Issues

• "engines" error message

  dereneaton/ipyrad#614 · Filter by author jesus-mavarez opened on Nov 14, 2025
  11

• problem installing on mac m4

  dereneaton/ipyrad#613 · Filter by author benfitz01 opened on Nov 3, 2025
  1

• Paired-end R1/R2 reads not merging in ddRAD assembly #step1

  dereneaton/ipyrad#612 · Filter by author manhbio opened on Oct 27, 2025
  12

• Mapping to Whole reference genome, ipyrad error step 3

  dereneaton/ipyrad#610 · Filter by author littlelimia opened on Oct 13, 2025
  5

• Step 7 error. integer division or modulo by zero

  dereneaton/ipyrad#606 · Filter by author jesus-mavarez opened on Sep 13, 2025
  1

• work with demultiplexed sequence

  dereneaton/ipyrad#604 · Filter by author alnusmeinata opened on Jun 26, 2025
  5

• Encountered an Error. Message: Can't recognize paired fastq files.

  dereneaton/ipyrad#601 · Filter by author ClaudiaPaetzold opened on May 23, 2025
  1

• 3D-GBS, not suitable with pair3rad, because SE data

  dereneaton/ipyrad#600 · Filter by author edgagnon opened on Apr 28, 2025
  2

• analysis.tetrad: Broken for toytree and updated Tetrad API

  dereneaton/ipyrad#599 · Filter by author isaacovercast opened on Apr 14, 2025
  1

• error in step 5

  dereneaton/ipyrad#592 · Filter by author onmikula opened on Feb 6, 2025
  1

• Error ipyrad step 3

  dereneaton/ipyrad#591 · Filter by author urigarciaunam opened on Feb 5, 2025
  1

• Files required for steps 4-7

  dereneaton/ipyrad#588 · Filter by author carlahurt opened on Jan 9, 2025
  3

• analysis.bpp - Toytree 3 compatibility

  dereneaton/ipyrad#586 · Filter by author isaacovercast opened on Dec 9, 2024

• No progress in struct.run

  dereneaton/ipyrad#584 · Filter by author Zombiekotze opened on Nov 29, 2024
  1

• ipa.raxml should have a draw function

  dereneaton/ipyrad#583 · Filter by author isaacovercast opened on Nov 9, 2024

• PCA cookbook is out of date

  dereneaton/ipyrad#579 · Filter by author isaacovercast opened on Sep 22, 2024

• Step 2 why is it trimming R1/R2 ?

  dereneaton/ipyrad#576 · Filter by author isaacovercast opened on Sep 12, 2024

• Support for muscle v5

  dereneaton/ipyrad#572 · Filter by author isaacovercast opened on Aug 21, 2024
  1

• ipa.pca: Include an optional 'default' group for imap to catch samples not included

  dereneaton/ipyrad#570 · Filter by author isaacovercast opened on Aug 7, 2024

• ipa.pca: Allow to pass in a pops file to populate imap

  dereneaton/ipyrad#569 · Filter by author isaacovercast opened on Aug 7, 2024

• analysis.treemix - toytree v3.0 compatibility

  dereneaton/ipyrad#559 · Filter by author isaacovercast opened on Apr 29, 2024

• problems downloading Pedicularis example data

  dereneaton/ipyrad#552 · Filter by author jesus-mavarez opened on Mar 22, 2024
  1

• ipyrad error step 6: ValueError: cannot copy sequence with size 298 to array axis with dimension 299

  dereneaton/ipyrad#551 · Filter by author IvonedeBem opened on Mar 20, 2024
  4

• *.ustr file and other files not generated when using a genome as a reference in the assembly method

  dereneaton/ipyrad#542 · Filter by author aroavaron opened on Jan 28, 2024
  10

• In Step 7: Message: ValueError: not enough values to unpack (expected 2, got 1)

  dereneaton/ipyrad#541 · Filter by author aroavaron opened on Jan 27, 2024
  5