Issues

• Seq with messy location and unknown time on usher tree

  yatisht/usher#440 · Filter by author xz-keg opened on Aug 11, 2026
  3

• Main Usher Tree Option Not Working

  yatisht/usher#439 · Filter by author ryhisner opened on Jul 16, 2026
  3

• Usher/Nextstrain Error: "Couldn't load JSONs for...."

  yatisht/usher#438 · Filter by author ryhisner opened on Jun 7, 2026
  6

• Inconsistent matUtils extract pathing: nwks segfault, JSONs hang infinitely, pbs write to invalid paths (not a dupe of #211)

  yatisht/usher#437 · Filter by author aofarrel opened on Jun 2, 2026

• usher-sampled: -T flag not respected by Taskflow executors → ~9000 threads on multi-core hosts

  yatisht/usher#433 · Filter by author Colossus opened on May 7, 2026
  3

• matUtils summary non-deterministic

  yatisht/usher#427 · Filter by author aofarrel opened on Jan 23, 2026
  3

• missing output from version 0.2.1 onwards (expanded subtrees)

  yatisht/usher#421 · Filter by author lsterck opened on Nov 17, 2025

• PE.1.2 branch not annotated on SC2 tree

  yatisht/usher#416 · Filter by author corneliusroemer opened on Sep 13, 2025

• Metadata of provided reference tree

  yatisht/usher#412 · Filter by author jcgrenier opened on Aug 21, 2025

• Regression (v0.6.6): usher creates tree with 0 branch length

  yatisht/usher#411 · Filter by author gp201 opened on Aug 19, 2025

• matOptimize with VCF hits SIGTRAP error condition on some input trees/VCFs

  yatisht/usher#406 · Filter by author AngieHinrichs opened on Jun 27, 2025

• Meaning of warning

  yatisht/usher#405 · Filter by author josephhughes opened on Jun 24, 2025
  9

• Support newer protobuf

  yatisht/usher#404 · Filter by author corneliusroemer opened on Jun 19, 2025

• New method to get seqs from Genbase

  yatisht/usher#401 · Filter by author xz-keg opened on Jun 5, 2025
  5

• Remove 6183, 9142 and 13339 from masked sites

  yatisht/usher#397 · Filter by author xz-keg opened on May 23, 2025
  1

• matUtils extract creates invalid MAT/NWK with branch lengths of 0

  yatisht/usher#392 · Filter by author aofarrel opened on Apr 1, 2025
  2

• Build for Apple silicon (ARM)

  yatisht/usher#391 · Filter by author corneliusroemer opened on Mar 31, 2025
  2

• Output nwk filenames are inconsistent

  yatisht/usher#389 · Filter by author aofarrel opened on Feb 14, 2025

• Segmentation fault

  yatisht/usher#388 · Filter by author guoqiangu opened on Dec 18, 2024

• debugging the macos-13 github runner workflow

  yatisht/usher#387 · Filter by author AngieHinrichs opened on Dec 4, 2024
  1

• Mask fewer sites, the mask sites include lots of false positives

  yatisht/usher#384 · Filter by author corneliusroemer opened on Nov 12, 2024
  3

• Conda boost-cpp dependancy clash

  yatisht/usher#379 · Filter by author jodyphelan opened on Aug 4, 2024
  1

• NC_045512 shows up in MAT when extracting from a WNV auspice tree

  yatisht/usher#378 · Filter by author jcw349 opened on Jul 1, 2024
  5

• does matUtils extract has -M function?

  yatisht/usher#376 · Filter by author liamxg opened on May 21, 2024
  3

• what is the cluster_span meaning?

  yatisht/usher#375 · Filter by author liamxg opened on May 20, 2024
  1