dec 30, 2025

• How to cluster and filter gene clusters across many genomes to infer their distribution

  soedinglab/spacedust#19 · Filter by author JoshPhd opened on Dec 24, 2025

• Problem of --cluster-size 1

  soedinglab/spacedust#17 · Filter by author lalintao opened on Nov 27, 2025
  2

• Error occurred when mapping the protein sequence to the structure database

  soedinglab/spacedust#16 · Filter by author longlu428 opened on Nov 19, 2025

• comparison accuracy of "spacedust clustersearch" decreases significantly when the targetdb increases

  soedinglab/spacedust#15 · Filter by author DUANZIHAOO opened on Nov 14, 2025
  2

• How can I create a custom reference database

  soedinglab/spacedust#14 · Filter by author neptuneyt opened on Nov 1, 2025

• No datafile could be found for /Database/FoldSeekDB/PDB100_member_to_set!

  soedinglab/spacedust#13 · Filter by author neptuneyt opened on Nov 1, 2025
  1

• Reduction of redundancy in gene clusters

  soedinglab/spacedust#12 · Filter by author lalintao opened on Oct 28, 2025
  2

• Whether spacedust supports MMseqs2-GPU version？

  soedinglab/spacedust#11 · Filter by author zhaorui-bi opened on Oct 8, 2025

• Cant find the Google Colab notebook in the paper

  soedinglab/spacedust#10 · Filter by author Shild94 opened on Oct 7, 2025
  2

• [Question] Paper doesn't mention fungal genomes--any reason it shouldn't work?

  soedinglab/spacedust#9 · Filter by author DaRinker opened on Sep 30, 2025
  2

• "Clusterhits failed. Invalid query lookup record." with .fna and .gff3 files from NCBI

  soedinglab/spacedust#7 · Filter by author SamuelSchwab opened on Jun 17, 2025
  8

• version tags

  soedinglab/spacedust#6 · Filter by author KerrinSteensen opened on Nov 5, 2024
  3

• Not enough GFF files are provided. Some results might be omitted Error: gff2db failed

  soedinglab/spacedust#4 · Filter by author abrozzi opened on Oct 11, 2024
  6

• Unable to run spacedust normally

  soedinglab/spacedust#3 · Filter by author Dx-wmc opened on Oct 14, 2023
  4

• Support for circular sequences

  soedinglab/spacedust#2 · Filter by author apcamargo opened on Sep 26, 2023