[INFO] cloning repository https://github.com/japality/japalityecho
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/japality/japalityecho" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fjapality%2Fjapalityecho", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fjapality%2Fjapalityecho'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] bff4cb348cf97d307a8cd05fea6598e413c6d767
[INFO] testing japality/japalityecho against master#ec6f9a5b4413f74386267ef8efc93712c2ce6db6 for pr-155739
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fjapality%2Fjapalityecho" "/workspace/builds/worker-6-tc1/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-6-tc1/source'...
[INFO] [stderr] done.
[INFO] started tweaking git repo https://github.com/japality/japalityecho
[INFO] finished tweaking git repo https://github.com/japality/japalityecho
[INFO] tweaked toml for git repo https://github.com/japality/japalityecho written to /workspace/builds/worker-6-tc1/source/Cargo.toml
[INFO] validating manifest of git repo https://github.com/japality/japalityecho on toolchain ec6f9a5b4413f74386267ef8efc93712c2ce6db6
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+ec6f9a5b4413f74386267ef8efc93712c2ce6db6" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+ec6f9a5b4413f74386267ef8efc93712c2ce6db6" "generate-lockfile" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Updating crates.io index
[INFO] [stderr]      Locking 75 packages to latest Rust 1.97.0-nightly compatible versions
[INFO] [stderr]       Adding libloading v0.8.9 (available: v0.9.0)
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+ec6f9a5b4413f74386267ef8efc93712c2ce6db6" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded once_cell v1.21.4
[INFO] [stderr]   Downloaded tempfile v3.27.0
[INFO] [stderr]   Downloaded getrandom v0.4.2
[INFO] [stderr]   Downloaded anstyle-query v1.1.5
[INFO] [stderr]   Downloaded bitflags v2.11.1
[INFO] [stderr]   Downloaded itoa v1.0.18
[INFO] [stderr]   Downloaded is_terminal_polyfill v1.70.2
[INFO] [stderr]   Downloaded anstyle-wincon v3.0.11
[INFO] [stderr]   Downloaded clap_lex v1.1.0
[INFO] [stderr]   Downloaded colorchoice v1.0.5
[INFO] [stderr]   Downloaded anstyle-parse v1.0.0
[INFO] [stderr]   Downloaded once_cell_polyfill v1.70.2
[INFO] [stderr]   Downloaded anstyle v1.0.14
[INFO] [stderr]   Downloaded anstream v1.0.0
[INFO] [stderr]   Downloaded quote v1.0.45
[INFO] [stderr]   Downloaded clap_derive v4.6.1
[INFO] [stderr]   Downloaded fastrand v2.4.1
[INFO] [stderr]   Downloaded semver v1.0.28
[INFO] [stderr]   Downloaded simd-adler32 v0.3.9
[INFO] [stderr]   Downloaded r-efi v6.0.0
[INFO] [stderr]   Downloaded clap v4.6.1
[INFO] [stderr]   Downloaded wit-bindgen v0.57.1
[INFO] [stderr]   Downloaded indexmap v2.14.0
[INFO] [stderr]   Downloaded wasip2 v1.0.3+wasi-0.2.9
[INFO] [stderr]   Downloaded hashbrown v0.17.1
[INFO] [stderr]   Downloaded clap_builder v4.6.0
[INFO] [stderr]   Downloaded libc v0.2.186
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc1/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:d429b63d4308055ea97f60fb1d3dfca48854a00942f1bd2ad806beaf015945ec" "/opt/rustwide/cargo-home/bin/cargo" "+ec6f9a5b4413f74386267ef8efc93712c2ce6db6" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] de61d7f725222da19822e132efd701a903bb07f8652d38011121e9f919386f88
[INFO] running `Command { std: "docker" "start" "-a" "de61d7f725222da19822e132efd701a903bb07f8652d38011121e9f919386f88", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "de61d7f725222da19822e132efd701a903bb07f8652d38011121e9f919386f88", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "de61d7f725222da19822e132efd701a903bb07f8652d38011121e9f919386f88", kill_on_drop: false }`
[INFO] [stdout] de61d7f725222da19822e132efd701a903bb07f8652d38011121e9f919386f88
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc1/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "RUSTDOCFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:d429b63d4308055ea97f60fb1d3dfca48854a00942f1bd2ad806beaf015945ec" "/opt/rustwide/cargo-home/bin/cargo" "+ec6f9a5b4413f74386267ef8efc93712c2ce6db6" "build" "--frozen" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] ad5382852c6c28326d374aa5a49b33f21955faab8bb1fbea070a6898a59acca3
[INFO] running `Command { std: "docker" "start" "-a" "ad5382852c6c28326d374aa5a49b33f21955faab8bb1fbea070a6898a59acca3", kill_on_drop: false }`
[INFO] [stderr]    Compiling proc-macro2 v1.0.106
[INFO] [stderr]    Compiling quote v1.0.45
[INFO] [stderr]    Compiling unicode-ident v1.0.24
[INFO] [stderr]    Compiling crossbeam-utils v0.8.21
[INFO] [stderr]    Compiling serde_core v1.0.228
[INFO] [stderr]    Compiling cfg-if v1.0.4
[INFO] [stderr]    Compiling rayon-core v1.13.0
[INFO] [stderr]    Compiling colorchoice v1.0.5
[INFO] [stderr]    Compiling is_terminal_polyfill v1.70.2
[INFO] [stderr]    Compiling crc32fast v1.5.0
[INFO] [stderr]    Compiling anstyle v1.0.14
[INFO] [stderr]    Compiling anstyle-query v1.1.5
[INFO] [stderr]    Compiling zmij v1.0.21
[INFO] [stderr]    Compiling anyhow v1.0.102
[INFO] [stderr]    Compiling clap_lex v1.1.0
[INFO] [stderr]    Compiling anstyle-parse v1.0.0
[INFO] [stderr]    Compiling serde v1.0.228
[INFO] [stderr]    Compiling adler2 v2.0.1
[INFO] [stderr]    Compiling heck v0.5.0
[INFO] [stderr]    Compiling simd-adler32 v0.3.9
[INFO] [stderr]    Compiling serde_json v1.0.149
[INFO] [stderr]    Compiling memchr v2.8.0
[INFO] [stderr]    Compiling either v1.15.0
[INFO] [stderr]    Compiling itoa v1.0.18
[INFO] [stderr]    Compiling libloading v0.8.9
[INFO] [stderr]    Compiling anstream v1.0.0
[INFO] [stderr]    Compiling miniz_oxide v0.8.9
[INFO] [stderr]    Compiling clap_builder v4.6.0
[INFO] [stderr]    Compiling crossbeam-epoch v0.9.18
[INFO] [stderr]    Compiling syn v2.0.117
[INFO] [stderr]    Compiling crossbeam-deque v0.8.6
[INFO] [stderr]    Compiling flate2 v1.1.9
[INFO] [stderr]    Compiling rayon v1.12.0
[INFO] [stderr]    Compiling serde_derive v1.0.228
[INFO] [stderr]    Compiling clap_derive v4.6.1
[INFO] [stderr]    Compiling clap v4.6.1
[INFO] [stderr]    Compiling japalityecho v0.3.0 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 29.62s
[INFO] running `Command { std: "docker" "inspect" "ad5382852c6c28326d374aa5a49b33f21955faab8bb1fbea070a6898a59acca3", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "ad5382852c6c28326d374aa5a49b33f21955faab8bb1fbea070a6898a59acca3", kill_on_drop: false }`
[INFO] [stdout] ad5382852c6c28326d374aa5a49b33f21955faab8bb1fbea070a6898a59acca3
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc1/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "RUSTDOCFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:d429b63d4308055ea97f60fb1d3dfca48854a00942f1bd2ad806beaf015945ec" "/opt/rustwide/cargo-home/bin/cargo" "+ec6f9a5b4413f74386267ef8efc93712c2ce6db6" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] e4582bdd46a43292ae1ecb43ff02867ccf36c07c5d77c3b22b5b4b5f79b279be
[INFO] running `Command { std: "docker" "start" "-a" "e4582bdd46a43292ae1ecb43ff02867ccf36c07c5d77c3b22b5b4b5f79b279be", kill_on_drop: false }`
[INFO] [stderr]    Compiling libc v0.2.186
[INFO] [stderr]    Compiling rustix v1.1.4
[INFO] [stderr]    Compiling getrandom v0.4.2
[INFO] [stderr]    Compiling linux-raw-sys v0.12.1
[INFO] [stderr]    Compiling bitflags v2.11.1
[INFO] [stderr]    Compiling fastrand v2.4.1
[INFO] [stderr]    Compiling once_cell v1.21.4
[INFO] [stderr]    Compiling tempfile v3.27.0
[INFO] [stderr]    Compiling japalityecho v0.3.0 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished `test` profile [unoptimized + debuginfo] target(s) in 9.01s
[INFO] running `Command { std: "docker" "inspect" "e4582bdd46a43292ae1ecb43ff02867ccf36c07c5d77c3b22b5b4b5f79b279be", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "e4582bdd46a43292ae1ecb43ff02867ccf36c07c5d77c3b22b5b4b5f79b279be", kill_on_drop: false }`
[INFO] [stdout] e4582bdd46a43292ae1ecb43ff02867ccf36c07c5d77c3b22b5b4b5f79b279be
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc1/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "RUSTDOCFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:d429b63d4308055ea97f60fb1d3dfca48854a00942f1bd2ad806beaf015945ec" "/opt/rustwide/cargo-home/bin/cargo" "+ec6f9a5b4413f74386267ef8efc93712c2ce6db6" "test" "--frozen", kill_on_drop: false }`
[INFO] [stdout] ffda9c8d10c666cbfba05906eba468abb244570f40ee78663849fe7ffc505e76
[INFO] running `Command { std: "docker" "start" "-a" "ffda9c8d10c666cbfba05906eba468abb244570f40ee78663849fe7ffc505e76", kill_on_drop: false }`
[INFO] [stderr]     Finished `test` profile [unoptimized + debuginfo] target(s) in 0.18s
[INFO] [stderr]      Running unittests src/lib.rs (/opt/rustwide/target/debug/deps/japalityecho-ac0fbc3b9266328a)
[INFO] [stdout] 
[INFO] [stdout] running 15 tests
[INFO] [stdout] test bloom::tests::inserted_key_has_positive_count ... ok
[INFO] [stdout] test bloom::tests::multiple_inserts_increase_count ... ok
[INFO] [stdout] test dbg::tests::edge_and_node_counts ... ok
[INFO] [stdout] test dbg::tests::correct_sequence_regions_integration ... ok
[INFO] [stdout] test bloom::tests::memory_is_reasonable ... ok
[INFO] [stdout] test bloom::tests::empty_filter_returns_zero ... ok
[INFO] [stdout] test dbg::tests::construction_from_simple_spectrum ... ok
[INFO] [stdout] test dbg::tests::encode_node_roundtrip ... ok
[INFO] [stdout] test dbg::tests::empty_spectrum_produces_empty_graph ... ok
[INFO] [stdout] test dbg::tests::no_correction_when_path_matches ... ok
[INFO] [stdout] test dbg::tests::multi_base_region_correction ... ok
[INFO] [stdout] test dbg::tests::region_boundary_checks ... ok
[INFO] [stdout] test dbg::tests::single_base_path_correction ... ok
[INFO] [stdout] test bloom::tests::low_false_positive_rate ... ok
[INFO] [stdout] test bloom::tests::counters_saturate_at_15 ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 15 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.06s
[INFO] [stdout] 
[INFO] [stderr]      Running unittests src/main.rs (/opt/rustwide/target/debug/deps/japalityecho-f0b287af1e15077d)
[INFO] [stdout] 
[INFO] [stdout] running 0 tests
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 0 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s
[INFO] [stdout] 
[INFO] [stderr]      Running tests/pipeline.rs (/opt/rustwide/target/debug/deps/pipeline-f6f29154f575a6f5)
[INFO] [stdout] 
[INFO] [stdout] running 76 tests
[INFO] [stdout] test detects_rna_seq_from_leading_bias_and_duplication_without_poly_t ... ok
[INFO] [stdout] test evaluate_cli_reports_json_metrics ... ok
[INFO] [stdout] test detects_single_cell_poly_t_signature ... ok
[INFO] [stdout] test cuda_request_reports_acceleration_preview ... ok
[INFO] [stdout] test inspect_paired_inputs_preserves_single_cell_r1_signal ... ok
[INFO] [stdout] test cpu_pipeline_repairs_errors_and_trims_adapters ... ok
[INFO] [stdout] test inspect_reports_cuda_scaffold_metadata ... ok
[INFO] [stdout] test detects_atac_from_strong_nextera_signal ... ok
[INFO] [stdout] test paired_end_pipeline_keeps_mates_synchronized ... ok
[INFO] [stdout] test cuda_full_backend_matches_cpu_behavior_when_available ... ok
[INFO] [stdout] test benchmark_mode_summarizes_repeated_cpu_runs ... ok
[INFO] [stdout] test paired_synthetic_evaluation_reports_publication_metrics ... ok
[INFO] [stdout] test benchmark_compare_reports_mode_deltas ... ok
[INFO] [stdout] test study_annotate_cli_reports_json_bundle ... ok
[INFO] [stdout] test history_report_summarizes_recorded_entries ... ok
[INFO] [stdout] test study_annotate_imports_sra_ena_style_metadata_exports ... ok
[INFO] [stdout] test study_annotate_chains_from_discovery_into_study_artifacts ... ok
[INFO] [stdout] test study_annotate_can_overwrite_existing_values ... ok
[INFO] [stdout] test study_discover_can_disable_recursive_scan ... ok
[INFO] [stdout] test study_annotate_enriches_manifest_without_overwriting_existing_values ... ok
[INFO] [stdout] test study_artifacts_cli_reports_json_bundle ... ok
[INFO] [stdout] test study_discover_cli_reports_json_bundle ... ok
[INFO] [stdout] test history_report_flags_threshold_breaches_against_baseline ... ok
[INFO] [stdout] test benchmark_history_appends_jsonl_records ... ok
[INFO] [stdout] test history_report_cli_exits_non_zero_for_configured_alert_status ... ok
[INFO] [stdout] test study_fetch_metadata_cli_expands_study_accession_json_bundle ... ok
[INFO] [stdout] test study_download_skips_existing_fastqs_on_resume ... ok
[INFO] [stdout] test illumina_adapter_signal_overrides_flat_quality_mgi_guess ... ok
[INFO] [stdout] test study_fetch_metadata_cli_reports_json_bundle ... ok
[INFO] [stdout] test study_fetch_metadata_cli_resolves_geo_sample_json_bundle ... ok
[INFO] [stdout] test study_fetch_metadata_expands_study_and_project_accessions ... ok
[INFO] [stdout] test paper_artifacts_cli_reports_json_bundle ... ok
[INFO] [stdout] test does_not_call_atac_from_trace_nextera_signal ... ok
[INFO] [stdout] test study_fetch_metadata_cli_reports_geo_fallback_json_bundle ... ok
[INFO] [stdout] test study_fetch_metadata_falls_back_to_full_geo_text_when_quick_text_has_no_public_accessions ... ok
[INFO] [stdout] test history_report_selects_latest_comparable_prefix_baseline ... ok
[INFO] [stdout] test study_fetch_metadata_resolves_geo_series_accession ... ok
[INFO] [stdout] test study_download_materializes_public_fastqs ... ok
[INFO] [stdout] test study_artifacts_generate_case_study_bundle ... ok
[INFO] [stdout] test study_fetch_metadata_records_failed_accessions_without_dropping_successes ... ok
[INFO] [stdout] test history_report_selects_latest_pass_baseline ... ok
[INFO] [stdout] test study_fetch_metadata_resume_reuses_existing_rows_and_statuses ... ok
[INFO] [stdout] test study_fetch_metadata_falls_back_to_single_accession_requests_when_chunk_is_empty ... ok
[INFO] [stdout] test study_discover_builds_inventory_template ... ok
[INFO] [stdout] test study_fetch_metadata_cli_resume_reports_json_bundle ... ok
[INFO] [stdout] test study_fetch_metadata_uses_cache_and_writes_status_bookkeeping ... ok
[INFO] [stdout] test study_ingest_cli_parses_native_alignment_reports ... ok
[INFO] [stdout] test paper_artifacts_generate_reproducible_bundle ... ok
[INFO] [stdout] test study_fetch_metadata_resume_fetches_only_new_accessions ... ok
[INFO] [stdout] test study_ingest_cli_parses_native_tool_outputs ... ok
[INFO] [stdout] test study_download_cli_reports_json_bundle ... ok
[INFO] [stdout] test study_ingest_rejects_conflicting_native_coverage_reports ... ok
[INFO] [stdout] test study_ingest_cli_parses_native_variant_benchmark_reports ... ok
[INFO] [stdout] test study_ingest_rejects_conflicting_native_variant_reports ... ok
[INFO] [stdout] test study_fetch_metadata_retries_failed_chunk_and_reports_attempts ... ok
[INFO] [stdout] test history_report_selects_latest_pass_baseline_with_prefix_filter ... ok
[INFO] [stdout] test study_fetch_metadata_writes_phase35_compatible_output ... ok
[INFO] [stdout] test study_manifest_bootstrap_preserves_relative_paths ... FAILED
[INFO] [stdout] test study_ingest_rejects_conflicting_structured_metrics ... ok
[INFO] [stdout] test study_ingest_parses_native_fastp_and_quast_outputs ... ok
[INFO] [stdout] test study_manifest_public_accession_export_falls_back_to_layout_placeholders ... ok
[INFO] [stdout] test study_manifest_bootstraps_public_accession_export ... ok
[INFO] [stdout] test study_manifest_cli_bootstraps_public_accession_export ... ok
[INFO] [stdout] test study_ingest_rejects_conflicting_native_alignment_reports ... ok
[INFO] [stdout] test study_ingest_parses_native_variant_benchmark_reports ... ok
[INFO] [stdout] test study_manifest_bootstrap_generates_canonical_manifest ... ok
[INFO] [stdout] test study_ingest_cli_parses_native_coverage_reports ... ok
[INFO] [stdout] test study_ingest_parses_native_coverage_reports ... ok
[INFO] [stdout] test study_manifest_cli_reports_json_bundle ... ok
[INFO] [stdout] test study_ingest_merges_structured_results_bundle ... ok
[INFO] [stdout] test synthetic_evaluation_reports_publication_metrics ... ok
[INFO] [stdout] test study_ingest_rejects_conflicting_native_quast_outputs ... ok
[INFO] [stdout] test study_ingest_parses_native_alignment_reports ... ok
[INFO] [stdout] test study_ingest_cli_reports_json_bundle ... ok
[INFO] [stdout] test publication_bundle_cli_emits_study_and_paper_artifacts ... ok
[INFO] [stdout] test study_ingest_merges_accession_metadata_with_native_tool_outputs ... ok
[INFO] [stdout] 
[INFO] [stdout] failures:
[INFO] [stdout] 
[INFO] [stdout] ---- study_manifest_bootstrap_preserves_relative_paths stdout ----
[INFO] [stdout] Error: No such file or directory (os error 2) at path "/opt/rustwide/workdir/target/.tmpcJMZQz"
[INFO] [stdout] 
[INFO] [stdout] Stack backtrace:
[INFO] [stdout]    0: <anyhow::Error as core::convert::From<std::io::error::Error>>::from
[INFO] [stdout]              at /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/anyhow-1.0.102/src/backtrace.rs:10:14
[INFO] [stdout]    1: <core::result::Result<(), anyhow::Error> as core::ops::try_trait::FromResidual<core::result::Result<core::convert::Infallible, std::io::error::Error>>>::from_residual
[INFO] [stdout]              at /rustc/ec6f9a5b4413f74386267ef8efc93712c2ce6db6/library/core/src/result.rs:2189:27
[INFO] [stdout]    2: pipeline::study_manifest_bootstrap_preserves_relative_paths
[INFO] [stdout]              at ./tests/pipeline.rs:3044:15
[INFO] [stdout]    3: pipeline::study_manifest_bootstrap_preserves_relative_paths::{closure#0}
[INFO] [stdout]              at ./tests/pipeline.rs:3041:59
[INFO] [stdout]    4: <pipeline::study_manifest_bootstrap_preserves_relative_paths::{closure#0} as core::ops::function::FnOnce<()>>::call_once
[INFO] [stdout]              at /rustc/ec6f9a5b4413f74386267ef8efc93712c2ce6db6/library/core/src/ops/function.rs:250:5
[INFO] [stdout]    5: <fn() -> core::result::Result<(), alloc::string::String> as core::ops::function::FnOnce<()>>::call_once
[INFO] [stdout]              at /rustc/ec6f9a5b4413f74386267ef8efc93712c2ce6db6/library/core/src/ops/function.rs:250:5
[INFO] [stdout]    6: test::__rust_begin_short_backtrace::<core::result::Result<(), alloc::string::String>, fn() -> core::result::Result<(), alloc::string::String>>
[INFO] [stdout]              at /rustc/ec6f9a5b4413f74386267ef8efc93712c2ce6db6/library/test/src/lib.rs:724:18
[INFO] [stdout]    7: test::run_test_in_process::{closure#0}
[INFO] [stdout]              at /rustc/ec6f9a5b4413f74386267ef8efc93712c2ce6db6/library/test/src/lib.rs:747:74
[INFO] [stdout]    8: <core::panic::unwind_safe::AssertUnwindSafe<test::run_test_in_process::{closure#0}> as core::ops::function::FnOnce<()>>::call_once
[INFO] [stdout]              at /rustc/ec6f9a5b4413f74386267ef8efc93712c2ce6db6/library/core/src/panic/unwind_safe.rs:275:9
[INFO] [stdout]    9: std::panicking::catch_unwind::do_call::<core::panic::unwind_safe::AssertUnwindSafe<test::run_test_in_process::{closure#0}>, core::result::Result<(), alloc::string::String>>
[INFO] [stdout]              at /rustc/ec6f9a5b4413f74386267ef8efc93712c2ce6db6/library/std/src/panicking.rs:581:40
[INFO] [stdout]   10: std::panicking::catch_unwind::<core::result::Result<(), alloc::string::String>, core::panic::unwind_safe::AssertUnwindSafe<test::run_test_in_process::{closure#0}>>
[INFO] [stdout]              at /rustc/ec6f9a5b4413f74386267ef8efc93712c2ce6db6/library/std/src/panicking.rs:544:19
[INFO] [stdout]   11: std::panic::catch_unwind::<core::panic::unwind_safe::AssertUnwindSafe<test::run_test_in_process::{closure#0}>, core::result::Result<(), alloc::string::String>>
[INFO] [stdout]              at /rustc/ec6f9a5b4413f74386267ef8efc93712c2ce6db6/library/std/src/panic.rs:359:14
[INFO] [stdout]   12: test::run_test_in_process
[INFO] [stdout]              at /rustc/ec6f9a5b4413f74386267ef8efc93712c2ce6db6/library/test/src/lib.rs:747:27
[INFO] [stdout]   13: test::run_test::{closure#0}
[INFO] [stdout]              at /rustc/ec6f9a5b4413f74386267ef8efc93712c2ce6db6/library/test/src/lib.rs:668:43
[INFO] [stdout]   14: test::run_test::{closure#1}
[INFO] [stdout]              at /rustc/ec6f9a5b4413f74386267ef8efc93712c2ce6db6/library/test/src/lib.rs:698:41
[INFO] [stdout]   15: std::sys::backtrace::__rust_begin_short_backtrace::<test::run_test::{closure#1}, ()>
[INFO] [stdout]              at /rustc/ec6f9a5b4413f74386267ef8efc93712c2ce6db6/library/std/src/sys/backtrace.rs:166:18
[INFO] [stdout]   16: std::thread::lifecycle::spawn_unchecked::<test::run_test::{closure#1}, ()>::{closure#1}::{closure#0}
[INFO] [stdout]              at /rustc/ec6f9a5b4413f74386267ef8efc93712c2ce6db6/library/std/src/thread/lifecycle.rs:70:13
[INFO] [stdout]   17: <core::panic::unwind_safe::AssertUnwindSafe<std::thread::lifecycle::spawn_unchecked<test::run_test::{closure#1}, ()>::{closure#1}::{closure#0}> as core::ops::function::FnOnce<()>>::call_once
[INFO] [stdout]              at /rustc/ec6f9a5b4413f74386267ef8efc93712c2ce6db6/library/core/src/panic/unwind_safe.rs:275:9
[INFO] [stdout]   18: std::panicking::catch_unwind::do_call::<core::panic::unwind_safe::AssertUnwindSafe<std::thread::lifecycle::spawn_unchecked<test::run_test::{closure#1}, ()>::{closure#1}::{closure#0}>, ()>
[INFO] [stdout]              at /rustc/ec6f9a5b4413f74386267ef8efc93712c2ce6db6/library/std/src/panicking.rs:581:40
[INFO] [stdout]   19: std::panicking::catch_unwind::<(), core::panic::unwind_safe::AssertUnwindSafe<std::thread::lifecycle::spawn_unchecked<test::run_test::{closure#1}, ()>::{closure#1}::{closure#0}>>
[INFO] [stdout]              at /rustc/ec6f9a5b4413f74386267ef8efc93712c2ce6db6/library/std/src/panicking.rs:544:19
[INFO] [stdout]   20: std::panic::catch_unwind::<core::panic::unwind_safe::AssertUnwindSafe<std::thread::lifecycle::spawn_unchecked<test::run_test::{closure#1}, ()>::{closure#1}::{closure#0}>, ()>
[INFO] [stdout]              at /rustc/ec6f9a5b4413f74386267ef8efc93712c2ce6db6/library/std/src/panic.rs:359:14
[INFO] [stdout]   21: std::thread::lifecycle::spawn_unchecked::<test::run_test::{closure#1}, ()>::{closure#1}
[INFO] [stdout]              at /rustc/ec6f9a5b4413f74386267ef8efc93712c2ce6db6/library/std/src/thread/lifecycle.rs:68:26
[INFO] [stdout]   22: <std::thread::lifecycle::spawn_unchecked<test::run_test::{closure#1}, ()>::{closure#1} as core::ops::function::FnOnce<()>>::call_once::{shim:vtable#0}
[INFO] [stdout]              at /rustc/ec6f9a5b4413f74386267ef8efc93712c2ce6db6/library/core/src/ops/function.rs:250:5
[INFO] [stdout]   23: <alloc::boxed::Box<dyn core::ops::function::FnOnce<(), Output = ()> + core::marker::Send> as core::ops::function::FnOnce<()>>::call_once
[INFO] [stdout]              at /rustc/ec6f9a5b4413f74386267ef8efc93712c2ce6db6/library/alloc/src/boxed.rs:2271:9
[INFO] [stdout]   24: <std::sys::thread::unix::Thread>::new::thread_start
[INFO] [stdout]              at /rustc/ec6f9a5b4413f74386267ef8efc93712c2ce6db6/library/std/src/sys/thread/unix.rs:118:17
[INFO] [stdout]   25: <unknown>
[INFO] [stdout]   26: clone
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] failures:
[INFO] [stdout]     study_manifest_bootstrap_preserves_relative_paths
[INFO] [stdout] 
[INFO] [stdout] test result: FAILED. 75 passed; 1 failed; 0 ignored; 0 measured; 0 filtered out; finished in 2.05s
[INFO] [stdout] 
[INFO] [stderr] error: test failed, to rerun pass `--test pipeline`
[INFO] running `Command { std: "docker" "inspect" "ffda9c8d10c666cbfba05906eba468abb244570f40ee78663849fe7ffc505e76", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "ffda9c8d10c666cbfba05906eba468abb244570f40ee78663849fe7ffc505e76", kill_on_drop: false }`
[INFO] [stdout] ffda9c8d10c666cbfba05906eba468abb244570f40ee78663849fe7ffc505e76
