{
  "agent_trace": {
    "codex_logs_available_local_only": true,
    "raw_logs_published": false
  },
  "collected_at": "2026-05-18T13:25:06.129260+00:00",
  "docker_cpus": 16,
  "docker_memory": "30g",
  "eval": {
    "error_code": null,
    "failed_tests": [
      "eval.tests.test_basic.TestSeqCommand.test_seq_nonexistent_file",
      "eval.tests.test_basic.TestSeqCommand.test_seq_strip_whitespace",
      "eval.tests.test_basic.TestSeqCommand.test_seq_fake_quality",
      "eval.tests.test_basic.TestSeqCommand.test_seq_x_lowercase_to_n",
      "eval.tests.test_basic.TestSeqCommand.test_seq_reverse_both_strands",
      "eval.tests.test_comp.TestCompCommand.test_comp_with_region_bed",
      "eval.tests.test_basic.TestSizeCommand.test_size_nonexistent_file",
      "eval.tests.test_comp.TestFqchkCommand.test_fqchk_nonexistent_file",
      "eval.tests.test_comp.TestCompCommand.test_comp_upper_only",
      "eval.tests.test_genomics.TestGcCommand.test_gc_nonexistent_file",
      "eval.tests.test_genomics.TestCutNCommand.test_cutn_nonexistent_file",
      "eval.tests.test_merge_split.TestHrunCommand.test_hrun_basic",
      "eval.tests.test_merge_split.TestHrunCommand.test_hrun_shows_usage",
      "eval.tests.test_merge_split.TestHrunCommand.test_hrun_output_format",
      "eval.tests.test_merge_split.TestHrunCommand.test_hrun_min_length",
      "eval.tests.test_merge_split.TestHrunCommand.test_hrun_stdin",
      "eval.tests.test_comp.TestCompCommand.test_comp_nonexistent_file",
      "eval.tests.test_sample_subseq.TestSubseqCommand.test_subseq_missing_region_file",
      "eval.tests.test_genomics.TestHetyCommand.test_hety_nonexistent_file",
      "eval.tests.test_telo.TestTeloCommand.test_telo_show_profile",
      "eval.tests.test_telo.TestTeloCommand.test_telo_max_drop",
      "eval.tests.test_telo.TestTeloCommand.test_telo_min_score",
      "eval.tests.test_telo.TestTeloCommand.test_telo_penalty",
      "eval.tests.test_merge_split.TestKfreqCommand.test_kfreq_stdin",
      "eval.tests.test_merge_split.TestKfreqCommand.test_kfreq_basic",
      "eval.tests.test_merge_split.TestKfreqCommand.test_kfreq_shows_usage",
      "eval.tests.test_merge_split.TestKfreqCommand.test_kfreq_output_format",
      "eval.tests.test_telo.TestTeloCommand.test_telo_custom_motif",
      "eval.tests.test_trimfq.TestTrimfqCommand.test_trimfq_nonexistent_file",
      "tests.test_info.test_fqchk_quality_distribution",
      "tests.test_analysis.test_hety_window_larger_than_sequence",
      "tests.test_analysis.test_gap_missing_file",
      "tests.test_analysis.test_gc_basic",
      "tests.test_info.test_comp_uppercase_only_flag",
      "tests.test_info.test_comp_with_regions",
      "tests.test_analysis.test_gc_stdin",
      "tests.test_analysis.test_hety_custom_window_step",
      "tests.test_analysis.test_hety_window_boundary",
      "tests.test_info.test_fqchk_simple_fastq",
      "tests.test_mutation_masking.test_mergefa_quality_threshold",
      "tests.test_mutation_masking.test_mergefa_double_het_identical",
      "tests.test_mutation_masking.test_famask_different_sequence_names",
      "tests.test_mutation_masking.test_mergefa_complex_iupac_codes",
      "tests.test_mutation_masking.test_mergefa_mask_n_mode",
      "tests.test_mutation_masking.test_mutfa_invalid_mutation_format",
      "tests.test_info.test_fqchk_q0_flag_all_qualities",
      "tests.test_analysis.test_gc_missing_file",
      "tests.test_analysis.test_hety_stdin",
      "tests.test_analysis.test_gc_short_regions",
      "tests.test_analysis.test_hety_lowercase_masking",
      "tests.test_analysis.test_hety_basic",
      "tests.test_mutation_masking.test_mutfa_line_wrapping",
      "tests.test_info.test_fqchk_stdin_input",
      "tests.test_mutation_masking.test_famask_line_wrapping",
      "tests.test_mutation_masking.test_mergefa_empty_sequences",
      "tests.test_mutation_masking.test_mergefa_flag_combination_error",
      "tests.test_mutation_masking.test_mergefa_haploid_mode",
      "tests.test_mutation_masking.test_mutfa_multi_sequence_mutations",
      "tests.test_mutation_masking.test_mergefa_unequal_sequence_lengths",
      "tests.test_pe_trim.test_trimfq_nonexistent_file",
      "tests.test_seq.test_both_forward_and_reverse",
      "tests.test_analysis.test_hety_tiny_window",
      "tests.test_analysis.test_hety_missing_file",
      "tests.test_mutation_masking.test_mutfa_missing_snp_file",
      "tests.test_mutation_masking.test_famask_missing_input_files",
      "tests.test_info.test_fqchk_fasta_input_ignored",
      "tests.test_analysis.test_listhet_missing_file",
      "tests.test_mutation_masking.test_mergefa_missing_input_files",
      "tests.test_mutation_masking.test_famask_empty_sequences",
      "tests.test_mutation_masking.test_mergefa_different_sequence_names",
      "tests.test_mutation_masking.test_mergefa_random_het_mode",
      "tests.test_pe_trim.test_mergepe_nonexistent_files",
      "tests.test_seq.test_both_strands_with_quality_masking",
      "tests.test_subseq_sample.test_sample_deterministic_with_seed",
      "tests.test_subseq_sample.test_sample_fraction_sampling",
      "tests.test_subseq_sample.test_sample_different_seeds_produce_different_output",
      "tests.test_seq.test_sampling_with_seed",
      "tests.test_seq.test_fake_quality_fasta_to_fastq",
      "tests.test_mutation_masking.test_mergefa_het_hom_interaction",
      "tests.test_info.test_fqchk_q30_threshold"
    ],
    "failed_tests_omitted": 51,
    "public_eval_path": "eval.json",
    "summary_path": "eval-summary.json",
    "test_branch_errors": {},
    "test_records": 440,
    "warnings": []
  },
  "host_machine": "x86_64",
  "host_system": "Linux",
  "inference_mode": "mini-swe-compatible-nointernet",
  "instance_id": "lh3__seqtk.94e7070",
  "metrics": {
    "almost_resolved": "False",
    "cached_input_tokens": "3393152",
    "calls": "71",
    "created_at": "2026-05-17T12:35:27.034971+00:00",
    "docker_cpus": "16",
    "docker_memory": "30g",
    "error_code": "",
    "estimated_cost_usd": "3.8773",
    "evaluator_problem": "False",
    "host_machine": "x86_64",
    "host_system": "Linux",
    "inference_mode": "mini-swe-compatible-nointernet",
    "input_tokens": "3534045",
    "instance_id": "lh3__seqtk.94e7070",
    "long_context_calls": "0",
    "model": "gpt-5.5",
    "n_resolved_tests": "300",
    "n_system_errors": "0",
    "n_tests": "429",
    "n_warnings": "0",
    "output_tokens": "49210",
    "paper_compliant": "False",
    "pricing_source": "https://developers.openai.com/api/docs/models/gpt-5.5",
    "reasoning_effort": "xhigh",
    "reasoning_output_tokens": "16750",
    "resolved": "False",
    "run_name": "cpx62-miniswecompat-xhigh-20260517T094700Z-lh3-seqtk",
    "run_version": "20260517T094700Z",
    "score": "0.6993006993006993",
    "session_ended_at": "2026-05-17T12:48:27.971Z",
    "session_started_at": "2026-05-17T12:35:30.181Z",
    "test_branch_errors": "{}",
    "total_tokens": "3583255",
    "wall_clock_seconds": "777"
  },
  "model": "gpt-5.5",
  "package": {
    "contents": [
      ".",
      "./compile.sh",
      "./executable",
      "./seqtk_py.py"
    ],
    "contents_omitted": 0,
    "submission_available_local_only": true
  },
  "paper_compliant": false,
  "paper_mode": false,
  "reasoning_effort": "xhigh",
  "run_name": "cpx62-miniswecompat-xhigh-20260517T094700Z-lh3-seqtk",
  "run_version": "20260517T094700Z",
  "usage_audit": {
    "available_local_artifact": true,
    "public_path": "usage-audit.json"
  }
}
