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  1. IGB
  2. IGBF-3912

Investigate: Unexpected behavior when adding subsequent custom genomes

    Details

    • Type: Bug
    • Status: To-Do (View Workflow)
    • Priority: Major
    • Resolution: Unresolved
    • Affects Version/s: None
    • Fix Version/s: None
    • Labels:
      None

      Description

      I've found a bug in IGB 10.1.0 that relates to the addition of custom genomes to IGB.

      What I found is that, while viewing a custom genome in IGB, attempting to add a subsequent custom genome to IGB adds that second genome to the chromosome list of the custom genome that was being viewed. Expected behavior is that the second custom genome would be added to the Species drop-down menu as a separate genome. This may be an issue with how IGB differentiates genomes based on the value populated in the Genome Version field because the two custom genomes I added had the same value for Genome Version (S_SPECIES_MMM_YYYY).

      This issue is appearing in 9.1.8 and beyond, though note that I did not test earlier releases.

      To reproduce the issue as I found it, do the following:

      1. Open IGB 9.1.8
      2. Click the "Open genome from file." (double helix) button along the top of IGB
      3. Click "Browse..."
      4. Select "GIC31_complete.fna", then click "Open"
      5. In the Genus field, type "Samplegic31"
      6. Click "OK"
      7. Drag and drop "GIC31_complete_proteins.gff" into IGB
      8. Click "Load Data"
      9. Click "Load Sequence"
      10. Observe the Chromosome list on the right side of IGB and notice one listing (strain_GIC31_complete_genome)
      11. Click the "Open genome from file." (double helix) button along the top of IGB
      12. Click "Browse..."
      13. Select "gsD_SM51.fna", then click "Open"
      14. In the Genus field, type "Samplesm51"
      15. Click "OK"
      16. Observe the Chromosome list on the right side of IGB and notice that same listing from earlier, plus 25 new scaffolds
      17. Click the Species drop-down menu in the top-right of IGB
      18. Observe only one custom genome where there should be two (Samplegic31 SPECIES)

        Attachments

        1. GIC31_complete.fna
          2.82 MB
          Paige Kulzer
        2. GIC31_complete_proteins.gff
          399 kB
          Paige Kulzer
        3. gsD_SM51.fna
          7.35 MB
          Paige Kulzer
        4. Screenshot 2024-09-18 at 14.23.00.png
          194 kB
          Paige Kulzer

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              • Assignee:
                nfreese Nowlan Freese
                Reporter:
                pkulzer Paige Kulzer
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                Dates

                • Created:
                  Updated: