109:scope: June 4 `lsmc` workspace setup, local fork-identity cleanup, `forked` cluster launch, catalog retry driver fixes, and the final DayOA evidence-manifest failure that blocked a near-complete workflow
110:applies_to: cwd=/Users/jmajor/projects/lsmc plus Codex/browser workflow around `Clone Daylily forks into lsmc`; reuse_rule=reuse for similar `lsmc-bio` DayOA/DYEC fork work, cluster bring-up, or retry/debug loops in these local clones, but re-check the live repo paths, cluster name, branch/SHA, and current workflow state before reusing exact statuses
132:## Task 3: fixed the DayOA evidence-manifest symlink boundary and turned the user’s “rerun everything until `rc=0`” ask into a command-state table plus targeted retries [chronicle memory]
136:- /Users/jmajor/.codex/memories/extensions/chronicle/resources/2026-06-04T04-49-00-yzum-10min-memory-summary.md (cwd=Codex chat `Clone Daylily forks into lsmc` plus local DayOA/DYEC worktrees, rollout_path=/Users/jmajor/.codex/memories/extensions/chronicle/resources/2026-06-04T04-49-00-yzum-10min-memory-summary.md, updated_at=2026-06-04T04:49:00+00:00, thread_id=None, `EvidenceManifestError`, `path.resolve()` root cause, focused tests, and `jem-dev` push at `ebc59c09d3ab72b12fb3ba40b601c1d0506bb4e1`) [chronicle memory]
156:- the DayOA evidence-manifest root cause on June 4 was specific: `path.resolve()` made symlinks under `results/day/...` appear outside the analysis root when they pointed at `/fsx/references/...`; the accepted fix preserved the local symlink path for root checks while still hashing target content, and focused verification included `test_evidence_manifest.py` (`30 passed`), `test_shell_wrapper_contracts.py`, and `bash -n bin/day_run` [Task 3]
347:# Task Group: daylily-ephemeral-cluster / daylily-omics-analysis June 2026 `dyec5128` BWA temp-dir tuning, DayOA/Sarek relaunch, and command-catalog validation [chronicle memory]
348:scope: June 3 `dyec5128` live compute tuning, `/scratch` versus `/dev/shm` diagnosis, DayOA/Sarek bootstrap fixes, and read-only command-catalog status reporting
349:applies_to: cwd=/Users/jmajor/.codex/worktrees/be82/daylily-ephemeral-cluster plus /Users/jmajor/projects/daylily/daylily-omics-analysis and browser/Codex workflow around `dyec5128`; reuse_rule=reuse for similar DayOA/DYEC HG003, `bwa_mem2`, Sarek relaunch, or catalog-validation questions in this repo family, but re-check the current cluster, live run ids, cache paths, and DRA/run-mount state before reusing exact status claims
361:## Task 2: treated DayOA/Sarek relaunch defects as bootstrap/setup work, not one-off run-local patching, and staged the DayOA -> DYEC release train [chronicle memory]
365:- /Users/jmajor/.codex/memories/extensions/chronicle/resources/2026-06-03T12-45-00-Bjgk-10min-memory-summary.md (cwd=browser workflow plus `Access sacct from ubuntu`, rollout_path=/Users/jmajor/.codex/memories/extensions/chronicle/resources/2026-06-03T12-45-00-Bjgk-10min-memory-summary.md, updated_at=2026-06-03T12:45:00+00:00, thread_id=None, DayOA `dyec5128_hg003_5x_ilmn_snv_dayoa2040_20260603T122856Z`, Sarek relaunch state, and headnode-bootstrap fix request) [chronicle memory]
376:- /Users/jmajor/.codex/memories/extensions/chronicle/resources/2026-06-03T14-07-00-PpcV-10min-memory-summary.md (cwd=browser workflow plus `/fsx/analysis_results/dyec5128/init/daylily-omics-analysis`, rollout_path=/Users/jmajor/.codex/memories/extensions/chronicle/resources/2026-06-03T14-07-00-PpcV-10min-memory-summary.md, updated_at=2026-06-03T14:07:00+00:00, thread_id=None, failed/not-run relaunch variant, DRA-run-command skip because run mounts were absent, and `dy-r -j 100` planning) [chronicle memory]
386:- when the user asks whether a DayOA/Sarek defect “could be fixed by the headnode setup script,” treat missing FSx directories, stale license paths, and shared-cache lock handling as bootstrap/setup fixes rather than preserving them as ad hoc run-local steps [Task 2]
394:- the DayOA/Sarek relaunch state worth preserving is that the benchmark used already-mounted references/FASTQs, so missing `/fsx/run_dir_mounts` in the compact preflight was expected for that shape; the real durable bootstrap fixes were the stale Sentieon license path in `~/.config/daylily/daylily_cli_global.yaml` and moving Sarek away from one shared writable Singularity cache into a per-user or per-analysis cache root under `/fsx/work/.../container_cache` [Task 2]
403:- symptom: DayOA/Sarek relaunch defects get patched manually per run and then recur on the next launch -> cause: bootstrap-owned config and cache-path problems were treated as analysis-local quirks -> fix: move standard FSx-directory creation, license-path repair, and non-shared cache roots into the headnode setup/bootstrap path [Task 2]
407:scope: June 3 DayOA source debugging around `benchmark:` stanzas on target aliases, rules without outputs, and explicit `localrules` membership
408:applies_to: cwd=/Users/jmajor/projects/daylily/daylily-omics-analysis plus related Codex worktrees under /Users/jmajor/.codex/worktrees/214e/daylily-omics-analysis; reuse_rule=reuse for similar DayOA retry failures, benchmark-output complaints, or source cleanup decisions in this repo family, but re-check the current dirty worktree, current release/tag state, and whether a rule does real executable work before removing benchmarks
425:- /Users/jmajor/.codex/memories/extensions/chronicle/resources/2026-06-03T15-58-00-siQi-10min-memory-summary.md (cwd=browser workflow plus `BCL-convert-expts`, rollout_path=/Users/jmajor/.codex/memories/extensions/chronicle/resources/2026-06-03T15-58-00-siQi-10min-memory-summary.md, updated_at=2026-06-03T15:58:00+00:00, thread_id=None, careful benchmark fix release state at DayOA `2.0.43` annotated tag) [chronicle memory]
449:- symptom: a completed DayOA output still fails on retry because a benchmark TSV is missing -> cause: a target alias or output-less local rule still declares `benchmark:` even though it does not perform benchmarkable work -> fix: inspect the rule body first and strip benchmarks only from the non-executable/alias cases [Task 1]
454:scope: June 3 `bcl2fq` queue bring-up, read-only DayOA BCL scratch-run monitoring, `/dev/shm` probe follow-up, and the user’s parallel docs/planning asks while a live run stayed under observation
455:applies_to: cwd=/Users/jmajor/.codex/worktrees/be82/daylily-ephemeral-cluster plus /Users/jmajor/projects/daylily/daylily-omics-analysis and browser/Codex workflow around the same run; reuse_rule=reuse for similar DYEC queue-capacity, DayOA scratch-output, or live-monitoring questions in this repo family, but re-check the active cluster, queue/node availability, and exact ledger/workset ids before reusing status claims
457:## Task 1: launched the single-lane `L003` scratch-backed DayOA run on `dyec0602bcl` and proved the queue was blocked on unavailable `bcl2fq` capacity rather than workflow failure [chronicle memory]
469:## Task 2: added `bcl2fq-i384-nvme-test`, ruled out `/dev/shm` plus `O_DIRECT` as the current blocker, and staged the next DayOA/DYEC release-train work [chronicle memory]
477:- bcl2fq-i384-nvme-test, c8id384, mr8id384, ParallelCluster validator, pytest -q tests/test_packaged_defaults.py tests/test_resources_extraction.py, PROBE-001, 3d294702, /dev/shm, shared-thread-odirect-output false, ldlm_completion_ast, Inspect DayOA and release state
478:## Task 3: verified `sacct` was unavailable from `ubuntu`, kept live Slurm monitoring read-only, and captured the user’s public-facing DayOA/DYEC docs expectations [chronicle memory]
482:- /Users/jmajor/.codex/memories/extensions/chronicle/resources/2026-06-03T08-36-00-seYm-10min-memory-summary.md (cwd=browser workflow plus Codex DayOA monitoring and docs-planning threads, rollout_path=/Users/jmajor/.codex/memories/extensions/chronicle/resources/2026-06-03T08-36-00-seYm-10min-memory-summary.md, updated_at=2026-06-03T08:36:00+00:00, thread_id=None, public-facing docs request, live `bcl2fq` monitoring, and no-intervention boundary) [chronicle memory]
493:- when the user drafts DayOA/DYEC documentation work, they want public-safe main docs with repo philosophy/design, Mermaid diagrams, concrete CLI/setup/allowed-command coverage, and language that makes clear DYEC is not locked to one workflow-manager style; completed or old plans/working docs should move out of the main docs surface into `docs/jem_working_docs/` / `docs/jerd_working_docs/` rather than staying mixed with current guidance [Task 3]
499:- the June 3 scratch-run path had a durable ledger/workset shape: a fresh DayOA workset with scratch support, `samples.tsv` generated from `BCLConvert_Data`, a dry-run that planned exactly one `run_bclconvert_lane` for `L003`, and a live `dy-r` launched in the required initialized tmux session with validation/provenance files already written before queue polling [Task 1]
502:- `dyec0602bcl` was the new cluster name for this work arc, and the visible run-mount evidence said the DRA became `AVAILABLE` after the earlier short wait timed out, with no duplicate mount created; the headnode-visible mount path was `/fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/` [Task 1]
518:scope: native DayOA tile-shard implementation, June 2 shard008 benchmark/release evidence, and the exact merge/ODIRECT contract the user expects before more BCL experiments
519:applies_to: cwd=/Users/jmajor/projects/daylily/daylily-omics-analysis plus /Users/jmajor/.codex/worktrees/be82/daylily-ephemeral-cluster and /Users/jmajor/.codex/worktrees/dyec-fsx-dra-mounts/daylily-ephemeral-cluster; reuse_rule=reuse for similar DayOA/DYEC BCL Convert tile-sharding, benchmark comparison, or launch-planning work in this repo family, but re-check the current DayOA tag, benchmark files, and whether the run is single-lane, compute-tuned, or full-flowcell
521:## Task 1: implemented native DayOA BCL Convert tile sharding and pushed the checked-in helper path
525:- rollout_summaries/2026-05-31T07-33-07-1FU5-dayoa_bclconvert_tile_sharding.md (cwd=/Users/jmajor/.codex/worktrees/dyec-fsx-dra-mounts/daylily-ephemeral-cluster, rollout_path=/Users/jmajor/.codex/sessions/2026/05/31/rollout-2026-05-31T00-33-07-019e7cf3-67f5-7070-9252-27e30fe08951.jsonl, updated_at=2026-06-01T20:07:57+00:00, thread_id=019e7cf3-67f5-7070-9252-27e30fe08951, native tile-shard helper/rule/config/docs/tests and pushed DayOA branch)
544:- /Users/jmajor/.codex/memories/extensions/chronicle/resources/2026-06-02T11-39-00-Utly-10min-memory-summary.md (cwd=browser workflow plus `/Users/jmajor/.codex/worktrees/be82/daylily-ephemeral-cluster`, rollout_path=/Users/jmajor/.codex/memories/extensions/chronicle/resources/2026-06-02T11-39-00-Utly-10min-memory-summary.md, updated_at=2026-06-02T11:39:00+00:00, thread_id=None, DayOA `2.0.37` / DYEC `5.1.25` release closeout, compute-tuned benchmark completion, and raw benchmark presentation correction) [chronicle memory]
545:- /Users/jmajor/.codex/memories/extensions/chronicle/resources/2026-06-02T11-29-00-MSaa-10min-memory-summary.md (cwd=browser workflow plus `/Users/jmajor/projects/daylily/daylily-omics-analysis`, rollout_path=/Users/jmajor/.codex/memories/extensions/chronicle/resources/2026-06-02T11-29-00-MSaa-10min-memory-summary.md, updated_at=2026-06-02T11:29:00+00:00, thread_id=None, release train through DayOA `2.0.37` and DYEC `5.1.25`, `shard008` pending state, and headnode bootstrap failure context) [chronicle memory]
550:- shard008_cpu_tuned_odirect_on, 2026-06-02T11:15:18Z, 2026-06-02T11:35:44Z, partition=i192mem, parallel_tiles=16, conversion=2, compression=8, decompression=8, bench_expts, fastq_sizes.tsv, raw benchmark fields, do not calculate, DayOA 2.0.37, DYEC 5.1.25
611:- native DayOA tile sharding is now a checked-in path: `workflow/rules/bclconvert.smk` adds `run_bclconvert_tile_shard` and `merge_bclconvert_tile_shards`, `run_bclconvert_lane.sh` accepts a `--tiles` regex for shard jobs, and `workflow/scripts/merge_bclconvert_tile_shards.py` validates shard headers, concatenates shard FASTQs in shard order, and aggregates shard CSV reports back to the lane tree [Task 1]
983:scope: standing shell/session defaults for local Mac work, remote Linux hosts, Daylily/DayOA/DAY-EC controllers, and the allowed boundary for SSM Run Command
994:- interactive shell, zsh, bash login shell, ubuntu, tmux, source dyoainit, dy-a, dy-r, Daylily, DayOA, DAY-EC, SSM Run Command, no root
1008:- /Users/jmajor/.codex/memories/extensions/ad_hoc/notes/20260530T131115Z-headnode-compute-ssh-exception.md (cwd=workflow scope across Daylily/DayOA/DYEC headnode debugging, rollout_path=/Users/jmajor/.codex/memories/extensions/ad_hoc/notes/20260530T131115Z-headnode-compute-ssh-exception.md, updated_at=2026-05-30T13:11:15+00:00, thread_id=None, explicit compute-node SSH exception from an already-approved headnode session) [ad-hoc note]
1012:- headnode, compute node, ssh <compute-node-name>, private cluster network, SSM to headnode first, ubuntu, Daylily, DayOA, DYEC
1013:## Task 4: tightened the DayOA `dy-r` contract to persistent tmux-only headnode execution and no direct `snakemake` [ad-hoc note]
1017:- /Users/jmajor/.codex/memories/extensions/ad_hoc/notes/20260602T211500Z-dayoa-dyr-passes-through.md (cwd=workflow scope across Daylily/DayOA headnode workflow work, rollout_path=/Users/jmajor/.codex/memories/extensions/ad_hoc/notes/20260602T211500Z-dayoa-dyr-passes-through.md, updated_at=2026-06-02T21:15:00+00:00, thread_id=None, `dy-r` as the supported Snakemake interface) [ad-hoc note]
1018:- /Users/jmajor/.codex/memories/extensions/ad_hoc/notes/20260602T211200Z-dayoa-agent-runbook.md (cwd=workflow scope across DayOA workflow work, rollout_path=/Users/jmajor/.codex/memories/extensions/ad_hoc/notes/20260602T211200Z-dayoa-agent-runbook.md, updated_at=2026-06-02T21:12:00+00:00, thread_id=None, persistent tmux contract, smoke command, and stop-on-contract-gap rule) [ad-hoc note]
1019:- /Users/jmajor/.codex/memories/extensions/ad_hoc/notes/20260602T211039Z-dayoa-dyr-tmux-contract.md (cwd=workflow scope across DayOA workflow work, rollout_path=/Users/jmajor/.codex/memories/extensions/ad_hoc/notes/20260602T211039Z-dayoa-dyr-tmux-contract.md, updated_at=2026-06-02T21:10:39+00:00, thread_id=None, separate-command tmux contract for `source dyoainit`, `dy-a`, and `dy-r`) [ad-hoc note]
1023:- dy-r, snakemake directly, persistent tmux, bash -il, source dyoainit, dy-a slurm hg38, dy-r help -p -k -j 1 -n, one-shot non-interactive SSM script, exact contract gap
1040:- when running Daylily, DayOA, or DAY-EC controllers/workflows -> use an interactive `ubuntu` tmux/login-shell pane and initialize as separate commands like `source dyoainit`, then `dy-a ...`, then `dy-r ...` so aliases/functions are defined before use [Task 1]
1042:- when running DayOA workflow commands -> never invoke `snakemake` directly; always use `dy-r` from a persistent, meaningfully named `tmux` session on the headnode, and send `source dyoainit`, `dy-a ...`, and `dy-r ...` as separate commands [Task 4]
1043:- when `source dyoainit`, `dy-a`, or `dy-r` is unavailable -> stop and report the exact contract gap instead of substituting raw `snakemake`, inferred config paths, or a new checkout [Task 4]
1046:- when Daylily/DayOA/DYEC work requires compute-node inspection -> reach the headnode through SSM first, then use `ssh <compute-node-name>` from that headnode session instead of treating direct laptop-to-compute SSH as allowed [Task 3]
1053:- the high-friction failure mode this note is avoiding is non-interactive controller launches where `dyoainit`, `dy-a`, or `dy-r` are unavailable because the alias/function surface never initialized [Task 1]
1054:- the strict DayOA workflow contract now preserved here is: headnode as `ubuntu`, persistent `tmux` session running `bash -il`, `cd` into the DayOA checkout, `source dyoainit`, `dy-a slurm hg38` or `hg38_broad`, then `dy-r <targets> <flags>`; use `dy-r help -p -k -j 1 -n` as the smoke/dry-run proof path [Task 4]
1055:- `dy-r` is the supported Snakemake wrapper for DayOA workflow work and passes targets/flags through; this applies to help, dry-runs, live runs, and unlock/recovery, so “never invoke `snakemake` directly” is a real workflow boundary, not a stylistic preference [Task 4]
1064:- symptom: a remote Daylily controller command fails because aliases/functions like `dy-a` or `dy-r` are missing -> cause: the command ran in a non-interactive shell or skipped `source dyoainit` -> fix: move into an interactive `ubuntu` tmux/login shell and run the environment setup as separate commands first [Task 1]
1069:- symptom: a DayOA workflow task drifts into raw `snakemake` or a one-shot SSM payload -> cause: the `dy-r`/persistent-tmux contract was treated as optional -> fix: re-enter the persistent initialized tmux pane and run the supported `source dyoainit` -> `dy-a` -> `dy-r` sequence instead [Task 4]
1073:scope: standing approval boundaries for Slurm, node-health, and workflow-job intervention during Dayhoff, DayOA, DYEC, and related workflow execution
1074:applies_to: cwd=workflow scope across Dayhoff, DayOA, DYEC, and related Slurm-backed execution; reuse_rule=reuse across similar workflow monitoring, benchmarking, and cluster-debugging tasks unless the user explicitly approves the exact Slurm or job intervention in the current thread
1080:- /Users/jmajor/.codex/memories/extensions/ad_hoc/notes/20260601T141000Z_no_slurm_interventions_without_approval.md (cwd=workflow scope across Dayhoff, DayOA, DYEC, and related workflow execution, rollout_path=/Users/jmajor/.codex/memories/extensions/ad_hoc/notes/20260601T141000Z_no_slurm_interventions_without_approval.md, updated_at=2026-06-01T14:10:00+00:00, thread_id=None, explicit no-Slurm-intervention rule and monitoring-only boundary) [ad-hoc note]
1088:- when Dayhoff, DayOA, DYEC, or related workflow execution touches Slurm -> do not fix, optimize, repair, or administer Slurm unless the exact intervention is proposed first and explicitly approved in the current thread [Task 1]
1287:scope: 2026-05-31 follow-up in the `lsmc/daylily-ursa` checkout covering the utility-command replay fix, the remaining downstream DayEC/DayOA failure boundary, and the Ursa-side Slurm-accounting config/ownership wiring
1288:applies_to: cwd=/Users/jmajor/projects/lsmc/daylily-ursa; reuse_rule=reuse for similar Ursa replay-acceptance, release-state, or Slurm-accounting handoff work in this checkout, but re-check the live production version, current ledger, and downstream DayEC/DayOA failure signature before reusing exact status claims
1300:## Task 2: proved the old Ursa replay-mount failure was fixed and isolated the remaining failure to DayEC/DayOA `dy-r help` [chronicle memory]
1304:- /Users/jmajor/.codex/memories/extensions/chronicle/resources/2026-05-31T15-08-00-nIIC-10min-memory-summary.md (cwd=browser workflow plus `/Users/jmajor/projects/lsmc/daylily-ursa`, rollout_path=/Users/jmajor/.codex/memories/extensions/chronicle/resources/2026-05-31T15-08-00-nIIC-10min-memory-summary.md, updated_at=2026-05-31T15:08:00+00:00, thread_id=None, utility-no-mount acceptance state, `4.0.38` release/deploy, and downstream DayEC/DayOA blocker) [chronicle memory]
1305:- /Users/jmajor/.codex/memories/extensions/chronicle/resources/2026-05-31T14-25-00-RNZv-10min-memory-summary.md (cwd=browser workflow plus `codex/owy-run-directory-analysis-20260528`, rollout_path=/Users/jmajor/.codex/memories/extensions/chronicle/resources/2026-05-31T14-25-00-RNZv-10min-memory-summary.md, updated_at=2026-05-31T14:25:00+00:00, thread_id=None, earlier tiny-prefix smoke state showing `dy-r help` returned `0` before export/registration failed under `simple-test`) [chronicle memory]
1309:- 4.0.38, 20260531T141115Z_ursa_run_directory_utility_no_mount_ledger.md, simple-test, mount_id=null, export_trigger=none, destination=null, .fail sidecars, dy-r -p -k -j 1 help, aggregate_report_components, workflow/rules/multiqc_final_wgs.smk, bootstrap_bclconvert
1331:- when the user asks “what is the status of your plan?” on an Ursa replay/debug thread -> answer from the active ledger and separate “Ursa side complete” from downstream DayEC/DayOA blockers instead of flattening everything into one status [Task 2]
1341:- the remaining blocker after the Ursa fix was downstream DayEC/DayOA execution rather than request acceptance: earlier evidence on `dyec-515` showed `dy-r -p -k -j 1 help` failing with wildcard-consistency errors at `aggregate_report_components` (`workflow/Snakefile` line 293; `workflow/rules/multiqc_final_wgs.smk` line 550) and `collect_rules_benchmark_data` (`workflow/rules/multiqc_final_wgs.smk` line 433), while the later `4.0.40` Chronicle window showed another fresh replay still only at `worker-spawn` / cluster-listing and not yet at a new terminal outcome [Task 2][Task 4]
1343:- the `sacct`/database provenance answer worth preserving is that the thread which launched `dy-r -p -k -j 1 help` did not create or modify a Slurm accounting DB; the question had to be answered from the visible stack evidence and thread boundary, not by assuming ownership from the presence of accounting-related work [Task 3]
1349:- symptom: a replay smoke test is described as “still failing” without distinguishing old versus new failure modes -> cause: the terminalized `.fail` path and downstream workflow error are conflated with the original Ursa mount/export-registration bug -> fix: report whether the replay now terminalizes cleanly first, then isolate any remaining DayEC/DayOA command failure separately [Task 2]
1493:applies_to: cwd=workflow scope across Daylily headnode, DayOA, and DayEC remote-shell work; reuse_rule=reuse for similar SSM/headnode diagnostics or edits unless the user explicitly asks for a one-off inline command shape
1503:- SSM quoting, daylily_ec.aws.ssm.run_shell, shlex.quote, heredoc, python -c, --config, base64 remote script, temporary script, bin/day_run, colr, dy-a, dy-r
1515:- for DayOA workflow dry-runs or reruns, prefer the supported repo wrapper or initialized tmux/login-shell path rather than direct non-interactive `bin/day_run` when env helpers like `colr`, `dy-a`, or `dy-r` are required [Task 1]
1552:- /Users/jmajor/.codex/memories/extensions/ad_hoc/notes/20260531T105246Z-bcl2fastq-to-bclconvert-mapping.md (cwd=workflow scope across DayOA/DYEC BCL Convert work, rollout_path=/Users/jmajor/.codex/memories/extensions/ad_hoc/notes/20260531T105246Z-bcl2fastq-to-bclconvert-mapping.md, updated_at=2026-05-31T10:52:46+00:00, thread_id=None, CLI-vs-sample-sheet mapping for legacy `bcl2fastq` behavior) [ad-hoc note]
1561:- /Users/jmajor/.codex/memories/extensions/ad_hoc/notes/20260531T115305Z-bclconvert-default-two-node-four-lane-setup.md (cwd=workflow scope across DayOA/DYEC BCL Convert benchmarking, rollout_path=/Users/jmajor/.codex/memories/extensions/ad_hoc/notes/20260531T115305Z-bclconvert-default-two-node-four-lane-setup.md, updated_at=2026-05-31T11:53:05+00:00, thread_id=None, default two-node four-lane benchmark layout and anti-tile-splitting caution) [ad-hoc note]
1572:- /Users/jmajor/.codex/memories/extensions/ad_hoc/notes/20260531T152700Z-bclconvert-tile-sharding-defaults.md (cwd=workflow scope across DayOA/DYEC BCL Convert benchmarking, rollout_path=/Users/jmajor/.codex/memories/extensions/ad_hoc/notes/20260531T152700Z-bclconvert-tile-sharding-defaults.md, updated_at=2026-05-31T15:27:00+00:00, thread_id=None, default natural shard series, `--tiles` rule, and clean-vs-concurrent timing notes) [ad-hoc note]
1601:## Task 8: fixed the `dy-r help` rule-contract path, clarified Slurm-accounting provenance, and sequenced DayOA `2.0.32` before DYEC `5.1.15` [chronicle memory]
1605:- /Users/jmajor/.codex/memories/extensions/chronicle/resources/2026-06-01T03-03-00-Czef-10min-memory-summary.md (cwd=browser workflow plus `/Users/jmajor/.codex/worktrees/be82/daylily-ephemeral-cluster`, rollout_path=/Users/jmajor/.codex/memories/extensions/chronicle/resources/2026-06-01T03-03-00-Czef-10min-memory-summary.md, updated_at=2026-06-01T03:03:00+00:00, thread_id=None, DYEC `5.1.15` corrective release/upload state, DayOA `2.0.32` dependency, cluster-replacement follow-up, and successful `d515_0531Tdyr_help_2030` proof) [chronicle memory]
1606:- /Users/jmajor/.codex/memories/extensions/chronicle/resources/2026-05-31T20-00-00-Cxzt-10min-memory-summary.md (cwd=browser workflow plus `/Users/jmajor/.codex/worktrees/be82/daylily-ephemeral-cluster`, rollout_path=/Users/jmajor/.codex/memories/extensions/chronicle/resources/2026-05-31T20-00-00-Cxzt-10min-memory-summary.md, updated_at=2026-05-31T20:00:00+00:00, thread_id=None, official benchmark pivot plus `dy-r help` success on DayOA `2.0.30` and local `dy-h` / `day-help` wrapper state) [chronicle memory]
1607:- /Users/jmajor/.codex/memories/extensions/chronicle/resources/2026-05-31T19-20-00-Dfjv-10min-memory-summary.md (cwd=browser workflow plus `/Users/jmajor/.codex/worktrees/be82/daylily-ephemeral-cluster`, rollout_path=/Users/jmajor/.codex/memories/extensions/chronicle/resources/2026-05-31T19-20-00-Dfjv-10min-memory-summary.md, updated_at=2026-05-31T19:20:00+00:00, thread_id=None, DayOA rule-contract fix, Ursa `4.0.39` release-worktree state, and explicit “no sacct DB created” clarification) [chronicle memory]
1611:- dy-r help, d515_0531Tdyr_help_2030, dayec-slurm-accounting-us-west-2d, sacct db, CreateStack, AWS account root, multiqc_for_raw_fastqs.smk, seqqc, test_rule_log_benchmark_contracts.py, daylily-omics-analysis 2.0.32, daylily-ephemeral-cluster 5.1.15, TWINE, twine upload, dy-h, day-help
1619:- when translating legacy `bcl2fastq` usage into the current DayOA/DYEC BCL Convert path -> keep thread/concurrency controls on the CLI and move cycle mask, mismatch, adapter, trimming, and index-read FASTQ behavior into `[BCLConvert_Settings]` in the sample sheet [Task 3]
1625:- when the user asks “did you create a sacct db?” or “did another agent do it?” -> answer from the exact observed stack/thread evidence and distinguish database-stack provenance from the `dy-r help` debugging thread [Task 8]
1630:- the rerun plan visible on 2026-05-30 kept Roche and hybrid work ledgered: `roche_snv_alignstats` needed the Sentieon SNV path instead of the Roche/GATK-oriented command, hybrid reruns stayed constrained by prior DayOA/runtime repairs, and unused DRA mounts plus leftover `/fsx` analysis data were treated as separate approval-gated cleanup surfaces [Task 1]
1637:- DayOA/DYEC benchmark thread accounting uses `heavy_threads = parallel_tiles * conversion_threads + compression_threads + decompression_threads`; the requested `32/4/32/32` shape therefore means `192` CPU-heavy workers [Task 3]
1648:- the `dy-r help` fix path moved through two distinct rule-contract issues: first `multiqc_for_raw_fastqs.smk` had static outputs but wildcarded `seqqc` log/benchmark paths, then a later remote proof showed DayOA `2.0.30` on `dyec-515` completed session `d515_0531Tdyr_help_2030` with exit code `0`, while local `dy-h` / `day-help` wrapper edits remained unreleased/tagged [Task 8]
1649:- the visible corrective release ordering on 2026-06-01 was DayOA `2.0.32` before DYEC `5.1.15`: the DYEC tag was annotated and matched commit `3b6cc5cc`, but the package index still showed only `5.1.11`, so packaging/upload had to run from the `TWINE` environment while leaving the validated `DAY-EC` runtime intact [Task 8]
1650:- the Slurm-accounting provenance note worth preserving is that `dayec-slurm-accounting-us-west-2d` already existed as `CREATE_COMPLETE` with endpoint `10.0.1.39:3306`, database `dayec_slurm_acct`, and user `slurm_acct` before the `dy-r help` debug path; the thread itself did not create or modify a `sacct` database [Task 8]
1659:- symptom: a legacy `bcl2fastq` recipe gets ported by looking for one-for-one CLI flags in BCL Convert -> cause: the DayOA/DYEC path splits thread controls onto the CLI and semantic demux/trimming behavior into `[BCLConvert_Settings]` -> fix: translate mask, mismatch, adapter, trimming, and index-read behavior into sample-sheet settings and keep concurrency flags explicit on the command line [Task 3]
1666:- symptom: a `dy-r help` or Slurm-accounting status answer blurs together local fixes, remote release state, and unrelated stack creation -> cause: local DayOA edits, published package state, and pre-existing AWS stack evidence were not separated -> fix: report which fixes are only local, which versions are actually released/uploaded, and which AWS resources predated the current debug thread [Task 8]
1669:scope: DYEC bootstrap/launcher contract fixes, DayOA and DYEC release publication, and follow-up package-index lookups where exact commit/tag/index state matters more than local version constants
1670:applies_to: cwd=/Users/jmajor/.codex/worktrees/be82/daylily-ephemeral-cluster plus /Users/jmajor/projects/daylily/daylily-omics-analysis; reuse_rule=reuse for similar DYEC/DayOA release, package publication, or current-version lookup work in this checkout family, but re-check live package-index state and exact tag/commit provenance before reusing exact version claims
1681:## Task 2: published DayOA `2.0.33`
1685:- rollout_summaries/2026-06-01T03-34-42-M3Il-day_clone_executing_entity_and_dyec_release_train.md (cwd=/Users/jmajor/.codex/worktrees/be82/daylily-ephemeral-cluster, rollout_path=/Users/jmajor/.codex/archived_sessions/rollout-2026-05-31T20-34-42-019e813f-7cef-7c80-b207-0a6f3586ea09.jsonl, updated_at=2026-06-01T14:55:51+00:00, thread_id=019e813f-7cef-7c80-b207-0a6f3586ea09, DayOA `2.0.33` commit/tag/build/upload/index verification with sdist ambiguity noted)
1699:## Task 4: mapped shorthand package names and queried live PyPI for current DYEC and DayOA versions
1708:## Task 5: filtered non-semver marker tags out of DayOA/DYEC version discovery and tightened exact package-version gating [chronicle memory]
1712:- /Users/jmajor/.codex/memories/extensions/chronicle/resources/2026-06-02T11-39-00-Utly-10min-memory-summary.md (cwd=browser workflow plus `/Users/jmajor/.codex/worktrees/be82/daylily-ephemeral-cluster`, rollout_path=/Users/jmajor/.codex/memories/extensions/chronicle/resources/2026-06-02T11-39-00-Utly-10min-memory-summary.md, updated_at=2026-06-02T11:39:00+00:00, thread_id=None, DayOA `2.0.37` / DYEC `5.1.25` release closeout, exact-package gating, and Dayhoff semver-filter test plan) [chronicle memory]
1734:- when the user asks whether a new tag would fix version inference and then says to apply the fix in both DayOA and DYEC, later broadening it to Dayhoff/services too -> prefer numeric-only semver tag filters across the repo family instead of letting marker tags or branch names participate in release-version discovery [Task 5]
1742:- DayOA `2.0.33` publication used the `TWINE` environment with `zsh -lic 'eval "$(conda shell.zsh hook)" && conda activate TWINE && python -m build && twup'`; commit `59195a45ec38777f39054051482b4ae0bc216977` was tagged as annotated `2.0.33`, and `python -m pip index versions daylily-omics-analysis` confirmed the package was visible even though the sdist upload path later returned `400 Bad Request` [Task 2]
1743:- the DYEC release train first cut `5.1.16` to carry the DayOA `2.0.33` pin and `day-clone` fix, then advanced the self-pins to `5.1.17`; annotated tags `5.1.16` and `5.1.17` were pushed, the focused validation stayed at `39 passed`, and `python -m pip index versions daylily-ephemeral-cluster` showed latest `5.1.17` after the final build/upload attempt [Task 3]
1744:- for current package-state questions, `pyproject.toml` is enough to map shorthand names (`dyec` -> `daylily-ephemeral-cluster`, DayOA -> `daylily-omics-analysis`), and live PyPI JSON at `https://pypi.org/pypi/<project>/json` is the reliable source for current release lists and latest versions; the later verification run reported latest `5.1.19` for DYEC and `2.0.34` for DayOA [Task 4]
1745:- the June 2 version-poisoning bug was a non-semver marker tag such as `lsmc-back-fork-cnd2` winning `setuptools_scm` / describe resolution; the durable fix direction was numeric-only tag filtering for DayOA and DYEC, plus the same semver filter principle for Dayhoff/service latest-tag discovery and manifest validation [Task 5]
1754:- symptom: a DayOA release thread assumes `source ./activate` should exist or that local tag state is enough -> cause: repo-specific release surface and package-index verification were not separated -> fix: use the repo’s actual Python env for tests, then verify commit, annotated tag, and index visibility explicitly [Task 2]
1841:- /Users/jmajor/.codex/memories/extensions/chronicle/resources/2026-05-30T12-23-00-XxZN-10min-memory-summary.md (cwd=browser workflow plus `Sleep 1`, rollout_path=/Users/jmajor/.codex/memories/extensions/chronicle/resources/2026-05-30T12-23-00-XxZN-10min-memory-summary.md, updated_at=2026-05-30T12:23:00+00:00, thread_id=None, ledger-path draft, Ursa/DayOA pin checks, and expanded ddev81 plan scope) [chronicle memory]
1845:- ddev80, ddev81, shared Cognito, shared Aurora, us-east-1, delete ddev80 only, no live build yet, services/pins.toml, extended_family_runtime_targets.yaml, Sandbox Deployment View, Dayhoff ddev80 cleanup ddev81 shared auth data Ursa DayOA ledger
1920:- the 2026-05-30 planning pass split Dayhoff dev-stack work into three durable concerns: destructive `ddev80` cleanup limited to its own AWS/local artifacts, generalized shared Cognito/Aurora config that must fail hard when incomplete, and a later `ddev81` deploy/release path that also needs Ursa/DayOA pin checks, service commit/push/tag/release-train rows, and Playwright login evidence up to expected external blockers such as Google redirect configuration [Task 1]
