Rabies Method-Sensitivity Report

summary

variants
4
execution mode
parallel
parallel workers
2
stable clades
2
changed clades
8
slurm planned jobs
4
slurm max memory MiB
1536
slurm array partitions
2
slurm job evidence files
36
slurm storage MiB
2
slurm largest storage variant
ginsi-gap-threshold
slurm output explosion risk
low
slurm output explosion high-risk variants
0
slurm tree retention status
no_action
slurm tree-set files
0
slurm merge ready
true
slurm mergeable variants
4
slurm fresh output jobs
4
slurm stale output jobs
0
slurm completed jobs
4
slurm stale jobs
0
slurm recovery status
clean
slurm rerunnable jobs
0
reproducibility passed
true
reproducibility checks
136
linked artifacts
32

artifacts

workflow-summary

dataset: Rabies method-sensitivity panel
variants: 4
execution mode: parallel
parallel workers: 2
stable clades across variants: 2
changed clades across variants: 8
auto-gap-threshold: model TPM2u+F+G4; unrooted serious conflicts 8; rooted engine RF 0
ginsi-gap-threshold: model TPM2u+F+G4; unrooted serious conflicts 8; rooted engine RF 0
auto-gappyout: model TPM2u+F+G4; unrooted serious conflicts 8; rooted engine RF 0
ginsi-gappyout: model TPM2u+F+G4; unrooted serious conflicts 8; rooted engine RF 0

conclusions

preprocessing_rooted_iqtree_topology: stable
claim: The rooted IQ-TREE topology stayed unchanged across every declared alignment and trimming variant.
evidence: 6 rooted pairwise preprocessing comparisons returned RF distance 0 and no rooting-only disagreements.
caution: This stability statement is limited to the compact nine-taxon rabies panel and the four declared preprocessing settings.

preprocessing_selected_model: stable
claim: The selected substitution model remained constant across the declared preprocessing matrix.
evidence: selected models: TPM2u+F+G4
caution: Model-selection stability here reflects one short rabies nucleoprotein panel rather than a general claim about all pathogen alignments.

rooted_engine_agreement: stable
claim: After explicit outgroup rooting, FastTree and IQ-TREE preserved the same rooted topology in every declared preprocessing variant.
evidence: rooted engine comparisons over outgroup bat_chile_rv108 returned RF distance 0 in every variant.
caution: Rooted agreement does not imply that every internal unrooted split or support value is interchangeable across engines.

unrooted_engine_sensitivity: changed
claim: Before rooting, the FastTree versus IQ-TREE comparison changed several internal clade conclusions on this rabies panel.
evidence: serious unrooted engine conflicts ranged up to 8 per variant, while stable shared clades per variant ranged from 2 to 2.
caution: The engine-sensitive clades are a warning against over-reading fine internal structure from one compact panel, especially when approximate and likelihood engines disagree before rooting.

reproducibility-audit

all passed: true
top-level checks: 136
failed top-level checks: 0
failed variants: 0

slurm-job-planning

planned jobs: 4
maximum estimated memory MiB: 1536
maximum estimated wallclock minutes: 35
total estimated core hours: 3.2
total estimated scratch MiB: 1024
total estimated output MiB: 4

slurm-array-partitioning

array partitions: 2
largest partition size: 2
partition scripts: 2
total array jobs: 4

slurm-job-evidence

job evidence packages: 4
job evidence artifact files: 36
job evidence total runtime seconds: 17.324942
job evidence total output bytes: 168260

slurm-storage-estimate

estimated retained storage MiB: 2
workflow outputs bytes: 161224
log bytes: 900
tree bytes: 7036
posterior sample bytes: 0
review artifact bytes: 1101231
largest variant by retained bytes: ginsi-gap-threshold

slurm-output-explosion-risk

overall risk status: low
global issues: 0
warning variants: 0
high-risk variants: 0
largest variant output share: 0.25
posterior sample bytes: 0

slurm-tree-retention-policy

overall policy status: no_action
tree-set files: 0
posterior sample files: 0
thinning required files: 0
compression required files: 0
largest tree set: variants/ginsi-gappyout/iqtree-support.nwk

slurm-merge-report

merge status: merge-ready
merge ready: true
mergeable variants: 4
failed merge checks: 0
merged stable clades: 2
merged changed clades: 8

slurm-output-freshness

all outputs fresh: true
fresh jobs: 4
stale jobs: 0
freshness checks: 12
failed freshness checks: 0

slurm-workflow-status

workflow status: succeeded
active run state: absent
completed jobs: 4
failed jobs: 0
pending jobs: 0
stale jobs: 0

slurm-failure-recovery

overall recovery status: clean
rerunnable jobs: 0
blocked jobs: 0
recovery partitions: 0
workflow state: succeeded
active run state: absent

artifacts

workflow summary: workflow-summary.tsv
variant summary: variant-summary.tsv
parallel execution summary: parallel-execution-summary.tsv
preprocessing rooted comparisons: preprocessing-rooted-comparisons.tsv
stable clades: stable-clades.tsv
changed clades: changed-clades.tsv
method conclusions: method-conclusion-summary.tsv
resolved config: workflow-config.resolved.json
workflow manifest: rabies-method-sensitivity.manifest.json
slurm job plan: slurm-job-plan.tsv
slurm estimation assumptions: slurm-estimation-assumptions.tsv
slurm planning summary: slurm-planning-summary.json
slurm array partitions: slurm-array-partitions.tsv
slurm array members: slurm-array-members.tsv
slurm array strategy: slurm-array-strategy.json
slurm job evidence index: slurm-job-evidence.tsv
slurm job evidence summary: slurm-job-evidence-summary.json
slurm storage categories: slurm-storage-categories.tsv
slurm storage variants: slurm-storage-variants.tsv
slurm storage summary: slurm-storage-report.json
slurm storage report: slurm-storage-report.html
slurm output explosion checks: slurm-output-explosion-checks.tsv
slurm output explosion variants: slurm-output-explosion-variants.tsv
slurm output explosion summary: slurm-output-explosion-report.json
slurm output explosion report: slurm-output-explosion-report.html
slurm tree retention checks: slurm-tree-retention-checks.tsv
slurm tree retention files: slurm-tree-retention-files.tsv
slurm tree retention summary: slurm-tree-retention-policy.json
slurm tree retention report: slurm-tree-retention-policy.html
slurm merge checks: slurm-merge-checks.tsv
slurm merge variants: slurm-merge-variants.tsv
slurm merge summary: slurm-merge-report.json
slurm merge report: slurm-merge-report.html
slurm output freshness: slurm-output-freshness.tsv
slurm output freshness checks: slurm-output-freshness-checks.tsv
slurm output freshness summary: slurm-output-freshness.json
slurm job status: slurm-job-status.tsv
slurm partition status: slurm-partition-status.tsv
slurm workflow status: slurm-workflow-status.json
slurm failure recovery jobs: slurm-failure-recovery-jobs.tsv
slurm failure recovery partitions: slurm-failure-recovery-partitions.tsv
slurm failure recovery summary: slurm-failure-recovery-report.json
slurm failure recovery report: slurm-failure-recovery-report.html
reproducibility checks: reproducibility-checks.tsv
reproducibility variant audit: reproducibility-variants.tsv
reproducibility audit: reproducibility-audit.json