{
  "agent_trace": {
    "codex_logs_available_local_only": true,
    "raw_logs_published": false
  },
  "collected_at": "2026-05-18T13:24:54.895152+00:00",
  "docker_cpus": 16,
  "docker_memory": "30g",
  "eval": {
    "error_code": null,
    "failed_tests": [
      "tests.test_fasta_ops.test_maskfasta_soft_mask",
      "tests.test_fasta_ops.test_maskfasta_soft_overrides_custom_char",
      "tests.test_harvest_bam_bed_conversions.test_bamtobed_t7_three_blocks_bed12",
      "tests.test_harvest_closest_extended.test_sortandnaming_t19",
      "tests.test_harvest_closest_extended.test_sortandnaming_t02",
      "tests.test_harvest_closest_extended.test_kclosest_t30",
      "tests.test_annotate.test_annotate_single_file_fraction_coverage",
      "tests.test_annotate.test_annotate_adjacent_non_overlapping_features",
      "tests.test_harvest_complement_flank_sort_multicov.test_sort_t08",
      "tests.test_harvest_closest.test_closest_t51",
      "tests.test_harvest_closest.test_closest_t68",
      "tests.test_harvest_bam_bed_conversions.test_bamtofastq_paired_end",
      "tests.test_harvest_closest.test_closest_t18",
      "tests.test_harvest_closest.test_closest_t35",
      "tests.test_harvest_closest_extended.test_kclosest_t15",
      "tests.test_harvest_fasta_groupby.test_getfasta_t05",
      "tests.test_harvest_closest_extended.test_sortandnaming_t20",
      "tests.test_fasta_ops.test_maskfasta_custom_mask_character",
      "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_annotate.test_annotate_bed3_format",
      "tests.test_harvest_closest_extended.test_sortandnaming_t03",
      "tests.test_harvest_closest.test_closest_t19",
      "tests.test_harvest_closest_extended.test_kclosest_t16",
      "tests.test_harvest_closest.test_closest_t69",
      "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_fasta_groupby.test_getfasta_t06",
      "tests.test_harvest_fasta_groupby.test_getfasta_t15",
      "tests.test_fasta_ops.test_nuc_basic_profile",
      "tests.test_harvest_closest_extended.test_sortandnaming_t21",
      "tests.test_fasta_ops.test_nuc_empty_bed",
      "tests.test_harvest_closest_extended.test_sortandnaming_t04",
      "tests.test_harvest_closest_extended.test_kclosest_t32",
      "tests.test_harvest_closest_extended.test_kclosest_t17",
      "tests.test_annotate.test_annotate_with_names_header",
      "tests.test_harvest_closest.test_closest_t70",
      "tests.test_annotate.test_annotate_features_extending_beyond_intervals",
      "tests.test_harvest_complement_flank_sort_multicov.test_multicov_t02",
      "tests.test_harvest_bam_bed_conversions.test_bamtobed_t9_deletion_and_intron_split",
      "tests.test_harvest_closest.test_closest_t41",
      "tests.test_harvest_closest.test_closest_t29",
      "tests.test_harvest_closest.test_closest_t15",
      "tests.test_harvest_fasta_groupby.test_getfasta_t07",
      "tests.test_harvest_fasta_groupby.test_getfasta_t134",
      "tests.test_fasta_ops.test_nuc_zero_length_intervals",
      "tests.test_fasta_ops.test_nuc_with_sequence_output",
      "tests.test_harvest_closest_extended.test_sortandnaming_t22",
      "tests.test_annotate.test_annotate_counts_mode",
      "tests.test_harvest_closest_extended.test_sortandnaming_t05",
      "tests.test_harvest_complement_flank_sort_multicov.test_multicov_t03",
      "tests.test_annotate.test_annotate_counts_with_names_header",
      "tests.test_harvest_closest_extended.test_kclosest_t18",
      "tests.test_harvest_closest_extended.test_kclosest_t33",
      "tests.test_harvest_closest.test_closest_t71",
      "tests.test_harvest_bam_bed_conversions.test_bamtobed_t10_deletion_splitD",
      "tests.test_harvest_closest.test_closest_t44",
      "tests.test_harvest_format_conversion.test_bamtobed_two_blocks_no_split",
      "tests.test_harvest_fasta_groupby.test_jaccard_t08",
      "tests.test_harvest_fasta_groupby.test_getfasta_t16",
      "tests.test_harvest_fasta_groupby.test_getfasta_t08",
      "tests.test_fasta_ops.test_nuc_interval_beyond_chromosome",
      "tests.test_annotate.test_annotate_both_mode",
      "tests.test_fasta_ops.test_nuc_pattern_matching",
      "tests.test_harvest_closest_extended.test_kclosest_t19",
      "tests.test_harvest_closest_extended.test_kclosest_t34",
      "tests.test_harvest_complement_flank_sort_multicov.test_multicov_t04",
      "tests.test_annotate.test_annotate_single_file_both_mode",
      "tests.test_harvest_closest_extended.test_sortandnaming_t06",
      "tests.test_harvest_closest_extended.test_kclosest_t2",
      "tests.test_harvest_bam_bed_conversions.test_bamtobed_t11_deletion_bed12",
      "tests.test_harvest_closest.test_closest_t47",
      "tests.test_harvest_complement_flank_sort_multicov.test_complement_t09",
      "tests.test_harvest_format_conversion.test_bamtobed_two_blocks_with_split",
      "tests.test_harvest_fasta_groupby.test_jaccard_t09",
      "tests.test_harvest_fasta_groupby.test_getfasta_t09",
      "tests.test_harvest_fasta_groupby.test_getfasta_t17"
    ],
    "failed_tests_omitted": 581,
    "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": "mini-swe-compatible-nointernet",
  "instance_id": "arq5x__bedtools2.dd57059",
  "metrics": {
    "almost_resolved": "False",
    "cached_input_tokens": "4623488",
    "calls": "55",
    "created_at": "2026-05-17T12:19:55.878955+00:00",
    "docker_cpus": "16",
    "docker_memory": "30g",
    "error_code": "",
    "estimated_cost_usd": "4.9141",
    "evaluator_problem": "False",
    "host_machine": "x86_64",
    "host_system": "Linux",
    "inference_mode": "mini-swe-compatible-nointernet",
    "input_tokens": "4856703",
    "instance_id": "arq5x__bedtools2.dd57059",
    "long_context_calls": "0",
    "model": "gpt-5.5",
    "n_resolved_tests": "424",
    "n_system_errors": "0",
    "n_tests": "1053",
    "n_warnings": "0",
    "output_tokens": "47875",
    "paper_compliant": "False",
    "pricing_source": "https://developers.openai.com/api/docs/models/gpt-5.5",
    "reasoning_effort": "xhigh",
    "reasoning_output_tokens": "11870",
    "resolved": "False",
    "run_name": "cpx62-miniswecompat-xhigh-20260517T094700Z-arq5x-bedtools2-attempt-2",
    "run_version": "20260517T094700Z",
    "score": "0.402659069325736",
    "session_ended_at": "2026-05-17T12:34:10.461Z",
    "session_started_at": "2026-05-17T12:20:00.113Z",
    "test_branch_errors": "{}",
    "total_tokens": "4904578",
    "wall_clock_seconds": "850"
  },
  "model": "gpt-5.5",
  "package": {
    "contents": [
      ".",
      "./bedtools_reimpl.py",
      "./compile.sh",
      "./executable"
    ],
    "contents_omitted": 0,
    "submission_available_local_only": true
  },
  "paper_compliant": false,
  "paper_mode": false,
  "reasoning_effort": "xhigh",
  "run_name": "cpx62-miniswecompat-xhigh-20260517T094700Z-arq5x-bedtools2-attempt-2",
  "run_version": "20260517T094700Z",
  "usage_audit": {
    "available_local_artifact": true,
    "public_path": "usage-audit.json"
  }
}
