Cross-species scRNA-seq Integration… Write a literature review on cross-species single-cell RNA-seq integration. Pull the primary methods papers and recent benchmarks. Output the report as a LaTeX doc and a compiled PDF. Dispatching five parallel literature-retrieval tracks — PubMed primary methods, bioRxiv preprints, OpenAlex citation counts, CELLxGENE multi-species atlas inventory, and orthology-free embedding methods.

In the generate_plan PubMed delegation step the agent writes "LIGER (31178118), Seurat v3 integration (31178118)" — the same PMID for two distinct primary methods papers. The same plan's OpenAlex step assigns them different DOIs (Seurat v3 10.1016/j.cell.2019.05.031, LIGER 10.1016/j.cell.2019.05.006), so the plan is internally inconsistent and at least one PMID is wrong. None of the PMIDs or DOIs in msg[10] trace to any in-window tool output — no PubMed/CrossRef/OpenAlex lookup has run (exec-log rows 04449b53, 57baea0a, 254f1378 are the two skill kernel.py auto-loads and the env-filter bash; msg[4] tool_results are skill-catalog listings only). The agent reads these findings and self-corrects in its next message. Acknowledged — the plan listed PMID 31178118 for both; the PubMed sub-agent caught the swap and the saved CSV carries the corrected pair (LIGER 31178122, Seurat v3 31178118).