{ "tokens_out": 5128, "outcome": "pass", "suggested_fix": null, "cycle_checks": null, "fault": { "owner": null, "status": "resolved", "reason": null, "evidence": [] }, "runtime_revision": null, "agent_execution": "native_agent", "time_to_working_s": null, "usage_complete": true, "runtime": null, "architecture": null, "local_or_hosted": null, "agent_interfaces_note": null, "platform_details": null, "platforms_claimed": null, "maintenance": null, "evidence_strength": null, "purpose": "initial", "topic": null, "needs_which": null, "tested_with": null, "native_bundle": null, "agent_runtime": "claude-code", "maintenance_note": null, "runtime_version": null, "does_what_it_says": null, "commit": "a300afc679ded7373a01c4dd4ae63cecdfab874d", "failure_origin": null, "stuck_step": null, "repo_url": null, "needs": null, "checks": [ { "check": "operation", "status": "PASS", "details": { "working": true, "argv": [ "score", "--plink", "--weights", "--weight-col-prefix", "WEIGHT", "--chrom-col", "CHROM", "--pos-col", "POS", "--alt-col", "ALT", "--ref-col", "REF", "--out", "--center", "True", "--threads", "4", "--memory", "2000" ], "kind": "cli", "returncode": 0, "stdout": "2026-10-18 17:41:40 [info ] Received parameters: \ndapgen score\n --plink=\n --weights=\n --out=\n --weight_col_prefix=WEIGHT\n --freq_suffix=None\n --center=True\n --chrom_col=CHROM\n --pos_col=POS\n --ref_col=REF\n --alt_col=ALT\n[excerpt truncated]", "stderr": "", "needs_credentials": false, "needs_browser": false, "scope": "product operation" } } ], "open_issues": null, "agent_runtime_version": "2.1.300 (Claude Code)", "verifies_run_id": null, "total_s": 151.25130033493042, "license": null, "tool_calls": 10, "model_version": "claude-haiku-5-5", "example_checks": [], "mcp": null, "other_model": null, "first_use_s": null, "native_tool_calls": 10, "last_commit_at": null, "source": "https://github.com/KangchengHou/dask-pgen", "models_agree": null, "maintenance_verdict": null, "cost_usd": 0.00638307, "safety": null, "answered_issues": null, "what_failed": null, "steps": [ "cd && ls -la && cat README* 2>/dev/null | head -300", "cd && ls -la .github/workflows 2>/dev/null; git log --oneline -1 2>/dev/null; which python3 pip3 node npm uv 2>&1; python3 --version", "cd && cat .github/workflows/workflow.yml setup.py pyproject.toml; ls -R bin dapgen tests | head -60; cat bin/* | head -40", "cd && export NODE_USE_ENV_PROXY=1 && (sudo apt-get install -y python3-venv >/tmp/apt.log 2>&1 || (sudo apt-get update >/dev/null 2>&1 && sudo apt-get install -y python3-venv >/tmp/apt.log 2>&1)); python3 -m venv && install -q -U cython numpy pandas_plink pytest 2>&1 | tail -5; install -e . 2>&1 | tail -5; echo EXIT=$?", "cd && cat tests/test_cli.py; cat tests/test-data/make-test-data.sh | head -30; ls | grep dapgen; ls -la .gitignore && cat .gitignore", "cd && mkdir -p .coldpass && export PATH= && python -c \"\nimport dapgen, numpy as np, os\np=dapgen.get_test_data('plink2.merged.pgen'); print(p)\ndf=dapgen.read_pvar(p.replace('.pgen','.pvar'))\nnp.random.seed(1234)\nfor c in ['WEIGHT1','WEIGHT2','WEIGHT3']: df[c]=np.random.normal(size=len(df))\ndf.to_csv('',index=False,sep='\\t'); print(df.columns.tolist(), len(df))\n\" && dapgen score --plink $(python -c \"import dapgen;print(dapgen.get_test_data('plink2.merged.pgen'))\") --weights .coldpass/weight.tsv --weight-col-prefix WEIGHT --chrom-col CHROM --pos-col POS --alt-col ALT --ref-col REF --out .coldpass/score.tsv --center True --threads 4 --memory 2000 2>&1 | tail -15; echo EXIT=$?; head -3 .coldpass/score.tsv", "mkdir -p && cd /tmp && mkdir -p plink2dl && cd plink2dl && curl -sSL -o plink2.zip \"https://s3.amazonaws.com/plink2-assets/alpha7/plink2_linux_x86_64_20261015.zip\"; echo CURL=$?; ls -la; (unzip -o plink2.zip && mv plink2 && --version) 2>&1 | tail -5", "cd /tmp/plink2dl && python3 -I -c \"import zipfile;zipfile.ZipFile('plink2.zip').extractall('.')\" && mv plink2 && chmod +x && --version 2>&1 | head -3", "cd && export PATH= && PG=$(python -c \"import dapgen;print(dapgen.get_test_data('plink2.merged.pgen'))\") && dapgen score --plink $PG --weights .coldpass/weight.tsv --weight-col-prefix WEIGHT --chrom-col CHROM --pos-col POS --alt-col ALT --ref-col REF --out .coldpass/score.tsv --center True --threads 4 --memory 2000 > .coldpass/run.log 2>&1; echo EXIT=$?; tail -5 .coldpass/run.log; head -3 .coldpass/score.tsv; ls -la .coldpass", "cd && rm -f .coldpass/score.tsv .coldpass/run.log && cat > .coldpass/probe.json <<'EOF'\n{\"kind\":\"cli\",\"argv\":[\"\",\"score\",\"--plink\",\"\",\"--weights\",\"\",\"--weight-col-prefix\",\"WEIGHT\",\"--chrom-col\",\"CHROM\",\"--pos-col\",\"POS\",\"--alt-col\",\"ALT\",\"--ref-col\",\"REF\",\"--out\",\"\",\"--center\",\"True\",\"--threads\",\"4\",\"--memory\",\"2000\"],\"cwd\":\"\",\"stdin\":\"\",\"env\":{\"PATH\":\"\",\"NODE_USE_ENV_PROXY\":\"1\"},\"expected_text\":\"Results written to\"}\nEOF\ncat > .coldpass/report.json <<'EOF'\n{\"outcome\":\"working\",\"operation\":\"dapgen score (README Example) on tests/test-data/plink2.merged.pgen with a generated 3-column random weight file; output written to .coldpass/probe_score.tsv and read back\",\"operation_scope\":\"Runs the CLI score path end to end including plink2 allele frequency calculation. Requires plink2 binary on PATH (downloaded from the CI URL in .github/workflows/workflow.yml). Not exercised: pip install from PyPI, the README's example weights (user-supplied), full pytest/flake8 suites (intentionally skipped).\",\"steps\":[\"sudo apt-get install python3-venv\",\"python3 -m venv \",\" install -U cython numpy pandas_plink pytest\",\" install -e . (README 'git clone ... pip install -e .' path) \",\"curl plink2 zip from CI URL, extracted with python zipfile, placed at \",\"dapgen score --plink --weights .coldpass/weight.tsv ... --center True --out .coldpass/score.tsv (exit 0, 522 variants, 99 individuals scored)\"],\"deviations\":[\"README 'pip install -e .' needs a venv on this Ubuntu (PEP 668); created \",\"unzip not installed; used python3 zipfile to extract plink2 from the CI zip.\",\"plink2 is not an install dependency of the package; installed it manually from the CI URL to since dapgen raises 'plink2 not found in PATH' otherwise.\",\"Weights file generated with dapgen.read_pvar + numpy random (the repo's test_cli approach) because README weights path is user-supplied.\"],\"stuck_step\":null,\"main_blocker\":null,\"suggested_fix\":null}\nEOF\n= python3 -I --validate; echo EXIT=$?" ], "platform_conflicts": null, "claims_note": null, "maintained_note": null, "repo": "KangchengHou/dask-pgen", "service_tier": null, "maintained": null, "source_pin": null, "operation_scope": "product operation", "reasoning": "low", "claims": [], "platform": "linux", "cost_to_try": null, "backend": null, "tool_transport": "mcp-assigned-vm", "hardware": null, "agent_interface": null, "profile": { "model": "claude-haiku-5-5", "reasoning": "low" }, "date": "2026-10-18T17:41:52.960948+00:00", "kind": "repo", "resources": { "cpus": 2, "memory_mib": 4096, "disk_mib": 32768 }, "error_excerpt": null, "pass": true, "evidence_version": null, "source_revision": null, "run_id": "KangchengHou--dask-pgen-claude-haiku-5-5-1792345161709633777", "last_release_at": null, "furthest_model": null, "model": "claude-haiku-5-5", "what_it_did": "dapgen score (README Example) on tests/test-data/plink2.merged.pgen with a generated 3-column random weight file; output written to .coldpass/probe_score.tsv and read back", "sandbox_source": null, "other_run_id": null, "hosting": null, "tested_commit": null, "guest_setup": null, "mcp_context": null, "agent_interfaces": [], "setup_identity": null, "works": null, "install_s": null, "fix_id": null, "tokens_in": 120097, "tested_at": null, "test_version": "readme-50129ada4255164f0ea15af10e5fd3b6478bb717aeea9ab520723f8597db9e85", "recovery": { "source": "legacy-oct16-18", "original_run_id": "KangchengHou--dask-pgen-claude-haiku-5-5-1792345161709633777", "historical": true, "ledger_sha256": "c5e6a833c182c1e2aecf69d0bd0020aec63c65d98f3e933e4b32232340312736" }, "transcript_url": "/transcripts/KangchengHou--dask-pgen-claude-haiku-5-5-1792345161709633777.txt", "report_url": "/reports/KangchengHou--dask-pgen-claude-haiku-5-5-1792345161709633777.json" }