{ "run_id": "openvax--isovar-claude-haiku-5-5-1793157301745896257", "date": "2026-10-28T03:35:36.051105+00:00", "repo": "openvax/isovar", "kind": "repo", "source": "https://github.com/openvax/isovar", "commit": "e6828ae5e4bbf14d79e2404f735247e08dbdae19", "model": "claude-haiku-5-5", "model_version": "claude-haiku-5-5", "test_version": "readme-c106c8a1fd8238b0e3df988f814e62bbf2335959186ef6bbc72a5c3bf9412da5", "pass": null, "outcome": "too_slow", "time_to_working_s": null, "total_s": 1234.3046653270721, "steps": [ "cd && pwd && ls -la && id -u && python3 --version && git -C . rev-parse HEAD 2>&1 | head -1; cat /etc/os-release | head -2", "cd && cat README.md | head -c 7000", "cd && tail -c +7000 README.md | head -c 7000", "cd && tail -c +14000 README.md; echo; echo ---; cat test.sh | head -60; cat .coldpass/* 2>/dev/null | head -5; ls /inputs 2>&1", "cd /tmp && python3 -m venv && -m pip install -q --upgrade pip 2>&1 | tail -3; -m pip install 2>&1 | tail -5", "cd /tmp && --help 2>&1 | head -40; echo ---; ls | head -50; echo ---; ls | head -30", "cd /tmp && timeout 20 curl -sI https://ftp.ensembl.org/pub/release-75/gtf/homo_sapiens/ 2>&1 | head -3; echo \"rc=$?\"; timeout 10 curl -s -o /dev/null -w \"%{http_code}\\n\" $CDP_URL/json/version; echo \"CDP=$CDP_URL\"", "mkdir -p && cd /tmp && nohup install --release 75 --species human > 2>&1 &\nsleep 5; tail -c 600 ; echo; curl -s $CDP_URL/json/version | head -c 300; echo; echo \"CDP http:\"; curl -s -o /dev/null -w \"%{http_code}\\n\" $CDP_URL/json/version", "cd && ls tests/ | head -40; grep -rl \"isovar run\\|\\\"run\\\"\" docs/command-line.md | head; sed -n '1,80p' docs/command-line.md | head -c 4000", "cd && ls -la tests/data/wlos0001_tp53 | head -30; sed -n '1,60p' tests/data/wlos0001_tp53/README.md | head -c 3000; echo; tail -3 | tail -c 400", "cd && wc -l examples/wlos0001_tp53.py && head -c 2500 examples/wlos0001_tp53.py; echo; echo ----; cat tests/data/wlos0001_tp53/wlos0001-tp53.vcf", "mkdir -p && cd && examples/wlos0001_tp53.py --output ; echo \"rc=$?\"; ls -la ; head -c 800 ", "sleep 60; cat | tr '\\r' '\\n' | tail -5 | cut -c1-300; ls -la 2>&1 | head; pgrep -fa pyensembl | head -3", "cd && find tests/data examples -name \"*.vcf*\" | head -30; echo ---; grep -n \"primary.chr1\" -r tests/*.py | head -5", "cd && cat tests/data/somatic-variant-with-2-supporting-rna-reads/single_variant.vcf | head -20; ls tests/data/somatic-variant-with-2-supporting-rna-reads/; echo ---; head -30 tests/data/real_rna/HG001.selected.vcf | cut -c1-200; ls tests/data/real_rna | head", "cd /tmp && run --help 2>&1 | head -60 | cut -c1-220", "sleep 120; cat | tr '\\r' '\\n' | tail -4 | cut -c1-200; ls -la | tail -n +4 | cut -c1-160", "for i in $(seq 1 25); do if ! pgrep -f \"pyensembl install\" >/dev/null; then break; fi; sleep 10; done; cat | tr '\\r' '\\n' | tail -3 | cut -c1-200; pgrep -f \"pyensembl install\" >/dev/null && echo STILL_RUNNING || echo DONE", "for i in $(seq 1 25); do if ! pgrep -f \"pyensembl install\" >/dev/null; then break; fi; sleep 10; done; tail -c 300 | tr '\\r' '\\n' | tail -2 | cut -c1-200; pgrep -f \"pyensembl install\" >/dev/null && echo STILL_RUNNING || echo DONE", "for i in $(seq 1 25); do if ! kill -0 2436 2>/dev/null; then break; fi; sleep 10; done; kill -0 2436 2>/dev/null && echo STILL_RUNNING || echo DONE; tail -c 400 | tr '\\r' '\\n' | tail -2 | cut -c1-200; ls | grep -c db", "mkdir -p && cd && run --vcf tests/data/somatic-variant-with-2-supporting-rna-reads/single_variant.vcf --bam tests/data/somatic-variant-with-2-supporting-rna-reads/rna.14.105849746.G.A.2-alt.sorted.bam --output --log-level WARNING; echo \"rc=$?\"; cat | cut -c1-400", "cd && grep -rn \"2-alt\\|single_variant\" tests/*.py | head -8; echo ---; grep -rln \"while True\\|schedule\\|--once\\|webhook\\|cron\" isovar/ | head; echo ---; grep -rn \"\\-\\-once\\|--now\\|webhook\\|cron\" isovar/*.py | head -5", "cd && sed -n 1,60p tests/test_somatic_variant_with_2_supporting_rna_reads.py | cut -c1-160", "mkdir -p && mkdir -p && cd && cat > probe.json <<'EOF'\n{\"kind\":\"cli\",\"argv\":[\"\",\"run\",\"--vcf\",\"tests/data/somatic-variant-with-2-supporting-rna-reads/single_variant.vcf\",\"--bam\",\"tests/data/somatic-variant-with-2-supporting-rna-reads/rna.14.105849746.G.A.2-alt.sorted.bam\",\"--output\",\"\",\"--log-level\",\"WARNING\"],\"cwd\":\"\",\"env\":{\"PYENSEMBL_CACHE_DIR\":\"\"},\"expected_file\":\"\",\"expected_text\":\"p.G559E\"}\nEOF\ncat > claims.json <<'EOF'\n[{\"kind\":\"claim\",\"claim\":\"The CSV has one row per variant, with the same columns as the DataFrame.\",\"source\":\"The CSV has one row per variant, with the same columns as the DataFrame.\",\"input\":\"single_variant.vcf with rna.14.105849746.G.A.2-alt.sorted.bam\",\"expected\":\"one CSV row for chr14 g.105849746G>A\",\"probe_kind\":\"cli\",\"argv\":[\"\",\"run\",\"--vcf\",\"tests/data/somatic-variant-with-2-supporting-rna-reads/single_variant.vcf\",\"--bam\",\"tests/data/somatic-variant-with-2-supporting-rna-reads/rna.14.105849746.G.A.2-alt.sorted.bam\",\"--output\",\"\",\"--log-level\",\"WARNING\"],\"env\":{\"PYENSEMBL_CACHE_DIR\":\"\"},\"expected_file\":\"\",\"expected_text\":\"chr14 g.105849746G>A\",\"cwd\":\"\"}]\nEOF\npython3 -I -c \"import json;json.load(open('probe.json'));json.load(open('claims.json'));print('json ok')\"", "cd && cat > examples.json <<'EOF'\n[{\"kind\":\"example\",\"claim\":\"Replay the published canine TP53 DNA call against original tumor RNA reads and export protein hypotheses\",\"source\":\"tests/data/wlos0001_tp53/README.md\",\"input\":\"python examples/wlos0001_tp53.py --output \",\"expected\":\"RNA alt reads at 5:32563056 and 245 protein hypotheses\",\"argv\":[\"\",\"examples/wlos0001_tp53.py\",\"--output\",\"\"],\"cwd\":\"\",\"env\":{},\"expected_text\":\"Protein hypotheses: 245\"}]\nEOF\ncat > cycles.json <<'EOF'\n{\"detected\":false,\"reason\":\"Entry points inspected: README quickstart (isovar run), isovar --help subcommands, and examples/. isovar is a one-shot batch CLI and Python API; it has no cron, scheduler, daemon, watch loop, --once/--now flag, or webhook. Source grep for schedule/while True/webhook/cron found only unrelated audit/SV modules, not a product trigger.\",\"checks\":[]}\nEOF\npython3 -I -c \"import json;json.load(open('examples.json'));json.load(open('cycles.json'));print('ok')\"; ls -la ", "cd && ls -la 2>&1 | head; = python3 -I --validate --replay 2>&1 | tail -c 5000; echo \"rc=${PIPESTATUS[0]}\"", "ls -la 2>&1 | head; cd && (= nohup python3 -I --validate > 2>&1 &) ; sleep 45; tail -c 3000 " ], "stuck_step": "/bin/bash -c 'o=$(mktemp);e=$(mktemp);/bin/bash --noprofile --norc -c \"$1\" \"$o\" 2>\"$e\";c=$?;cat \"$o\";cat \"$e\" >&2;rm -f \"$o\" \"$e\";exit $c' coldpass 'exec /usr/bin/env -i USER=agent LOGNAME=agent USERNAME=agent '\"'\"'GIT_AUTHOR_NAME=Coldpass Cold Agent'\"'\"' '\"'\"'GIT_COMMITTER_NAME=Coldpass Cold Agent'\"'\"' GIT_CONFIG_NOSYSTEM=1 GIT_CONFIG_SYSTEM=/dev/null GIT_CONFIG_GLOBAL=/dev/null GIT_CONFIG_COUNT=4 GIT_CONFIG_KEY_0=user.name '\"'\"'GIT_CONFIG_VALUE_0=Coldpass Cold Agent'\"'\"' GIT_CONFIG_KEY_1=user.email GIT_CONFIG_KEY_2=user.useConfigOnly GIT_CONFIG_VALUE_2=true GIT_CONFIG_KEY_3=credential.helper GIT_CONFIG_VALUE_3= HOME= PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin LANG=C.UTF-8 SHELL=/bin/bash = XDG_CONFIG_HOME= NPM_CONFIG_CACHE=/var PIP_CACHE_DIR=/var CARGO_HOME=/var GOCACHE=/var GOMODCACHE=/var CDP_URL=http://:9226 =http://:9226 /bin/bash --noprofile --norc -c '\"'\"'cd && ls -la 2>&1 | head; cd && (= nohup python3 -I --validate > 2>&1 &) ; sleep 45; tail -c 3000 '\"'\"''", "error_excerpt": "exceeds time budget", "what_it_did": null, "suggested_fix": "Inspect the last guest command and installer output; prefer the smallest documented setup and useful operation for the next attempt.", "tokens_in": null, "tokens_out": null, "cost_usd": null, "usage_complete": true, "checks": [], "safety": { "version": "z2x-1", "rules_version": "z2x-1", "summary": "Review signals: 1 connection review, 80 hardcoded secret.", "expected": "Reviewed as expected for a test run: attempted writes that failed, so nothing was written.", "findings": [ { "kind": "connection-review", "count": 1, "note": "Repository processes attempted these non-loopback connections; proxies can hide the final hostname.", "location_count": 1, "path": "193.62.193.169:443", "process_count": 1, "processes": [ { "address": "193.62.193.169:443", "executable": "", "owner": "repo", "pid": "4010", "source": "isovar" } ] }, { "kind": "hardcoded-secret", "count": 80, "note": "Gitleaks found a possible hardcoded secret; value withheld.", "location_count": 11 } ], "context": [], "limitations": [ "A short run cannot establish that code is safe.", "Connections show IP addresses; proxies can hide the final hostname.", "Tracing covers dispatched commands and their children, not the whole OS; guest root can interfere with tracing." ], "static": { "dependency_note": "OSV scanned supported lockfiles; unpinned dependencies and unsupported formats are outside this check." }, "evidence_url": "/safety/?run=openvax--isovar-claude-haiku-5-5-1793157301745896257", "evidence_file": "/data/safety/openvax--isovar-claude-haiku-5-5-1793157301745896257.json.gz" }, "agent_execution": "native_agent", "agent_runtime": null, "agent_runtime_version": null, "tool_transport": null, "platform": "linux", "reasoning": "low", "service_tier": null, "resources": null, "native_tool_calls": null, "native_bundle": null, "architecture": null, "backend": "hyperv", "platform_details": { "backend": "hyperv", "os": "linux" }, "platform_conflicts": null, "sandbox_source": null, "source_pin": { "commit": "e6828ae5e4bbf14d79e2404f735247e08dbdae19", "url": "https://github.com/openvax/isovar" }, "purpose": "initial", "profile": { "model": "claude-haiku-5-5", "reasoning": "low" }, "fault": { "owner": "unknown", "status": "pending", "reason": "exceeds time budget" }, "fix_id": null, "verifies_run_id": null, "hosting": null, "operation_scope": null, "tool_calls": 27, "guest_setup": null, "runtime": null, "runtime_version": null, "runtime_revision": null, "source_revision": null, "evidence_version": null, "failure_origin": null, "evidence_strength": "nothing_checked", "works": "untested", "install_s": null, "first_use_s": null, "mcp": "none", "needs": [], "needs_which": null, "agent_interface": [], "license": "Apache-2.0", "repo_url": "https://github.com/openvax/isovar", "cost_to_try": null, "hardware": null, "what_failed": "exceeds time budget", "local_or_hosted": "local", "cycle_checks": null, "claims": null, "claims_note": null, "example_checks": null, "does_what_it_says": null, "maintenance": { "last_commit_at": "2026-10-27T23:31:04Z", "commits_90d": 421, "merged_prs_90d": 175, "open_issues": 41, "open_prs": 1, "reply_share": null, "reply_threads": 0, "median_reply_hours": null, "last_release_at": "2026-10-27T02:24:32Z", "archived": false, "verdict": "maintained", "note": "actively maintained: last commit 0 days ago; 421 commits and 175 merged PRs in 90 days; 41 open issues, 1 open PRs; latest release 2026-10-27" }, "maintenance_verdict": "maintained", "maintenance_note": "actively maintained: last commit 0 days ago; 421 commits and 175 merged PRs in 90 days; 41 open issues, 1 open PRs; latest release 2026-10-27", "maintained": "active", "maintained_note": "last commit 0 days ago; 11 open issues, 16 answered or closed", "last_commit_at": "2026-10-28T03:04:56Z", "last_release_at": "2026-10-27T02:24:32Z", "open_issues": 11, "answered_issues": 16, "platforms_claimed": [ "linux" ], "topic": "other", "agent_interfaces": [], "agent_interfaces_note": "README metadata is a discovery hint, not pinned documentation proof. Observed interfaces were exercised in this run. An empty list means unknown.", "mcp_context": null, "tested_at": "2026-10-28T03:35:36.051105+00:00", "tested_commit": "e6828ae5e4bbf14d79e2404f735247e08dbdae19", "tested_with": { "agent": null, "agent_version": null, "model": "claude-haiku-5-5", "model_route": "claude-haiku-5-5", "reasoning": "low", "os": "linux", "backend": "hyperv", "transport": null }, "setup_identity": { "repo": "openvax/isovar", "source": "https://github.com/openvax/isovar", "commit": "e6828ae5e4bbf14d79e2404f735247e08dbdae19", "source_revision": null, "os": "linux", "architecture": null, "backend": "hyperv", "model": "claude-haiku-5-5", "model_version": "claude-haiku-5-5", "agent_execution": "native_agent", "agent_runtime": null, "agent_runtime_version": null, "tool_transport": null, "runtime": null, "runtime_version": null, "runtime_revision": null, "sandbox_source": null, "guest_setup": null, "source_pin": { "commit": "e6828ae5e4bbf14d79e2404f735247e08dbdae19", "url": "https://github.com/openvax/isovar" }, "platform_details": { "os": "linux", "backend": "hyperv" }, "platform_conflicts": null, "reasoning": "low", "service_tier": null, "resources": null, "operation": null, "operation_scope": null, "hosting": null, "kind": "repo", "test_version": "readme-c106c8a1fd8238b0e3df988f814e62bbf2335959186ef6bbc72a5c3bf9412da5", "evidence_version": null }, "other_model": null, "other_run_id": null, "models_agree": null, "furthest_model": null, "transcript_url": "/transcripts/openvax--isovar-claude-haiku-5-5-1793157301745896257.txt", "report_url": "/reports/openvax--isovar-claude-haiku-5-5-1793157301745896257.json" }