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Mapping Error

Tags

  • type: bug
  • status: stalled
  • priority: medium
  • assigned: zachs, fredm, flisso
  • keywords: gn2, genenetwork2, genenetwork 2, mapping

Reproduction

  • Go to https://staging.genenetwork.org/
  • For 'Species' select "Arabidopsis (Arabidopsis thaliana, araTha1)"
  • For 'Group' select "BayXSha(RIL by sib-mating)"
  • For 'Type' select "arabidopsis seeds"
  • For 'Dataset' select "Arabidopsis BayXShaXRIL_expr_reg _ATH1"
  • Leave 'Get Any' blank
  • Enter "*" for "Combined"
  • Click "Search"
  • On the search results page, click on "AT1G01010"
  • Expand the "Mapping Tools" section
  • For 'Chromosome' select "All"
  • For 'Minor Allele ≥' enter "0.05"
  • For 'Use LOCO' select "Yes"
  • Ignore covariates
  • Click "Compute"

Expected

The system would compute the maps and display the mapping diagram(s) and data.

Actual

The computation fails with:

      GeneNetwork 2.11-rc2  https://staging.genenetwork.org/loading ( 6:50PM UTC Jul 03, 2024) 
Traceback (most recent call last):
  File "/gnu/store/jsvqai0gz6fn40k7kx3r12yq4hzfini6-profile/lib/python3.10/site-packages/flask/app.py", line 1523, in full_dispatch_request
    rv = self.dispatch_request()
  File "/gnu/store/jsvqai0gz6fn40k7kx3r12yq4hzfini6-profile/lib/python3.10/site-packages/flask/app.py", line 1509, in dispatch_request
    return self.ensure_sync(self.view_functions[rule.endpoint])(**req.view_args)
  File "/gnu/store/jsvqai0gz6fn40k7kx3r12yq4hzfini6-profile/lib/python3.10/site-packages/gn2/wqflask/views.py", line 812, in loading_page
    for sample in samples:
TypeError: 'NoneType' object is not iterable

Updates

This is likely just because the genotype file doesn't exist in the necessary format (BIMBAM). We probably need to convert the R/qtl2 genotypes to BIMBAM.

Stalled

This is currently stalled, until we can upload genotypes via the uploader.

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