[INFO] fetching crate genemancer 0.2.5...
[INFO] testing genemancer-0.2.5 against beta-2026-04-21 for beta-1.96-2
[INFO] extracting crate genemancer 0.2.5 into /workspace/builds/worker-5-tc2/source
[INFO] started tweaking crates.io crate genemancer 0.2.5
[INFO] removed 0 missing tests
[INFO] finished tweaking crates.io crate genemancer 0.2.5
[INFO] tweaked toml for crates.io crate genemancer 0.2.5 written to /workspace/builds/worker-5-tc2/source/Cargo.toml
[INFO] validating manifest of crates.io crate genemancer 0.2.5 on toolchain beta-2026-04-21
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+beta-2026-04-21" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate crates.io crate genemancer 0.2.5 already has a lockfile, it will not be regenerated
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+beta-2026-04-21" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc2/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" "+beta-2026-04-21" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] e626a87a2fc91acec537b6f33f3f56e8f09695284f8071eda7b03462ce08290e
[INFO] running `Command { std: "docker" "start" "-a" "e626a87a2fc91acec537b6f33f3f56e8f09695284f8071eda7b03462ce08290e", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "e626a87a2fc91acec537b6f33f3f56e8f09695284f8071eda7b03462ce08290e", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "e626a87a2fc91acec537b6f33f3f56e8f09695284f8071eda7b03462ce08290e", kill_on_drop: false }`
[INFO] [stdout] e626a87a2fc91acec537b6f33f3f56e8f09695284f8071eda7b03462ce08290e
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc2/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=warn" "-e" "RUSTDOCFLAGS=--cap-lints=warn" "-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" "+beta-2026-04-21" "build" "--frozen" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] b3d4ca027e36fc63b37050cdc6ceca618752e5a39304bbdd2c0985d5d45ccf3a
[INFO] running `Command { std: "docker" "start" "-a" "b3d4ca027e36fc63b37050cdc6ceca618752e5a39304bbdd2c0985d5d45ccf3a", kill_on_drop: false }`
[INFO] [stderr]    Compiling unicode-ident v1.0.24
[INFO] [stderr]    Compiling libc v0.2.182
[INFO] [stderr]    Compiling libm v0.2.16
[INFO] [stderr]    Compiling foldhash v0.2.0
[INFO] [stderr]    Compiling num-traits v0.2.19
[INFO] [stderr]    Compiling bitflags v2.11.0
[INFO] [stderr]    Compiling zlib-rs v0.6.2
[INFO] [stderr]    Compiling bit-vec v0.8.0
[INFO] [stderr]    Compiling proc-macro2 v1.0.106
[INFO] [stderr]    Compiling memchr v2.8.0
[INFO] [stderr]    Compiling hashbrown v0.16.1
[INFO] [stderr]    Compiling zerocopy v0.8.40
[INFO] [stderr]    Compiling thiserror v2.0.18
[INFO] [stderr]    Compiling lexical-util v1.0.7
[INFO] [stderr]    Compiling semver v1.0.27
[INFO] [stderr]    Compiling quote v1.0.44
[INFO] [stderr]    Compiling ash v0.38.0+1.3.281
[INFO] [stderr]    Compiling cc v1.2.56
[INFO] [stderr]    Compiling rustc_version v0.4.1
[INFO] [stderr]    Compiling crossbeam-channel v0.5.15
[INFO] [stderr]    Compiling syn v2.0.117
[INFO] [stderr]    Compiling indexmap v2.13.0
[INFO] [stderr]    Compiling bstr v1.12.1
[INFO] [stderr]    Compiling naga v28.0.0
[INFO] [stderr]    Compiling khronos-egl v6.0.0
[INFO] [stderr]    Compiling smallvec v1.15.1
[INFO] [stderr]    Compiling unicode-width v0.1.14
[INFO] [stderr]    Compiling foldhash v0.1.5
[INFO] [stderr]    Compiling bytes v1.11.1
[INFO] [stderr]    Compiling parking_lot_core v0.9.12
[INFO] [stderr]    Compiling hashbrown v0.15.5
[INFO] [stderr]    Compiling codespan-reporting v0.12.0
[INFO] [stderr]    Compiling noodles-core v0.19.0
[INFO] [stderr]    Compiling pathfinder_simd v0.5.5
[INFO] [stderr]    Compiling lexical-parse-integer v1.0.6
[INFO] [stderr]    Compiling lexical-write-integer v1.0.6
[INFO] [stderr]    Compiling yeslogic-fontconfig-sys v6.0.0
[INFO] [stderr]    Compiling bit-set v0.8.0
[INFO] [stderr]    Compiling spirv v0.3.0+sdk-1.3.268.0
[INFO] [stderr]    Compiling freetype-sys v0.20.1
[INFO] [stderr]    Compiling gpu-descriptor-types v0.2.0
[INFO] [stderr]    Compiling wgpu-hal v28.0.1
[INFO] [stderr]    Compiling presser v0.3.1
[INFO] [stderr]    Compiling rustc-hash v1.1.0
[INFO] [stderr]    Compiling lexical-write-float v1.0.6
[INFO] [stderr]    Compiling gpu-descriptor v0.3.2
[INFO] [stderr]    Compiling lexical-parse-float v1.0.6
[INFO] [stderr]    Compiling ordered-float v4.6.0
[INFO] [stderr]    Compiling parking_lot v0.12.5
[INFO] [stderr]    Compiling futures-core v0.3.32
[INFO] [stderr]    Compiling raw-window-handle v0.6.2
[INFO] [stderr]    Compiling profiling v1.0.17
[INFO] [stderr]    Compiling renderdoc-sys v1.1.0
[INFO] [stderr]    Compiling futures-sink v0.3.32
[INFO] [stderr]    Compiling glow v0.16.0
[INFO] [stderr]    Compiling pin-project-lite v0.2.17
[INFO] [stderr]    Compiling dirs-sys v0.5.0
[INFO] [stderr]    Compiling futures-channel v0.3.32
[INFO] [stderr]    Compiling lexical-core v1.0.6
[INFO] [stderr]    Compiling dlib v0.5.3
[INFO] [stderr]    Compiling wgpu-core v28.0.1
[INFO] [stderr]    Compiling futures-task v0.3.32
[INFO] [stderr]    Compiling slab v0.4.12
[INFO] [stderr]    Compiling futures-io v0.3.32
[INFO] [stderr]    Compiling font-kit v0.14.3
[INFO] [stderr]    Compiling jpeg-decoder v0.3.2
[INFO] [stderr]    Compiling weezl v0.1.12
[INFO] [stderr]    Compiling plotters-backend v0.3.7
[INFO] [stderr]    Compiling walkdir v2.5.0
[INFO] [stderr]    Compiling gif v0.12.0
[INFO] [stderr]    Compiling pathfinder_geometry v0.5.1
[INFO] [stderr]    Compiling dirs v6.0.0
[INFO] [stderr]    Compiling wgpu v28.0.0
[INFO] [stderr]    Compiling flate2 v1.1.9
[INFO] [stderr]    Compiling anyhow v1.0.102
[INFO] [stderr]    Compiling float-ord v0.3.2
[INFO] [stderr]    Compiling noodles-bgzf v0.46.0
[INFO] [stderr]    Compiling png v0.17.16
[INFO] [stderr]    Compiling clap_lex v1.0.0
[INFO] [stderr]    Compiling iana-time-zone v0.1.65
[INFO] [stderr]    Compiling clap_builder v4.5.60
[INFO] [stderr]    Compiling bytemuck_derive v1.10.2
[INFO] [stderr]    Compiling thiserror-impl v2.0.18
[INFO] [stderr]    Compiling zerocopy-derive v0.8.40
[INFO] [stderr]    Compiling futures-macro v0.3.32
[INFO] [stderr]    Compiling noodles-csi v0.54.0
[INFO] [stderr]    Compiling futures-util v0.3.32
[INFO] [stderr]    Compiling bytemuck v1.25.0
[INFO] [stderr]    Compiling noodles-sam v0.82.0
[INFO] [stderr]    Compiling noodles-tabix v0.60.0
[INFO] [stderr]    Compiling chrono v0.4.44
[INFO] [stderr]    Compiling wgpu-types v28.0.0
[INFO] [stderr]    Compiling image v0.24.9
[INFO] [stderr]    Compiling clap_derive v4.5.55
[INFO] [stderr]    Compiling plotters-bitmap v0.3.7
[INFO] [stderr]    Compiling tokio-macros v2.6.0
[INFO] [stderr]    Compiling futures-executor v0.3.32
[INFO] [stderr]    Compiling plotters-svg v0.3.7
[INFO] [stderr]    Compiling ttf-parser v0.20.0
[INFO] [stderr]    Compiling clap v4.5.60
[INFO] [stderr]    Compiling tokio v1.49.0
[INFO] [stderr]    Compiling futures v0.3.32
[INFO] [stderr]    Compiling noodles-bam v0.86.0
[INFO] [stderr]    Compiling noodles-bed v0.32.0
[INFO] [stderr]    Compiling glob v0.3.3
[INFO] [stderr]    Compiling half v2.7.1
[INFO] [stderr]    Compiling plotters v0.3.7
[INFO] [stderr]    Compiling gpu-allocator v0.28.0
[INFO] [stderr]    Compiling wgpu-core-deps-windows-linux-android v28.0.0
[INFO] [stderr]    Compiling genemancer v0.2.5 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 2m 49s
[INFO] running `Command { std: "docker" "inspect" "b3d4ca027e36fc63b37050cdc6ceca618752e5a39304bbdd2c0985d5d45ccf3a", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "b3d4ca027e36fc63b37050cdc6ceca618752e5a39304bbdd2c0985d5d45ccf3a", kill_on_drop: false }`
[INFO] [stdout] b3d4ca027e36fc63b37050cdc6ceca618752e5a39304bbdd2c0985d5d45ccf3a
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc2/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=warn" "-e" "RUSTDOCFLAGS=--cap-lints=warn" "-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" "+beta-2026-04-21" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 1a88e1fbcd75a0edb9740fdc20b3c8185b65481a638067e02b69de9387a9b838
[INFO] running `Command { std: "docker" "start" "-a" "1a88e1fbcd75a0edb9740fdc20b3c8185b65481a638067e02b69de9387a9b838", kill_on_drop: false }`
[INFO] [stderr]    Compiling bitflags v2.11.0
[INFO] [stderr]    Compiling rustix v1.1.4
[INFO] [stderr]    Compiling getrandom v0.4.1
[INFO] [stderr]    Compiling linux-raw-sys v0.12.1
[INFO] [stderr]    Compiling spirv v0.3.0+sdk-1.3.268.0
[INFO] [stderr]    Compiling gpu-descriptor-types v0.2.0
[INFO] [stderr]    Compiling wgpu-types v28.0.0
[INFO] [stderr]    Compiling noodles-sam v0.82.0
[INFO] [stderr]    Compiling font-kit v0.14.3
[INFO] [stderr]    Compiling gpu-descriptor v0.3.2
[INFO] [stderr]    Compiling plotters v0.3.7
[INFO] [stderr]    Compiling naga v28.0.0
[INFO] [stderr]    Compiling noodles-bam v0.86.0
[INFO] [stderr]    Compiling tempfile v3.26.0
[INFO] [stderr]    Compiling wgpu-hal v28.0.1
[INFO] [stderr]    Compiling wgpu-core-deps-windows-linux-android v28.0.0
[INFO] [stderr]    Compiling wgpu-core v28.0.1
[INFO] [stderr]    Compiling wgpu v28.0.0
[INFO] [stderr]    Compiling genemancer v0.2.5 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished `test` profile [unoptimized + debuginfo] target(s) in 1m 36s
[INFO] running `Command { std: "docker" "inspect" "1a88e1fbcd75a0edb9740fdc20b3c8185b65481a638067e02b69de9387a9b838", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "1a88e1fbcd75a0edb9740fdc20b3c8185b65481a638067e02b69de9387a9b838", kill_on_drop: false }`
[INFO] [stdout] 1a88e1fbcd75a0edb9740fdc20b3c8185b65481a638067e02b69de9387a9b838
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc2/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=warn" "-e" "RUSTDOCFLAGS=--cap-lints=warn" "-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" "+beta-2026-04-21" "test" "--frozen", kill_on_drop: false }`
[INFO] [stdout] 94fb402b2df0b4248afc1359b2375f29db2899ca9880673e8ed9ae7b06a21104
[INFO] running `Command { std: "docker" "start" "-a" "94fb402b2df0b4248afc1359b2375f29db2899ca9880673e8ed9ae7b06a21104", kill_on_drop: false }`
[INFO] [stderr]     Finished `test` profile [unoptimized + debuginfo] target(s) in 0.28s
[INFO] [stderr]      Running unittests src/main.rs (/opt/rustwide/target/debug/deps/genemancer-f828ce5da924a7cd)
[INFO] [stdout] 
[INFO] [stdout] running 66 tests
[INFO] [stdout] test call_targets::tests::merge_sample_counts_with_cap_adds_without_truncation ... ok
[INFO] [stdout] test call_targets::tests::rejects_conflicting_read_group_to_sample_mappings ... ok
[INFO] [stdout] test call_targets::tests::rg_map_overrides_header_sample_mappings ... ok
[INFO] [stdout] test call_targets::tests::merge_sample_counts_with_cap_truncates_deterministically ... ok
[INFO] [stdout] test call_targets_gpu::tests::auto_mode_ignores_explicit_overrides ... ok
[INFO] [stdout] test call_targets_gpu::tests::auto_tuning_for_datacenter_exceeds_defaults ... ok
[INFO] [stdout] test call_targets_gpu::tests::backend_mask_maps_explicit_backends ... ok
[INFO] [stdout] test call_targets_gpu::tests::classify_gpu_tier_prefers_integrated_device_type ... ok
[INFO] [stdout] test call_targets_gpu::tests::cpu_aggregation_counts_expected_cells ... ok
[INFO] [stdout] test call_targets_gpu::tests::deferred_startup_relief_triggers_on_elapsed_threshold ... ok
[INFO] [stdout] test call_targets_gpu::tests::deferred_startup_relief_requires_ready_chunks ... ok
[INFO] [stdout] test call_targets_gpu::tests::effective_chunk_batch_threshold_caps_deferred_mode ... ok
[INFO] [stdout] test call_targets_gpu::tests::deferred_startup_relief_triggers_on_pending_threshold ... ok
[INFO] [stdout] test call_targets_gpu::tests::effective_chunk_batch_threshold_keeps_baseline_when_not_deferred ... ok
[INFO] [stdout] test call_targets_gpu::tests::hybrid_mode_applies_utilization_and_cuda_toggle_overrides ... ok
[INFO] [stdout] test call_targets::tests::rejects_bgzf_reference_without_gzi_index ... ok
[INFO] [stdout] test call_targets_gpu::tests::flush_ready_chunks_non_forced_yields_on_writer_backpressure ... ok
[INFO] [stdout] test call_targets_gpu::tests::deferred_startup_relief_stops_after_gpu_batch_seen ... ok
[INFO] [stdout] test cnloh::tests::canonical_chrom_filter_matches_autosomes_and_sex_chromosomes ... ok
[INFO] [stdout] test call_targets_gpu::tests::flush_ready_chunks_caps_non_forced_pending_batches ... ok
[INFO] [stdout] test cnloh::tests::accumulates_reference_span_into_expected_bins ... ok
[INFO] [stdout] test cnloh::tests::normalizes_chr_prefix_case_insensitive ... ok
[INFO] [stdout] test cnloh::tests::palette_is_unique_for_first_24_chromosomes ... ok
[INFO] [stdout] test cnloh::tests::parses_marker_tab_format ... ok
[INFO] [stdout] test cnloh::tests::parses_marker_dot_format ... ok
[INFO] [stdout] test gff_gtf::tests::converts_simple_gff_to_gtf ... ok
[INFO] [stdout] test introns::tests::extracts_introns_from_multi_exon_transcript ... ok
[INFO] [stdout] test introns::tests::merges_overlapping_exons_before_introns ... ok
[INFO] [stdout] test introns::tests::skips_single_exon_transcripts ... ok
[INFO] [stdout] test fasta_prep::tests::returns_original_when_reference_already_indexed ... ok
[INFO] [stdout] test introns::tests::errors_when_exon_lacks_transcript_id ... ok
[INFO] [stdout] test merge_bam::tests::trims_reads_with_soft_clips ... ok
[INFO] [stdout] test merge_bam::tests::bed_all_mode_does_not_duplicate_records_across_overlapping_regions ... ok
[INFO] [stdout] test fasta_prep::tests::prepares_sorted_and_indexed_reference_when_unindexed ... ok
[INFO] [stdout] test pod5::tests::detects_glob_characters ... ok
[INFO] [stdout] test pod5::tests::keep_all_when_percent_100 ... ok
[INFO] [stdout] test pod5::tests::keep_none_when_percent_0 ... ok
[INFO] [stdout] test merge_bam::tests::writes_index_when_requested ... ok
[INFO] [stdout] test merge_bam::tests::filters_by_read_group ... ok
[INFO] [stdout] test tests::derives_introns_output_path_from_gtf_gz ... ok
[INFO] [stdout] test tests::derives_introns_output_path_from_plain_gtf ... ok
[INFO] [stdout] test split_bam::tests::splits_records_into_region_outputs ... ok
[INFO] [stdout] test merge_bam::tests::merges_inputs_in_coordinate_order ... ok
[INFO] [stdout] test split_bam::tests::writes_unassigned_output_for_non_overlapping_reads ... ok
[INFO] [stdout] test call_targets_gpu::tests::classify_gpu_tier_detects_datacenter_by_name ... ok
[INFO] [stdout] test split_bam::tests::applies_min_overlap_fraction_filter ... ok
[INFO] [stdout] test tests::parses_call_targets_gpu_with_tuning_overrides ... ok
[INFO] [stdout] test tests::parses_cnloh_detect_with_include_noncanonical ... ok
[INFO] [stdout] test tests::parses_pod5_subsample_with_multiple_inputs ... ok
[INFO] [stdout] test tests::parses_call_targets_gpu_with_required_gpu_flag ... ok
[INFO] [stdout] test tests::parses_call_targets_gpu_with_cuda_backend ... ok
[INFO] [stdout] test tests::parses_pod5_inspect_subcommand ... ok
[INFO] [stdout] test tests::parses_pod5_subsample_with_repeated_input_flags ... ok
[INFO] [stdout] test tests::parses_cnloh_detect_with_log_output ... ok
[INFO] [stdout] test tests::rejects_pod5_subsample_percent_above_hundred ... ok
[INFO] [stdout] test tests::rejects_call_targets_gpu_wgpu_upload_utilization_over_100 ... ok
[INFO] [stdout] test vcf::tests::rejects_duplicate_member_across_sets ... ok
[INFO] [stdout] test tests::parses_vcf_diff_multisample_args ... ok
[INFO] [stdout] test fasta_prep::tests::prepares_from_gz_reference ... ok
[INFO] [stdout] test tests::rejects_call_targets_min_alt_fraction_above_one ... ok
[INFO] [stdout] test tests::rejects_split_bam_min_overlap_fraction_above_one ... ok
[INFO] [stdout] test vcf::tests::rejects_single_set ... ok
[INFO] [stdout] test vcf::tests::rejects_ambiguous_multi_file_basename ... ok
[INFO] [stdout] test vcf::tests::validates_multi_file_mode_with_unique_basenames ... ok
[INFO] [stdout] test vcf::tests::validates_multisample_mode_with_two_sets ... ok
[INFO] [stdout] test cnloh::tests::writes_single_colored_cnv_plot ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 66 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 3.17s
[INFO] [stdout] 
[INFO] [stderr]      Running tests/cnloh_parity_baseline.rs (/opt/rustwide/target/debug/deps/cnloh_parity_baseline-73b680d81127a38f)
[INFO] [stdout] 
[INFO] [stdout] running 1 test
[INFO] [stderr] cnloh detect: start sample=parity_tiny data_type=WGS genome_build=Hg38 sample_mode=Aggregate variant_mode=Marker
[INFO] [stderr] cnloh detect: validating 2 BAM input(s)
[INFO] [stderr] cnloh detect: variant evidence plan=vcf (tests/data/cnloh_fixture/sample.vcf, sample=demo, sample_count=1) resolved_elapsed=113.39µs
[INFO] [stderr] cnloh detect: loading marker database from tests/data/cnloh_fixture/markers (custom path)
[INFO] [stderr] cnloh detect: marker load using 8 worker(s) across 24 files (host_parallelism=8)
[INFO] [stderr] cnloh detect: marker load [1/24] chr1 queued (tests/data/cnloh_fixture/markers/chr1)
[INFO] [stderr] cnloh detect: marker load [2/24] chr2 queued (tests/data/cnloh_fixture/markers/chr2)
[INFO] [stderr] cnloh detect: marker load [3/24] chr3 queued (tests/data/cnloh_fixture/markers/chr3)
[INFO] [stderr] cnloh detect: marker load [4/24] chr4 queued (tests/data/cnloh_fixture/markers/chr4)
[INFO] [stderr] cnloh detect: marker load [5/24] chr5 queued (tests/data/cnloh_fixture/markers/chr5)
[INFO] [stderr] cnloh detect: marker load [6/24] chr6 queued (tests/data/cnloh_fixture/markers/chr6)
[INFO] [stderr] cnloh detect: marker load [7/24] chr7 queued (tests/data/cnloh_fixture/markers/chr7)
[INFO] [stderr] cnloh detect: marker load [8/24] chr8 queued (tests/data/cnloh_fixture/markers/chr8)
[INFO] [stderr] cnloh detect: marker load [9/24] chr9 queued (tests/data/cnloh_fixture/markers/chr9)
[INFO] [stderr] cnloh detect: marker load [10/24] chr10 queued (tests/data/cnloh_fixture/markers/chr10)
[INFO] [stderr] cnloh detect: marker load [11/24] chr11 queued (tests/data/cnloh_fixture/markers/chr11)
[INFO] [stderr] cnloh detect: marker load [12/24] chr12 queued (tests/data/cnloh_fixture/markers/chr12)
[INFO] [stderr] cnloh detect: marker load [13/24] chr13 queued (tests/data/cnloh_fixture/markers/chr13)
[INFO] [stderr] cnloh detect: marker load [14/24] chr14 queued (tests/data/cnloh_fixture/markers/chr14)
[INFO] [stderr] cnloh detect: marker load [15/24] chr15 queued (tests/data/cnloh_fixture/markers/chr15)
[INFO] [stderr] cnloh detect: marker load [16/24] chr16 queued (tests/data/cnloh_fixture/markers/chr16)
[INFO] [stderr] cnloh detect: marker load [17/24] chr17 queued (tests/data/cnloh_fixture/markers/chr17)
[INFO] [stderr] cnloh detect: marker load [18/24] chr18 queued (tests/data/cnloh_fixture/markers/chr18)
[INFO] [stderr] cnloh detect: marker load [19/24] chr19 queued (tests/data/cnloh_fixture/markers/chr19)
[INFO] [stderr] cnloh detect: marker load [20/24] chr20 queued (tests/data/cnloh_fixture/markers/chr20)
[INFO] [stderr] cnloh detect: marker load [21/24] chr21 queued (tests/data/cnloh_fixture/markers/chr21)
[INFO] [stderr] cnloh detect: marker load [22/24] chr22 queued (tests/data/cnloh_fixture/markers/chr22)
[INFO] [stderr] cnloh detect: marker load [23/24] chrX queued (tests/data/cnloh_fixture/markers/chrX)
[INFO] [stderr] cnloh detect: marker load [24/24] chrY queued (tests/data/cnloh_fixture/markers/chrY)
[INFO] [stderr] cnloh detect: marker load mode=codes-only (VCF/SNP filter path; pileup index skipped)
[INFO] [stderr] cnloh detect: marker load [1/24] chr1 done rows_seen=1 parsed=1 added=1 dup_skipped=0 cumulative_targets=1 elapsed=121.11µs progress=4.2% path=tests/data/cnloh_fixture/markers/chr1
[INFO] [stderr] cnloh detect: marker load [2/24] chr2 done rows_seen=1 parsed=1 added=1 dup_skipped=0 cumulative_targets=2 elapsed=29.92µs progress=8.3% path=tests/data/cnloh_fixture/markers/chr2
[INFO] [stderr] cnloh detect: marker load [3/24] chr3 done rows_seen=1 parsed=1 added=1 dup_skipped=0 cumulative_targets=3 elapsed=23.49µs progress=12.5% path=tests/data/cnloh_fixture/markers/chr3
[INFO] [stderr] cnloh detect: marker load [4/24] chr4 done rows_seen=1 parsed=1 added=1 dup_skipped=0 cumulative_targets=4 elapsed=24.86µs progress=16.7% path=tests/data/cnloh_fixture/markers/chr4
[INFO] [stderr] cnloh detect: marker load [5/24] chr5 done rows_seen=1 parsed=1 added=1 dup_skipped=0 cumulative_targets=5 elapsed=21.53µs progress=20.8% path=tests/data/cnloh_fixture/markers/chr5
[INFO] [stderr] cnloh detect: marker load [6/24] chr6 done rows_seen=1 parsed=1 added=1 dup_skipped=0 cumulative_targets=6 elapsed=23.16µs progress=25.0% path=tests/data/cnloh_fixture/markers/chr6
[INFO] [stderr] cnloh detect: marker load [7/24] chr7 done rows_seen=1 parsed=1 added=1 dup_skipped=0 cumulative_targets=7 elapsed=34.52µs progress=29.2% path=tests/data/cnloh_fixture/markers/chr7
[INFO] [stderr] cnloh detect: marker load [8/24] chr8 done rows_seen=1 parsed=1 added=1 dup_skipped=0 cumulative_targets=8 elapsed=28.66µs progress=33.3% path=tests/data/cnloh_fixture/markers/chr8
[INFO] [stderr] cnloh detect: marker load [14/24] chr14 done rows_seen=1 parsed=1 added=1 dup_skipped=0 cumulative_targets=11 elapsed=96.68µs progress=37.5% path=tests/data/cnloh_fixture/markers/chr14
[INFO] [stderr] cnloh detect: marker load [13/24] chr13 done rows_seen=1 parsed=1 added=1 dup_skipped=0 cumulative_targets=12 elapsed=50.85µs progress=41.7% path=tests/data/cnloh_fixture/markers/chr13
[INFO] [stderr] cnloh detect: marker load [16/24] chr16 done rows_seen=1 parsed=1 added=1 dup_skipped=0 cumulative_targets=12 elapsed=33.30µs progress=45.8% path=tests/data/cnloh_fixture/markers/chr16
[INFO] [stderr] cnloh detect: marker load [11/24] chr11 done rows_seen=1 parsed=1 added=1 dup_skipped=0 cumulative_targets=12 elapsed=5.04ms progress=50.0% path=tests/data/cnloh_fixture/markers/chr11
[INFO] [stderr] cnloh detect: marker load [15/24] chr15 done rows_seen=1 parsed=1 added=1 dup_skipped=0 cumulative_targets=13 elapsed=200.62µs progress=54.2% path=tests/data/cnloh_fixture/markers/chr15
[INFO] [stderr] cnloh detect: marker load [21/24] chr21 done rows_seen=1 parsed=1 added=1 dup_skipped=0 cumulative_targets=14 elapsed=35.06µs progress=58.3% path=tests/data/cnloh_fixture/markers/chr21
[INFO] [stderr] cnloh detect: marker load [9/24] chr9 done rows_seen=1 parsed=1 added=1 dup_skipped=0 cumulative_targets=15 elapsed=7.57ms progress=62.5% path=tests/data/cnloh_fixture/markers/chr9
[INFO] [stderr] cnloh detect: marker load [22/24] chr22 done rows_seen=1 parsed=1 added=1 dup_skipped=0 cumulative_targets=16 elapsed=38.28µs progress=66.7% path=tests/data/cnloh_fixture/markers/chr22
[INFO] [stderr] cnloh detect: marker load [23/24] chrX done rows_seen=1 parsed=1 added=1 dup_skipped=0 cumulative_targets=18 elapsed=37.63µs progress=70.8% path=tests/data/cnloh_fixture/markers/chrX
[INFO] [stderr] cnloh detect: marker load [18/24] chr18 done rows_seen=1 parsed=1 added=1 dup_skipped=0 cumulative_targets=20 elapsed=414.25µs progress=75.0% path=tests/data/cnloh_fixture/markers/chr18
[INFO] [stderr] cnloh detect: marker load [19/24] chr19 done rows_seen=1 parsed=1 added=1 dup_skipped=0 cumulative_targets=21 elapsed=404.24µs progress=79.2% path=tests/data/cnloh_fixture/markers/chr19
[INFO] [stderr] cnloh detect: marker load [24/24] chrY done rows_seen=1 parsed=1 added=1 dup_skipped=0 cumulative_targets=21 elapsed=37.11µs progress=83.3% path=tests/data/cnloh_fixture/markers/chrY
[INFO] [stderr] cnloh detect: marker load [20/24] chr20 done rows_seen=1 parsed=1 added=1 dup_skipped=0 cumulative_targets=21 elapsed=318.95µs progress=87.5% path=tests/data/cnloh_fixture/markers/chr20
[INFO] [stderr] cnloh detect: marker load [17/24] chr17 done rows_seen=1 parsed=1 added=1 dup_skipped=0 cumulative_targets=22 elapsed=612.46µs progress=91.7% path=tests/data/cnloh_fixture/markers/chr17
[INFO] [stderr] cnloh detect: marker load [12/24] chr12 done rows_seen=1 parsed=1 added=1 dup_skipped=0 cumulative_targets=23 elapsed=3.85ms progress=95.8% path=tests/data/cnloh_fixture/markers/chr12
[INFO] [stderr] cnloh detect: marker load [10/24] chr10 done rows_seen=1 parsed=1 added=1 dup_skipped=0 cumulative_targets=24 elapsed=7.00ms progress=100.0% path=tests/data/cnloh_fixture/markers/chr10
[INFO] [stderr] cnloh detect: marker database loaded targets=24 elapsed=10.22ms
[INFO] [stderr] cnloh detect: output directory=/tmp/.tmpS58Zt6
[INFO] [stderr] cnloh detect: read filters skip_duplicates=true skip_secondary=true skip_supplementary=true
[INFO] [stderr] cnloh detect: chromosome filter include_noncanonical=false
[INFO] [stderr] cnloh detect: coverage bin window=2000000bp (override with --cov-window-size)
[INFO] [stderr] cnloh detect: scanning BAMs for coverage (requested_threads=4)
[INFO] [stderr] cnloh detect: bam scan start inputs=2 marker_pileup=false workers=2
[INFO] [stderr] cnloh detect: reference model validated across 2 BAM(s) contigs=2 elapsed=560.82µs
[INFO] [stderr] cnloh detect: coverage bin model window=2000000bp total_bins=2
[INFO] [stderr] cnloh detect: finished tests/data/small2.bam
[INFO] [stderr]   records_seen=2 retained=2 skipped=0
[INFO] [stderr]   marker_sites=0 nonzero_bins=1 decode_workers=1
[INFO] [stderr]   elapsed=1.03ms
[INFO] [stderr] cnloh detect: finished tests/data/small1.bam
[INFO] [stderr]   records_seen=2 retained=2 skipped=0
[INFO] [stderr]   marker_sites=0 nonzero_bins=1 decode_workers=1
[INFO] [stderr]   elapsed=1.46ms
[INFO] [stderr] cnloh detect: parallel scan stats workers=2 wall=2.29ms summed_bam=2.49ms est_speedup=1.09x
[INFO] [stderr] cnloh detect: loading variants from VCF tests/data/cnloh_fixture/sample.vcf sample=demo
[INFO] [stderr] cnloh detect: VCF variants loaded count=1 elapsed=48.49µs
[INFO] [stderr] cnloh detect: canonical chromosome filter removed variants=0 coverage_refs=0 coverage_bins=0 reference_contigs=0
[INFO] [stderr] cnloh detect: BAM scan done elapsed=2.37ms workers=2 wall=2.29ms summed_bam=2.49ms records_seen=4 retained=4 skipped=0 (unmapped=0 qc_fail=0 duplicate=0 secondary=0 supplementary=0 missing_ref_id=0 invalid_ref_id=0 missing_start=0 zero_reference_span=0)
[INFO] [stderr] cnloh detect: marker filtering complete kept=1 dropped_non_markers=0 plot_variant_source=marker_filtered plot_variant_count=1 elapsed=6.53µs
[INFO] [stderr] cnloh detect: marker/VAF preprocessing raw_depth=0.100 min_cov=8 min_mac=3 (subchrom-style preprocessing output only)
[INFO] [stderr] cnloh detect: writing outputs variant=/tmp/.tmpS58Zt6/parity_tiny.WGS.variant_evidence.tsv vaf_preprocessed=/tmp/.tmpS58Zt6/parity_tiny.WGS.vaf_preprocessed.tsv maf=/tmp/.tmpS58Zt6/parity_tiny.WGS.maf.tsv vaf_segments=/tmp/.tmpS58Zt6/parity_tiny.WGS.vaf_segments.tsv roh_segments=/tmp/.tmpS58Zt6/parity_tiny.WGS.roh_segments.tsv vaf_roh_segments=/tmp/.tmpS58Zt6/parity_tiny.WGS.vaf_roh_segments.tsv marker_chrom_stats=/tmp/.tmpS58Zt6/parity_tiny.WGS.marker_chrom_stats.tsv coverage=/tmp/.tmpS58Zt6/parity_tiny.WGS.coverage_summary.tsv coverage_bins=/tmp/.tmpS58Zt6/parity_tiny.WGS.coverage_bins.tsv coverage_segments=/tmp/.tmpS58Zt6/parity_tiny.WGS.coverage_segments.tsv coverage_vaf_segments=/tmp/.tmpS58Zt6/parity_tiny.WGS.coverage_vaf_segments.tsv events=/tmp/.tmpS58Zt6/parity_tiny.WGS.events.tsv summary=/tmp/.tmpS58Zt6/parity_tiny.WGS.analysis_start.txt
[INFO] [stderr] cnloh detect: write phase 1/2 (core outputs) starting
[INFO] [stderr] cnloh detect: write phase 1/2 complete files=5 wall=774.99µs coverage=104.87µs coverage_bins=85.16µs marker_chrom_stats=538.82µs vaf_preprocessed=134.62µs variant=138.18µs
[INFO] [stderr] cnloh detect: building derived VAF/ROH/coverage segmentation tables
[INFO] [stderr] cnloh detect: derived step start marker_preprocessed_points=1 min_bins=100 min_size=1000000 min_tf=0.100
[INFO] [stderr] cnloh detect: derived step complete maf_count=1 elapsed=1.40µs
[INFO] [stderr] cnloh detect: derived step complete vaf_segments=1 elapsed=3.25µs
[INFO] [stderr] cnloh detect: derived step complete roh_segments=0 elapsed=1.40µs
[INFO] [stderr] cnloh detect: derived step complete merged_vaf_roh_segments=1 elapsed=11.54µs
[INFO] [stderr] cnloh detect: derived step complete coverage_segments=2 elapsed=34.58µs
[INFO] [stderr] cnloh detect: derived step complete events=2 elapsed=18.64µs
[INFO] [stderr] cnloh detect: derived tables complete maf_rows=1 vaf_segments=1 roh_segments=0 merged_vaf_roh_segments=1 coverage_segments=2 coverage_vaf_segments=2 events=2 elapsed=109.18µs
[INFO] [stderr] cnloh detect: write phase 2/2 (derived outputs) starting
[INFO] [stderr] cnloh detect: write phase 2/2 complete files=7 wall=6.10ms coverage_segments=98.27µs coverage_vaf_segments=150.46µs events=115.49µs maf=86.09µs roh_segments=85.23µs vaf_roh_segments=93.46µs vaf_segments=87.74µs
[INFO] [stderr] cnloh detect: rendering CNV plot to /tmp/.tmpS58Zt6/parity_tiny.WGS.CNV.png (plot_tf=true source=marker_filtered variants=1 coverage_bins=2 window=2000000bp)
[INFO] [stderr] cnloh detect: CNV plot stats points_plotted=1/1 seq_depth=0.100 coverage_min_cov=1 variant_median_cov=40.000 variant_min_cov=10 min_cov_used=1 est_tumour_fraction=0.910 predicted_sex=unknown
[INFO] [stderr] cnloh detect: complete elapsed=3.01s sample=parity_tiny data_type=WGS genome_build=Hg38 panel_bin=WGS preset marker_source=custom path variant_evidence=vcf (tests/data/cnloh_fixture/sample.vcf, sample=demo, sample_count=1) bams=2 scan_workers=2 scan_wall=2.29ms summed_bam=2.49ms marker_targets=24 marker_variants=1 dropped_non_markers=0 plot_variant_source=marker_filtered plot_variant_count=1 include_noncanonical=false dropped_noncanonical_variants=0 dropped_noncanonical_coverage_refs=0 dropped_noncanonical_coverage_bins=0 dropped_noncanonical_reference_contigs=0 coverage_refs=2 coverage_bins=2 coverage_window_bp=2000000 records_seen=4 retained=4 skipped=0 (unmapped=0 qc_fail=0 duplicate=0 secondary=0 supplementary=0 missing_ref_id=0 invalid_ref_id=0 missing_start=0 zero_reference_span=0) plot=/tmp/.tmpS58Zt6/parity_tiny.WGS.CNV.png
[INFO] [stdout] cnloh detect started: sample=parity_tiny
[INFO] [stdout]   variant_evidence=vcf (tests/data/cnloh_fixture/sample.vcf, sample=demo, sample_count=1)
[INFO] [stdout]   marker_targets=24 marker_variants=1 dropped_non_markers=0
[INFO] [stdout]   plot_variant_source=marker_filtered plot_variant_count=1
[INFO] [stdout]   include_noncanonical=false dropped_noncanonical_variants=0 dropped_noncanonical_coverage_refs=0 dropped_noncanonical_coverage_bins=0 dropped_noncanonical_reference_contigs=0
[INFO] [stdout]   coverage_bams=2 coverage_refs=2 coverage_bins=2 coverage_window_bp=2000000 scan_workers=2 scan_wall=2.29ms summed_bam=2.49ms records_seen=4 retained=4 skipped=0
[INFO] [stdout]   skip_breakdown: unmapped=0 qc_fail=0 duplicate=0 secondary=0 supplementary=0 missing_ref_id=0 invalid_ref_id=0 missing_start=0 zero_reference_span=0
[INFO] [stdout]   wrote: /tmp/.tmpS58Zt6/parity_tiny.WGS.variant_evidence.tsv
[INFO] [stdout]          /tmp/.tmpS58Zt6/parity_tiny.WGS.vaf_preprocessed.tsv
[INFO] [stdout]          /tmp/.tmpS58Zt6/parity_tiny.WGS.maf.tsv
[INFO] [stdout]          /tmp/.tmpS58Zt6/parity_tiny.WGS.vaf_segments.tsv
[INFO] [stdout]          /tmp/.tmpS58Zt6/parity_tiny.WGS.roh_segments.tsv
[INFO] [stdout]          /tmp/.tmpS58Zt6/parity_tiny.WGS.vaf_roh_segments.tsv
[INFO] [stdout]          /tmp/.tmpS58Zt6/parity_tiny.WGS.marker_chrom_stats.tsv
[INFO] [stdout]          /tmp/.tmpS58Zt6/parity_tiny.WGS.coverage_summary.tsv
[INFO] [stdout]          /tmp/.tmpS58Zt6/parity_tiny.WGS.coverage_bins.tsv
[INFO] [stdout]          /tmp/.tmpS58Zt6/parity_tiny.WGS.analysis_start.txt
[INFO] [stdout]          /tmp/.tmpS58Zt6/parity_tiny.WGS.coverage_segments.tsv
[INFO] [stdout]          /tmp/.tmpS58Zt6/parity_tiny.WGS.coverage_vaf_segments.tsv
[INFO] [stdout]          /tmp/.tmpS58Zt6/parity_tiny.WGS.events.tsv
[INFO] [stdout]   plots: enabled=true cnv_plot=/tmp/.tmpS58Zt6/parity_tiny.WGS.CNV.png
[INFO] [stdout]   log_output: disabled
[INFO] [stdout]   NEXT: review CNV plot and calibrate thresholds for cohort-specific sensitivity
[INFO] [stdout] test cnloh_parity_baseline_tiny_fixture_outputs_expected_artifacts ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 1 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 3.02s
[INFO] [stdout] 
[INFO] [stderr]      Running tests/gtf_to_introns.rs (/opt/rustwide/target/debug/deps/gtf_to_introns-d5d1ed45b793748a)
[INFO] [stdout] 
[INFO] [stdout] running 2 tests
[INFO] [stdout] test derives_default_output_for_gzipped_gtf ... ok
[INFO] [stdout] test writes_expected_introns_for_plain_gtf ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 2 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.02s
[INFO] [stdout] 
[INFO] running `Command { std: "docker" "inspect" "94fb402b2df0b4248afc1359b2375f29db2899ca9880673e8ed9ae7b06a21104", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "94fb402b2df0b4248afc1359b2375f29db2899ca9880673e8ed9ae7b06a21104", kill_on_drop: false }`
[INFO] [stdout] 94fb402b2df0b4248afc1359b2375f29db2899ca9880673e8ed9ae7b06a21104
