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Re-map score sets with mapped variants that have neither a mapping nor an error #820

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Description

@bencap

Problem

Three of the 1,170 mapped score sets in the public dump have mapped variants with both post_mapped and error_message null. They came from dcd-mapping runs that were killed during BLAT alignment, most likely out of memory, before the mapper could report a reason, and the worker stored null for the missing error.

Both causes are gone on the code shipping in 2026.3.0:

  • dcd_mapping2 runs BLAT with shell=False, a timeout and an output file (align.py:185), so BLAT's output is no longer held in memory.
  • RT (the allele-centric mapping work on feature/bencap/allele-centric-mapping-and-storage)'s mapping job requires a typed outcome on every mapped record and fails the job when one is missing (worker/jobs/variant_processing/mapping.py), so a null/null row can't be written.

Scope

  • After 2026.3.0 deploys, find the score sets whose current mappings have neither a mapping nor an error.
  • Re-run mapping for those score sets.

Acceptance criteria

  • The query for current mapping records with no post-mapped allele and no error returns no rows in prod.
  • The affected score sets are listed in this issue, with their re-mapping job ids.

Activity

  1. added theissue type on Aug 7, 2026
  2. added this to the R2026.4 milestone on Sep 24, 2026
  3. changed the title [-]Mapping worker can silently persist error_message: null on total mapping failure (BLAT OOM)[/-] [+]Re-map score sets with mapped variants that have neither a mapping nor an error[/+] on Sep 24, 2026
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