Metadata
| Status | done ‖ paused |
|---|---|
| Created | 2026-06-18T08:44:06.503845837+00:00 |
| Completed | 2026-06-18T08:51:20.991075812+00:00 |
| Tags | manuscript, submission |
Description
Edit the active LaTeX manuscript so the abstract, Results mouse paragraph, Discussion, Methods mouse note, and Fig. 4C caption state the sequence-similar subtelomere / zygotene bouquet finding directly. Keep signal-stripping controls only as Methods mechanics, not as abstract/results/caption caveats.
Validation
- The explicit strike phrases are absent from submission/paper.tex.
- Abstract contains: Sequence-similar subtelomeres cluster in three dimensions, peaking at the zygotene bouquet.
- Mouse Results contains: Contact rises into zygotene and falls thereafter (rho series 0.419 / 0.614 / 0.576 / 0.245), matching the bouquet.
- Fig. 4C caption says per-pair Spearman peaks at the zygotene bouquet.
- Mouse Methods contains only the strict-MAPQ method note about removing the paralogous PHR body.
- submission make is attempted and the result is recorded.
Depends on
- (none)
Required by
- (none)
Log
- 2026-06-18T08:44:06.470184407+00:00 Task paused
- 2026-06-18T08:44:18.784657787+00:00 Applied focused patch to submission/paper.tex: replaced abstract 3D hedge with zygotene bouquet finding; removed mouse Results zygotene-peak hedge; changed Fig. 4C caption to 'per-pair Spearman peaks at the zygotene bouquet'; reduced mouse Methods control text to strict-MAPQ method note; removed result/caption control defenses.
- 2026-06-18T08:46:37.816182905+00:00 Validation grep passed: explicit strike phrases absent; required abstract, mouse Results, Fig. 4C caption, and strict-MAPQ Methods replacement text present. Initial plain make failed before reading paper.tex because active Guix TeX profile lacks pdflatex.fmt/GUIX_TEXMF. Temporary Guix TeX shell reached LaTeX pass 1 and failed on missing multirow.sty, so continuing by adding class dependencies to the temporary shell.
- 2026-06-18T08:49:28.934151332+00:00 Build validation status: available-package Guix shell now reaches jnl.cls imports and fails on algorithm.sty. This is after resolving pdflatex.fmt/GUIX_TEXMF, geometry, multirow, mathrsfs, manyfoot, etc. Checking broad texlive package before recording final environment blocker.
- 2026-06-18T08:50:35.253436620+00:00 Final build note: plain make fails before manuscript processing because current ~/.guix-profile has texlive-bin without pdflatex.fmt/GUIX_TEXMF. A temporary Guix shell with available class dependencies reaches jnl.cls and fails at missing algorithm.sty; broad texlive would download ~3.4 GB, so stopped. Source-level validation passed; build remains an environment/toolchain blocker.
- 2026-06-18T08:51:20.991083697+00:00 Task marked as done