Issues

• AF2 memory problem

  sokrypton/ColabFold#862 · Filter by author johnnypainter123 opened on Oct 15, 2026

• DB setup script fails when setting 'GPU=1'. Error = Invalid mask mode. No sequence lookup created!

  sokrypton/ColabFold#859 · Filter by author TomG75 opened on Oct 12, 2026

• ImportError: cannot import name 'decoded_ccd' from 'alphafold3.constants' (unknown location)

  sokrypton/ColabFold#857 · Filter by author vladislove2020 opened on Oct 5, 2026
  2

• MSA result download repeatedly times out after job reaches complete

  sokrypton/ColabFold#856 · Filter by author pngu1 opened on Sep 23, 2026

• ColabFold MSA Server Data Retention Question

  sokrypton/ColabFold#855 · Filter by author rano1256 opened on Sep 23, 2026

• RosettaFold2 Notebook Crashing due to Import Error

  sokrypton/ColabFold#850 · Filter by author AndrewLutsky opened on Sep 2, 2026
  1

• mmseqs expandaln issues: Cannot close data file /path/to/output/res_exp.xy

  sokrypton/ColabFold#847 · Filter by author LouisaMe09 opened on Aug 17, 2026
  2

• Inconsistent results from colabfold_search public API: random query-only A3M files

  sokrypton/ColabFold#845 · Filter by author LouisaMe09 opened on Jul 29, 2026
  2

• "Timeout while submitting to MSA server" This has been going on for a day. How do I fix it?

  sokrypton/ColabFold#843 · Filter by author ruichaomao opened on Jul 9, 2026
  3

• Segmentation fault / MLIR optimization error on NVIDIA RTX 5090 (Blackwell) with LocalColabFold 1.6.1

  sokrypton/ColabFold#841 · Filter by author Karol007 opened on Jul 1, 2026
  3

• ConnectTimeoutError to api.colabfold.com when using Boltz --use_msa_server

  sokrypton/ColabFold#839 · Filter by author Kj-23 opened on Jun 30, 2026

• Can not connect to the MSA server

  sokrypton/ColabFold#838 · Filter by author Jennyhu666 opened on Jun 30, 2026
  13

• Failed to mmap memory dataSize

  sokrypton/ColabFold#837 · Filter by author Little-Ghost opened on Jun 19, 2026

• Outlook: Will local colabfold_batch running at multi-thread GPU mode be online soon?

  sokrypton/ColabFold#834 · Filter by author Triiumpher opened on Jun 15, 2026

• issue about MSA server storage space

  sokrypton/ColabFold#827 · Filter by author ioj-91 opened on May 14, 2026
  5

• How to make colabfold_batch use more CPU cores for large ensemble generation?

  sokrypton/ColabFold#826 · Filter by author nematiaram opened on May 12, 2026

• ColabFold __ImportError

  sokrypton/ColabFold#825 · Filter by author lvxy97 opened on Apr 29, 2026
  8

• Confused about requirements for speed

  sokrypton/ColabFold#824 · Filter by author gabedol opened on Apr 22, 2026
  4

• IndentationError in colabfold.plot (plot_msa_v2)

  sokrypton/ColabFold#822 · Filter by author danielgarzonotero opened on Mar 30, 2026
  2

• colabfold_search v1.6.1 crashes using only paired or unpaired

  sokrypton/ColabFold#821 · Filter by author GBLille opened on Mar 30, 2026

• MSA requests remain in PENDING state (ColabFold server, Boltz2)

  sokrypton/ColabFold#820 · Filter by author dashatskiy opened on Mar 25, 2026
  2

• latest docker pull failed #tag unpublished

  sokrypton/ColabFold#818 · Filter by author Triiumpher opened on Mar 19, 2026

• Multimer error on ColabFold 1.6.0

  sokrypton/ColabFold#817 · Filter by author QuentinDuvertCurie opened on Mar 16, 2026
  3

• Bioemu colabfold notebook issue

  sokrypton/ColabFold#816 · Filter by author gulati-siddhant opened on Feb 27, 2026

• pairing endpoint + mode=env

  sokrypton/ColabFold#815 · Filter by author williamberman opened on Feb 26, 2026
  2