{"submission_id":"6ee7b1e2-a34d-4b71-88b5-3d5cdda49850","submission_revision_id":"b8e0e574-77a9-4467-bed9-b0803046db5e","revision_version":7,"submission_status":"submitted","submitted_at":"2026-09-19T00:04:01.587953Z","submitter_name":"Xingda Lyu","submitter_email":"xlyu18@uw.edu","task":{"status":"submitted","version":7,"extra_fields":{"difficulty_self_test":{"model":"GPT-6 Astra (High)","harness":"Codex","estimated_score":"<1%"}},"submitted_at":"2026-09-19T00:04:01.587953+00:00","industry_domain":"Life Sciences — Genomics & Sequence Analysis","task_short_name":"bacterial_genome_finishing_instance_1","operating_system":"Linux","task_description":"Objective: Finish a bacterial genome assembly from an upstream multi-assembler sequencing handoff and produce a complete, reference-grade genome representation.\n\nStarting State: You are given one automated draft assembly, 12 alternative candidate assemblies, sampled Oxford Nanopore MinION long reads (~25×), sampled paired-end Illumina short reads (~100× combined R1+R2), anonymous sequencing metadata, and a preinstalled offline Linux genome-finishing toolchain.\n\nInstructions & Rules: Reconcile conflicting candidate structures using the supplied long- and short-read evidence. Recover the complete biological replicon set, resolve structural disagreements and repeats, polish sequence errors, determine circular/linear topology and chromosome/plasmid/other role for every final replicon, and document the evidence supporting the final decisions. Use only the supplied task files and offline tools. Do not fetch external sequences, metadata, databases, or software. Keep final record IDs anonymous, preserve uncertainty where the supplied evidence is insufficient, and do not claim analyses that were not actually run.\n\nRequired Output: Create exactly:\n1. output/final_assembly.fasta\n2. output/replicon_summary.tsv\n3. output/qc_report.md\n\nreplicon_summary.tsv must contain exactly one row per FASTA record and use the exact header:\nreplicon_id    length_bp    circular    role    long_read_support    short_read_support    notes\n\nreplicon_id and length_bp must match the FASTA exactly. Allowed circular values are true, false, and uncertain. Allowed role values are chromosome, plasmid, other, and uncertain. Both read-support fields must be nonempty.\n\nqc_report.md must be nonempty Markdown containing:\n# Assembly QC report\n## Evidence\n## Decisions\n## Limitations","software_licensing":"Free/Open Source","evaluation_criteria":null,"verification_method":"Use the supplied deterministic, reference-aware evaluator.\n\nFull credit (score = 1.0) requires exact one-to-one biological equivalence to the hidden finished-genome reference and valid required deliverables. Every genuine replicon must be present exactly once; there may be no missing, extra, duplicate, split, fused, or internally rearranged sequence; there must be zero substitutions, insertions, or deletions; and topology and biological role must be correct for every replicon. Circular reference replicons may differ by circular-origin rotation and/or reverse complement. Linear reference replicons may differ only by forward/reverse-complement orientation and may not be circularly rotated.\n\nFor a non-exact submission, the score is 0 if core finished-genome scientific validity fails: the submitted records cannot form a complete reciprocal one-to-one mapping to all genuine reference replicons; genuine biological material is missing; spurious or duplicated biological material is present; a replicon is split or multiple replicons are fused; a major internal inversion/rearrangement is present; or a linear replicon is represented with an illegal circular-origin rotation. Every non-empty submitted FASTA record participates in this core inventory regardless of record length, so a separate additional record cannot escape the core validity check merely because it is short.\n\nAfter reciprocal matching, any separate unmatched submitted FASTA record is treated as a core scientific-validity failure. If at least 90% of that unmatched record is explained by exactly one genuine reference replicon, it is classified as duplicated/redundant biological material; otherwise it is classified as spurious/extra biological material. This rule applies to separate additional FASTA records and does not convert ordinary local substitutions or insertions/deletions within an otherwise correctly matched replicon into catastrophic inventory failures.\n\nIf core scientific validity passes, compute substitutions, inserted bases, and deleted bases across the matched replicons after applying the allowed circular-origin and orientation equivalences. Let:\n\nerror_rate = total_error_bases / total_reference_bases\n\nFor a nonzero error rate:\n\nconsensus_quality_score = min(1, 1e-5 / error_rate)\n\nZero base errors give:\n\nconsensus_quality_score = 1\n\nThe 1e-5 error-rate anchor corresponds approximately to Q50, or one consensus error per 100,000 bases, as a finished-genome quality reference point.\n\nThe partial scientific score is:\n\nconsensus_quality_score × topology_fraction × role_fraction\n\nwhere topology_fraction is the fraction of genuine replicons with correct circular/linear topology and role_fraction is the fraction with correct biological role. Each genuine replicon is weighted equally rather than by sequence length, so a small genuine replicon is not made negligible simply because it contributes few total bases.\n\nA QC-report-only contract failure caps an otherwise valid partial score at 0.90. A missing or unparseable final_assembly.fasta, or a missing, unparseable, or scientifically unmatchable replicon_summary.tsv, scores 0. All non-exact scores are capped below 1.0.\n\nMandatory FASTA/TSV format failures return score 0 before downstream scientific analyses. Checks that were not executed are explicitly marked not_executed, with unavailable diagnostic values recorded as null rather than represented as observed scientific failures. Candidate-output failures and evaluator infrastructure failures are reported separately. Infrastructure failures are not counted as model zero scores.\n\nThe evaluator is deterministic and code-based. The genuine reference positive control scores 1.0 with full_pass = true and core scientific validity passing.\n\nThe current parser/I/O repair preserves the scientific scoring functions, matching rules, thresholds, quality anchor, and hidden reference. Regression validation used the original 48 synthetic/reference-derived fixtures, each evaluated twice. All 48 fixture scores were unchanged from the original evaluator, and all 48 repeated result JSONs were byte-identical. For 41 fixtures, the complete result JSON was also unchanged from the historical result.\n\nAll 259 original checks were retained: 244 passed unchanged, while 15 old assertions or diagnostic comparisons had documented expected contract differences arising from early format rejection in seven fixtures. Those seven fixtures still scored 0; downstream checks were explicitly recorded as not executed. No additional unexpected regression failures or infrastructure failures were recorded. The legacy harness exit code and original assertion outcomes are preserved in the evidence package; this is not presented as 259/259 unchanged assertions passing. A separate supplemental boundary suite recorded 22 passing tests.\n\nThe original anti-cherry-picking and variant-generalization evidence is retained with its original version attribution. Current validation reports and raw regression records distinguish historical evidence from executions of the repaired evaluator.\n\nThe validation suite explicitly includes separate extra and duplicated FASTA records at 500, 999, 1000, 1500, and 1999 bp. All such cases receive score 0 and fail core scientific validity as required, confirming that no short additional record is silently ignored. At the same time, ordinary polishing errors remain non-catastrophic: a single SNP, 1-bp insertion, or 1-bp deletion in an otherwise correct finished genome receives a high non-full-pass score rather than zero. These tested cases demonstrate that the evaluator distinguishes failures of the biological genome object from residual base-level polishing errors.","software_and_version":"Autocycler 0.7.0; minimap2 2.31-r1302; samtools 1.23.1; BWA 0.7.19; Racon 1.5.0; Polypolish 0.7.1; Pypolca 0.4.0; MUMmer 4.0.1; SeqKit 2.13.0; Seqtk 1.5; Flye 2.9.6; Raven 1.8.3; Miniasm 0.3; Minipolish 0.2.1","specific_requirements":null,"expected_completion_time":null},"files":[{"file_id":"2ae7962a-b853-4098-b3b6-45a165230985","filename":"bacterial_genome_finishing_instance_1_reference_and_evaluation.zip","category":"reference_output","content_type":"application/zip","size_bytes":3425008},{"file_id":"c1141110-0a48-4a0a-857d-8053316defc3","filename":"bacterial_genome_finishing_instance_1_difficulty_evidence.zip","category":"difficulty_self_test_evidence","content_type":"application/zip","size_bytes":7459635},{"file_id":"510f7f03-b024-4c4b-bd49-4d7107f08e94","filename":"bacterial_genome_finishing_instance_1_input.zip","category":"input_materials","content_type":"application/zip","size_bytes":644136672}],"deep_review":{"overall_verdict":"Strong Accept","review_text":"**Overall Verdict:** Strong Accept — The submission is complete, professionally constructed, safely reachable, and supported by authentic inputs, a reproducible offline toolchain path, a hidden reference, and a deterministic validated evaluator.\n\n**Completeness Check:**\n- Instruction: Complete — The objective, evidence constraints, offline boundary, required artifacts, exact TSV schema, allowed classifications, and QC headings are unambiguous.\n- Inputs: Complete — The solver archive contains exactly the stated draft, 12 candidate assemblies, candidate manifest, anonymous metadata, 14,737 valid long reads, and 1,401,009 synchronized short-read pairs; sequence alphabets, FASTQ structure, pairing, manifest lengths, and target coverage were consistent.\n- Toolchain: Complete — Open-source Linux tools, versioned environment definitions, installation and verification recipes, realized package records, resource limits, and historical offline smoke evidence are supplied. Fresh deployment verification remains a routine integration step rather than a contributor-side gap.\n- Reference output: Complete — A valid six-record hidden FASTA and matching manifest provide exact lengths, topology, and biological roles. The reference positive control scores 1.0.\n- Rubric: Complete — The deterministic evaluator covers format contracts, reciprocal replicon inventory, structural validity, consensus errors, topology, roles, and QC requirements, with regression, boundary, repeatability, and infrastructure-error evidence.\n\n**File and Task Reachability:**\nAttachment classification: `reachable`. Task classification: `reachable`. The inspected attachments were `bacterial_genome_finishing_instance_1_input.zip`, `bacterial_genome_finishing_instance_1_reference_and_evaluation.zip`, and `bacterial_genome_finishing_instance_1_difficulty_evidence.zip`. Their downloaded sizes matched the manifest; all were readable ZIP containers with valid CRCs, safe relative paths, and no link, device, or encryption barriers. Internal hash manifests passed for all 323 covered members, all 142 JSON files parsed, TSV schemas were consistent, nested archives were readable and path-safe, and all compressed read streams decompressed successfully. Submitted programs and scripts were statically inventoried but never executed; noncritical historical logs and transcripts were integrity-checked rather than interpreted line by line. No required content remained unreviewed.\n\nThe end-to-end path is viable on one Linux machine: expose only the solver input and preinstalled offline tools, reconcile and polish the assembly into the three contracted outputs, then stage the hidden reference and run the supplied evaluator against the output directory. Recorded resource use and the stated 16-CPU/32-GiB ceiling support practical execution. License keys, accounts, tokens, and other credentials are not required from the contributor. Confidential, proprietary, or internal material may be evaluated as submitted evidence without requiring additional disclosure.\n\n**Special Screening:**\n`public_benchmark` — Submitted provenance identifies the source reads and finished reference as public scientific/INSDC records. The risk is materially mitigated by anonymized solver-visible identifiers, strict separation of reference/evaluator assets, and an offline solver environment. This classification relies on the supplied provenance; external public-source verification was not performed under the review constraints.\n\n**Recommended Changes:**\nThe submission provides unusually thorough integrity, provenance, leakage, reproducibility, and evaluator-validation evidence. No changes are required.","reviewed_at":"2026-09-19T00:36:20.920735Z"},"claim":null}