{
  "agent_trace": {
    "codex_logs_available_local_only": true,
    "raw_logs_published": false,
    "summary_path": "agent-summary.json"
  },
  "codex_version": "codex-cli 0.131.0",
  "collected_at": "2026-05-19T20:23:04.527347+00:00",
  "docker_cpus": 16,
  "docker_memory": "30g",
  "eval": {
    "error_code": null,
    "failed_tests": [
      "tests.test_harvest_closest_extended.test_sortandnaming_t02",
      "tests.test_fasta_ops.test_maskfasta_soft_mask",
      "tests.test_fasta_ops.test_maskfasta_soft_overrides_custom_char",
      "tests.test_harvest_closest_extended.test_kclosest_t30",
      "tests.test_harvest_closest_extended.test_sortandnaming_t19",
      "tests.test_harvest_complement_flank_sort_multicov.test_sort_t08",
      "tests.test_annotate.test_annotate_single_file_fraction_coverage",
      "tests.test_harvest_bam_bed_conversions.test_bamtobed_t7_three_blocks_bed12",
      "tests.test_harvest_closest.test_closest_t51",
      "tests.test_annotate.test_annotate_adjacent_non_overlapping_features",
      "tests.test_harvest_closest.test_closest_t68",
      "tests.test_harvest_closest.test_closest_t35",
      "tests.test_harvest_bam_bed_conversions.test_bamtofastq_paired_end",
      "tests.test_harvest_closest_extended.test_kclosest_t19",
      "tests.test_harvest_closest.test_closest_t26",
      "tests.test_harvest_fasta_groupby.test_getfasta_t05",
      "tests.test_fasta_ops.test_maskfasta_custom_mask_character",
      "tests.test_harvest_closest_extended.test_sortandnaming_t20",
      "tests.test_harvest_closest_extended.test_sortandnaming_t03",
      "tests.test_fasta_ops.test_nuc_error_missing_fasta",
      "tests.test_annotate.test_annotate_multiple_files_fraction_coverage",
      "tests.test_harvest_closest_extended.test_kclosest_t31",
      "tests.test_harvest_closest.test_closest_t69",
      "tests.test_annotate.test_annotate_bed3_format",
      "tests.test_harvest_bam_bed_conversions.test_bamtobed_t8_split_vs_bed12",
      "tests.test_harvest_bam_bed_conversions.test_bedtobam_t1_basic_conversion",
      "tests.test_harvest_complement_flank_sort_multicov.test_multicov_t01",
      "tests.test_harvest_closest.test_closest_t38",
      "tests.test_harvest_closest.test_closest_t59",
      "tests.test_harvest_closest.test_closest_t29",
      "tests.test_harvest_closest_extended.test_kclosest_t24",
      "tests.test_harvest_fasta_groupby.test_getfasta_t06",
      "tests.test_harvest_closest_extended.test_sortandnaming_t21",
      "tests.test_harvest_closest_extended.test_sortandnaming_t04",
      "tests.test_fasta_ops.test_nuc_basic_profile",
      "tests.test_fasta_ops.test_nuc_empty_bed",
      "tests.test_harvest_closest_extended.test_kclosest_t32",
      "tests.test_annotate.test_annotate_with_names_header",
      "tests.test_annotate.test_annotate_features_extending_beyond_intervals",
      "tests.test_harvest_closest.test_closest_t70",
      "tests.test_harvest_complement_flank_sort_multicov.test_multicov_t02",
      "tests.test_harvest_closest.test_closest_t41",
      "tests.test_harvest_bam_bed_conversions.test_bamtobed_t9_deletion_and_intron_split",
      "tests.test_harvest_closest_extended.test_kclosest_t25",
      "tests.test_harvest_fasta_groupby.test_jaccard_t05",
      "tests.test_harvest_closest.test_closest_t32",
      "tests.test_harvest_fasta_groupby.test_getfasta_t07",
      "tests.test_harvest_format_conversion.test_bamtofastq_paired_end",
      "tests.test_harvest_closest_extended.test_sortandnaming_t22",
      "tests.test_harvest_closest_extended.test_sortandnaming_t05",
      "tests.test_harvest_closest_extended.test_kclosest_t33",
      "tests.test_fasta_ops.test_nuc_with_sequence_output",
      "tests.test_fasta_ops.test_nuc_zero_length_intervals",
      "tests.test_annotate.test_annotate_counts_with_names_header",
      "tests.test_harvest_complement_flank_sort_multicov.test_multicov_t03",
      "tests.test_annotate.test_annotate_both_mode",
      "tests.test_harvest_closest_extended.test_kclosest_t2",
      "tests.test_harvest_bam_bed_conversions.test_bamtobed_t10_deletion_splitD",
      "tests.test_harvest_closest.test_closest_t44",
      "tests.test_harvest_fasta_groupby.test_getfasta_t15",
      "tests.test_harvest_fasta_groupby.test_getfasta_t08",
      "tests.test_harvest_fasta_groupby.test_jaccard_t06",
      "tests.test_harvest_closest_extended.test_kclosest_t28",
      "tests.test_harvest_format_conversion.test_bed12tobed6_one_block",
      "tests.test_fasta_ops.test_nuc_pattern_matching",
      "tests.test_fasta_ops.test_nuc_interval_beyond_chromosome",
      "tests.test_harvest_closest_extended.test_sortandnaming_t06",
      "tests.test_harvest_closest_extended.test_kclosest_t34",
      "tests.test_harvest_complement_flank_sort_multicov.test_multicov_t04",
      "tests.test_annotate.test_annotate_same_strand_filtering",
      "tests.test_annotate.test_annotate_single_file_both_mode",
      "tests.test_harvest_closest_extended.test_kclosest_t3",
      "tests.test_harvest_bam_bed_conversions.test_bamtobed_t11_deletion_bed12",
      "tests.test_harvest_complement_flank_sort_multicov.test_complement_t09",
      "tests.test_harvest_closest.test_closest_t47",
      "tests.test_harvest_fasta_groupby.test_getfasta_t134",
      "tests.test_harvest_closest_extended.test_kclosest_t29",
      "tests.test_harvest_fasta_groupby.test_getfasta_t09",
      "tests.test_harvest_format_conversion.test_bed12tobed6_two_blocks",
      "tests.test_harvest_fasta_groupby.test_jaccard_t07"
    ],
    "failed_tests_omitted": 549,
    "public_eval_path": "eval.json",
    "summary_path": "eval-summary.json",
    "test_branch_errors": {},
    "test_records": 1093,
    "warnings": []
  },
  "host_machine": "x86_64",
  "host_system": "Linux",
  "inference_mode": "paper-prompt-nointernet",
  "instance_id": "arq5x__bedtools2.dd57059",
  "metrics": {
    "almost_resolved": "False",
    "cached_input_tokens": "2227584",
    "calls": "41",
    "codex_version": "codex-cli 0.131.0",
    "created_at": "2026-05-18T23:39:08.212550+00:00",
    "docker_cpus": "16",
    "docker_memory": "30g",
    "error_code": "",
    "estimated_cost_usd": "",
    "evaluator_problem": "False",
    "host_machine": "x86_64",
    "host_system": "Linux",
    "inference_mode": "paper-prompt-nointernet",
    "input_tokens": "2426552",
    "instance_id": "arq5x__bedtools2.dd57059",
    "long_context_calls": "0",
    "model": "gpt-5.5",
    "n_resolved_tests": "455",
    "n_system_errors": "0",
    "n_tests": "1053",
    "n_warnings": "0",
    "output_tokens": "39319",
    "paper_compliant": "False",
    "pricing_source": "",
    "reasoning_effort": "xhigh",
    "reasoning_output_tokens": "7053",
    "resolved": "False",
    "run_name": "cpx62-paperprompt-xhigh-shard-1-of-5-20260518T232006Z-arq5x-bedtools2",
    "run_version": "20260518T232006Z",
    "score": "0.43209876543209874",
    "session_ended_at": "2026-05-18T23:49:44.764Z",
    "session_started_at": "2026-05-18T23:39:16.447Z",
    "test_branch_errors": "{}",
    "total_tokens": "2465871",
    "wall_clock_seconds": "628"
  },
  "model": "gpt-5.5",
  "package": {
    "contents": [
      ".",
      "./.git",
      "./.git/COMMIT_EDITMSG",
      "./.git/HEAD",
      "./.git/branches",
      "./.git/config",
      "./.git/description",
      "./.git/hooks",
      "./.git/hooks/applypatch-msg.sample",
      "./.git/hooks/commit-msg.sample",
      "./.git/hooks/fsmonitor-watchman.sample",
      "./.git/hooks/post-update.sample",
      "./.git/hooks/pre-applypatch.sample",
      "./.git/hooks/pre-commit.sample",
      "./.git/hooks/pre-merge-commit.sample",
      "./.git/hooks/pre-push.sample",
      "./.git/hooks/pre-rebase.sample",
      "./.git/hooks/pre-receive.sample",
      "./.git/hooks/prepare-commit-msg.sample",
      "./.git/hooks/push-to-checkout.sample",
      "./.git/hooks/update.sample",
      "./.git/index",
      "./.git/info",
      "./.git/info/exclude",
      "./.git/logs",
      "./.git/logs/HEAD",
      "./.git/logs/refs",
      "./.git/logs/refs/heads",
      "./.git/logs/refs/heads/master",
      "./.git/objects",
      "./.git/objects/27",
      "./.git/objects/27/295ffef33183bf4d6805a7526b7b91d0a449b2",
      "./.git/objects/2e",
      "./.git/objects/2e/978062e9b978a66e0cf2caec374f8b64966981",
      "./.git/objects/34",
      "./.git/objects/34/61805a42f957c757426dce3096c5dbbe5aff0a",
      "./.git/objects/3b",
      "./.git/objects/3b/ddbd652dcc3785cb1db504217ac7267b648ee6",
      "./.git/objects/3d",
      "./.git/objects/3d/993880fa31861ca6dfc5842d00ffda1131f211",
      "./.git/objects/3f",
      "./.git/objects/3f/222390bcc7ad132cc082462cd6e946daea1e3e",
      "./.git/objects/44",
      "./.git/objects/44/698c5d693eab140d23cce831d0dc942aa70181",
      "./.git/objects/47",
      "./.git/objects/47/3a41ebcc9221b6c86cde6c7e187b97ab5586f8",
      "./.git/objects/51",
      "./.git/objects/51/2c39656cccefa58fd4663365242ce8e22a7a1d",
      "./.git/objects/58",
      "./.git/objects/58/d2e380fe5b7a90ac820156faf606c71feed4d5",
      "./.git/objects/5a",
      "./.git/objects/5a/6bdced951cb01e62ad785c76110b1bf59816ec",
      "./.git/objects/64",
      "./.git/objects/64/69bedb6829eee78d14d294ea7f77506553716e",
      "./.git/objects/68",
      "./.git/objects/68/f3584491c208ee2cbded88eaad35dc9b155642",
      "./.git/objects/6b",
      "./.git/objects/6b/eb2708f4cfc4e723bab8dcaf1482aca1fcaee8",
      "./.git/objects/6d",
      "./.git/objects/6d/c87865d2e0d6a45470ea66a2ddc2cb53701ba4",
      "./.git/objects/80",
      "./.git/objects/80/8943cee55bd676cf378a34ae232fd2286ce0e0",
      "./.git/objects/8d",
      "./.git/objects/8d/2f71949058d2bde279254b393bbe44eaa62976",
      "./.git/objects/8e",
      "./.git/objects/8e/03a623eb8d50da534a93fb70855a32a2c5998a",
      "./.git/objects/94",
      "./.git/objects/94/c1aab6688055677a70b5ef6e4ada830b8a621d",
      "./.git/objects/ad",
      "./.git/objects/ad/bc418946dad20bd0cea89a7688370ebec3c76f",
      "./.git/objects/b2",
      "./.git/objects/b2/812e183146a102190b5235a00b698eac08f145",
      "./.git/objects/c1",
      "./.git/objects/c1/de3ff9ba7a6fb3900135f4eabcd6dce784fec8",
      "./.git/objects/c1/f05c388553548ead4d2a44a947b58ebc5a17a4",
      "./.git/objects/d8",
      "./.git/objects/d8/a7e6b7144d8d56c179ad74b9f920e21ec3d1cb",
      "./.git/objects/e3",
      "./.git/objects/e3/c27d93f8fcd6158879019c06b2a3c16b40e237",
      "./.git/objects/fa",
      "./.git/objects/fa/0bb85d9a56cd8281c183f22e6a2329a5c9254e",
      "./.git/objects/info",
      "./.git/objects/pack",
      "./.git/refs",
      "./.git/refs/heads",
      "./.git/refs/heads/master",
      "./.git/refs/tags",
      "./LICENSE",
      "./README.md",
      "./bedtools.py",
      "./compile.sh",
      "./data",
      "./data/aluY.chr1.bed.gz",
      "./data/gerp.chr1.bed.gz",
      "./data/knownGene.hg18.chr21.bed",
      "./data/knownGene.hg18.chr21.short.bed",
      "./data/refseq.chr1.exons.bed.gz",
      "./data/simpleRepeats.chr1.bed.gz",
      "./executable",
      "./genomes",
      "./genomes/human.hg18.genome",
      "./genomes/human.hg19.genome",
      "./genomes/human.hg38.genome",
      "./genomes/mouse.mm10.genome",
      "./genomes/mouse.mm8.genome",
      "./genomes/mouse.mm9.genome",
      "./tutorial",
      "./tutorial/answers.html",
      "./tutorial/answers.md",
      "./tutorial/bedtools.html",
      "./tutorial/bedtools.md",
      "./tutorial/bootstrap.css",
      "./tutorial/template.class.html",
      "./tutorial/template.html"
    ],
    "contents_omitted": 0,
    "submission_available_local_only": true
  },
  "paper_compliant": false,
  "paper_mode": true,
  "reasoning_effort": "xhigh",
  "run_name": "cpx62-paperprompt-xhigh-shard-1-of-5-20260518T232006Z-arq5x-bedtools2",
  "run_version": "20260518T232006Z",
  "usage_audit": {
    "available_local_artifact": true,
    "public_path": "usage-audit.json"
  }
}
