Issues

• Conda not solving for 1.8.1, nothing provides __cuda

  bug
  jtamames/SqueezeMeta#1051 · Filter by author fpusan opened on Oct 26, 2026

• Error in make_databases.pl

  jtamames/SqueezeMeta#1050 · Filter by author marinamartinezalvaro opened on Oct 20, 2026
  3

• fastp hanging up

  bug
  jtamames/SqueezeMeta#1049 · Filter by author carleton-envbiotech opened on Oct 1, 2026
  3

• Step 4 Diamond finished abnormally

  jtamames/SqueezeMeta#1048 · Filter by author ecronmiller opened on Sep 17, 2026
  5

• Support for eggNOG v7

  jtamames/SqueezeMeta#1046 · Filter by author NaokiShibata opened on Sep 8, 2026
  4

• Step 5 Resume bug

  bug
  jtamames/SqueezeMeta#1045 · Filter by author MicroSeq opened on Sep 2, 2026
  1

• Unknown option: force_overwrite for sqm_reads.pl

  enhancementSQM_reads
  jtamames/SqueezeMeta#1015 · Filter by author SimonChen1997 opened on Jan 22, 2026
  2

• HMMER3 step 5 slow and seems to not use multiple processors?

  enhancement
  jtamames/SqueezeMeta#1012 · Filter by author dutchscientist opened on Dec 8, 2025
  11

• Add a --notax flag to SqueezeMeta, sqm_reads and sqm_longreads

  enhancement
  jtamames/SqueezeMeta#966 · Filter by author fpusan opened on Apr 7, 2025

• Feature Request: Gene Clustering for Non-Redundant Gene Catalog

  jtamames/SqueezeMeta#919 · Filter by author fconstancias opened on Jan 8, 2025
  6

• Workflow, tool version outline

  enhancement
  jtamames/SqueezeMeta#825 · Filter by author s-junguy opened on Apr 11, 2024
  7

• "zip file is corrupt" when loading a zipped project into SQMtools

  bugSQMtools
  jtamames/SqueezeMeta#755 · Filter by author fpusan opened on Nov 19, 2023
  4

• Add the taxonomic category "Kingdom" for eukaryotes

  enhancementTaxonomic annotation
  jtamames/SqueezeMeta#747 · Filter by author glenjasper opened on Nov 8, 2023
  4

• Using dedupe.sh to identify and remove contigs contained in others (merged mode)

  Assemblyenhancementmerged modeseqmerge mode
  jtamames/SqueezeMeta#701 · Filter by author eperezv opened on Jun 26, 2023
  3

• sqm_longreads yields wrong mcount table

  bugsqm_longreadsSQM_reads
  jtamames/SqueezeMeta#686 · Filter by author jllavin77 opened on May 19, 2023
  10

• 04.rundiamond.pl error while using sqm_annot.pl

  jtamames/SqueezeMeta#558 · Filter by author PuspenduSardar opened on Oct 10, 2022
  8

• Support for EggNOG version 5.0.2

  databasesenhancement
  jtamames/SqueezeMeta#506 · Filter by author mdehollander opened on Jun 20, 2022
  2

• sqm_reads2tables.py problem

  enhancement
  jtamames/SqueezeMeta#477 · Filter by author fpeti11 opened on May 4, 2022
  13