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

Status: Open.

#438 In yatisht/usher;

· ryhisner opened on Jun 7, 2026

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

Status: Open.

#437 In yatisht/usher;

· aofarrel opened on Jun 2, 2026

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

Status: Open.

#433 In yatisht/usher;

· Colossus opened on May 7, 2026

matUtils summary non-deterministic

Status: Open.

#427 In yatisht/usher;

· aofarrel opened on Jan 23, 2026

missing output from version 0.2.1 onwards (expanded subtrees)

Status: Open.

#421 In yatisht/usher;

· lsterck opened on Nov 17, 2025

PE.1.2 branch not annotated on SC2 tree

Status: Open.

#416 In yatisht/usher;

· corneliusroemer opened on Sep 13, 2025

Metadata of provided reference tree

Status: Open.

#412 In yatisht/usher;

· jcgrenier opened on Aug 21, 2025

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

Status: Open.

#411 In yatisht/usher;

· gp201 opened on Aug 19, 2025

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

Status: Open.

#406 In yatisht/usher;

· AngieHinrichs opened on Jun 27, 2025

Meaning of warning

Status: Open.

#405 In yatisht/usher;

· josephhughes opened on Jun 24, 2025

Support newer protobuf

Status: Open.

#404 In yatisht/usher;

· corneliusroemer opened on Jun 19, 2025

New method to get seqs from Genbase

Status: Open.

#401 In yatisht/usher;

· xz-keg opened on Jun 5, 2025