[INFO] fetching crate genemancer 0.2.5... [INFO] testing genemancer-0.2.5 against try#dec9417b8611e34e787a3e4c37686b5131f9e5c5 for pr-154210-1 [INFO] extracting crate genemancer 0.2.5 into /workspace/builds/worker-2-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-2-tc2/source/Cargo.toml [INFO] validating manifest of crates.io crate genemancer 0.2.5 on toolchain dec9417b8611e34e787a3e4c37686b5131f9e5c5 [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+dec9417b8611e34e787a3e4c37686b5131f9e5c5" "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" "+dec9417b8611e34e787a3e4c37686b5131f9e5c5" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-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" "+dec9417b8611e34e787a3e4c37686b5131f9e5c5" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 87b6811f7415f546d6ef38459fe2c2bf673e7fcd1de1869a95d1070537816e27 [INFO] running `Command { std: "docker" "start" "-a" "87b6811f7415f546d6ef38459fe2c2bf673e7fcd1de1869a95d1070537816e27", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "87b6811f7415f546d6ef38459fe2c2bf673e7fcd1de1869a95d1070537816e27", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "87b6811f7415f546d6ef38459fe2c2bf673e7fcd1de1869a95d1070537816e27", kill_on_drop: false }` [INFO] [stdout] 87b6811f7415f546d6ef38459fe2c2bf673e7fcd1de1869a95d1070537816e27 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-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=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" "+dec9417b8611e34e787a3e4c37686b5131f9e5c5" "build" "--frozen" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] c3eca06b08513abb203ec5ca4be26e7492d632b0eaba017cfc066f1c52b464ca [INFO] running `Command { std: "docker" "start" "-a" "c3eca06b08513abb203ec5ca4be26e7492d632b0eaba017cfc066f1c52b464ca", kill_on_drop: false }` [INFO] [stderr] Compiling foldhash v0.2.0 [INFO] [stderr] Compiling simd-adler32 v0.3.8 [INFO] [stderr] Compiling bit-vec v0.8.0 [INFO] [stderr] Compiling proc-macro2 v1.0.106 [INFO] [stderr] Compiling num-traits v0.2.19 [INFO] [stderr] Compiling zlib-rs v0.6.2 [INFO] [stderr] Compiling zerocopy v0.8.40 [INFO] [stderr] Compiling lexical-util v1.0.7 [INFO] [stderr] Compiling thiserror v2.0.18 [INFO] [stderr] Compiling ash v0.38.0+1.3.281 [INFO] [stderr] Compiling bstr v1.12.1 [INFO] [stderr] Compiling crossbeam-channel v0.5.15 [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 hashbrown v0.15.5 [INFO] [stderr] Compiling hashbrown v0.16.1 [INFO] [stderr] Compiling miniz_oxide v0.8.9 [INFO] [stderr] Compiling pathfinder_simd v0.5.5 [INFO] [stderr] Compiling bit-set v0.8.0 [INFO] [stderr] Compiling codespan-reporting v0.12.0 [INFO] [stderr] Compiling freetype-sys v0.20.1 [INFO] [stderr] Compiling lexical-write-integer v1.0.6 [INFO] [stderr] Compiling lexical-parse-integer v1.0.6 [INFO] [stderr] Compiling quote v1.0.44 [INFO] [stderr] Compiling parking_lot_core v0.9.12 [INFO] [stderr] Compiling yeslogic-fontconfig-sys v6.0.0 [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-hal v28.0.1 [INFO] [stderr] Compiling presser v0.3.1 [INFO] [stderr] Compiling syn v2.0.117 [INFO] [stderr] Compiling indexmap v2.13.0 [INFO] [stderr] Compiling noodles-core v0.19.0 [INFO] [stderr] Compiling rustc-hash v1.1.0 [INFO] [stderr] Compiling gpu-descriptor v0.3.2 [INFO] [stderr] Compiling lexical-parse-float v1.0.6 [INFO] [stderr] Compiling lexical-write-float v1.0.6 [INFO] [stderr] Compiling fdeflate v0.3.7 [INFO] [stderr] Compiling parking_lot v0.12.5 [INFO] [stderr] Compiling glow v0.16.0 [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 dirs-sys v0.5.0 [INFO] [stderr] Compiling ordered-float v4.6.0 [INFO] [stderr] Compiling wgpu-core v28.0.1 [INFO] [stderr] Compiling weezl v0.1.12 [INFO] [stderr] Compiling litrs v1.0.0 [INFO] [stderr] Compiling lexical-core v1.0.6 [INFO] [stderr] Compiling jpeg-decoder v0.3.2 [INFO] [stderr] Compiling font-kit v0.14.3 [INFO] [stderr] Compiling dirs v6.0.0 [INFO] [stderr] Compiling wgpu v28.0.0 [INFO] [stderr] Compiling float-ord v0.3.2 [INFO] [stderr] Compiling clap_builder v4.5.60 [INFO] [stderr] Compiling chrono v0.4.44 [INFO] [stderr] Compiling ttf-parser v0.20.0 [INFO] [stderr] Compiling gif v0.12.0 [INFO] [stderr] Compiling pathfinder_geometry v0.5.1 [INFO] [stderr] Compiling document-features v0.2.12 [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 clap_derive v4.5.55 [INFO] [stderr] Compiling tokio-macros v2.6.0 [INFO] [stderr] Compiling flate2 v1.1.9 [INFO] [stderr] Compiling tokio v1.49.0 [INFO] [stderr] Compiling futures-util v0.3.32 [INFO] [stderr] Compiling noodles-bgzf v0.46.0 [INFO] [stderr] Compiling png v0.17.16 [INFO] [stderr] Compiling bytemuck v1.25.0 [INFO] [stderr] Compiling noodles-csi v0.54.0 [INFO] [stderr] Compiling wgpu-types v28.0.0 [INFO] [stderr] Compiling clap v4.5.60 [INFO] [stderr] Compiling noodles-tabix v0.60.0 [INFO] [stderr] Compiling noodles-sam v0.82.0 [INFO] [stderr] Compiling image v0.24.9 [INFO] [stderr] Compiling noodles-bed v0.32.0 [INFO] [stderr] Compiling noodles-bam v0.86.0 [INFO] [stderr] Compiling futures-executor v0.3.32 [INFO] [stderr] Compiling plotters-bitmap v0.3.7 [INFO] [stderr] Compiling futures v0.3.32 [INFO] [stderr] Compiling plotters v0.3.7 [INFO] [stderr] Compiling half v2.7.1 [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 48.05s [INFO] running `Command { std: "docker" "inspect" "c3eca06b08513abb203ec5ca4be26e7492d632b0eaba017cfc066f1c52b464ca", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "c3eca06b08513abb203ec5ca4be26e7492d632b0eaba017cfc066f1c52b464ca", kill_on_drop: false }` [INFO] [stdout] c3eca06b08513abb203ec5ca4be26e7492d632b0eaba017cfc066f1c52b464ca [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-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=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" "+dec9417b8611e34e787a3e4c37686b5131f9e5c5" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 66ddc2d5a828ed1c5d9842ee1ee64f19b87b66a993960dd6a90b89ab87be1da4 [INFO] running `Command { std: "docker" "start" "-a" "66ddc2d5a828ed1c5d9842ee1ee64f19b87b66a993960dd6a90b89ab87be1da4", kill_on_drop: false }` [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 font-kit v0.14.3 [INFO] [stderr] Compiling noodles-sam v0.82.0 [INFO] [stderr] Compiling tempfile v3.26.0 [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 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 25.21s [INFO] running `Command { std: "docker" "inspect" "66ddc2d5a828ed1c5d9842ee1ee64f19b87b66a993960dd6a90b89ab87be1da4", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "66ddc2d5a828ed1c5d9842ee1ee64f19b87b66a993960dd6a90b89ab87be1da4", kill_on_drop: false }` [INFO] [stdout] 66ddc2d5a828ed1c5d9842ee1ee64f19b87b66a993960dd6a90b89ab87be1da4 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-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=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" "+dec9417b8611e34e787a3e4c37686b5131f9e5c5" "test" "--frozen", kill_on_drop: false }` [INFO] [stdout] 71f8e5a3c47377c0b104e9907d5d0b58cbc84dfce70c095f96e1a38d4718d624 [INFO] running `Command { std: "docker" "start" "-a" "71f8e5a3c47377c0b104e9907d5d0b58cbc84dfce70c095f96e1a38d4718d624", kill_on_drop: false }` [INFO] [stderr] Finished `test` profile [unoptimized + debuginfo] target(s) in 0.21s [INFO] [stderr] Running unittests src/main.rs (/opt/rustwide/target/debug/deps/genemancer-7291f6c42e3c33fd) [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::merge_sample_counts_with_cap_truncates_deterministically ... ok [INFO] [stdout] test call_targets::tests::rg_map_overrides_header_sample_mappings ... ok [INFO] [stdout] test call_targets_gpu::tests::auto_tuning_for_datacenter_exceeds_defaults ... ok [INFO] [stdout] test call_targets::tests::rejects_conflicting_read_group_to_sample_mappings ... ok [INFO] [stdout] test call_targets_gpu::tests::auto_mode_ignores_explicit_overrides ... ok [INFO] [stdout] test call_targets_gpu::tests::backend_mask_maps_explicit_backends ... ok [INFO] [stdout] test call_targets_gpu::tests::classify_gpu_tier_detects_datacenter_by_name ... 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_requires_ready_chunks ... ok [INFO] [stdout] test call_targets_gpu::tests::deferred_startup_relief_stops_after_gpu_batch_seen ... 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_triggers_on_pending_threshold ... ok [INFO] [stdout] test call_targets_gpu::tests::effective_chunk_batch_threshold_caps_deferred_mode ... 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::flush_ready_chunks_non_forced_yields_on_writer_backpressure ... ok [INFO] [stdout] test cnloh::tests::accumulates_reference_span_into_expected_bins ... ok [INFO] [stdout] test call_targets_gpu::tests::hybrid_mode_applies_utilization_and_cuda_toggle_overrides ... ok [INFO] [stdout] test cnloh::tests::parses_marker_dot_format ... ok [INFO] [stdout] test cnloh::tests::parses_marker_tab_format ... ok [INFO] [stdout] test call_targets_gpu::tests::flush_ready_chunks_caps_non_forced_pending_batches ... ok [INFO] [stdout] test cnloh::tests::palette_is_unique_for_first_24_chromosomes ... ok [INFO] [stdout] test introns::tests::extracts_introns_from_multi_exon_transcript ... ok [INFO] [stdout] test cnloh::tests::canonical_chrom_filter_matches_autosomes_and_sex_chromosomes ... ok [INFO] [stdout] test call_targets::tests::rejects_bgzf_reference_without_gzi_index ... ok [INFO] [stdout] test merge_bam::tests::trims_reads_with_soft_clips ... 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 gff_gtf::tests::converts_simple_gff_to_gtf ... ok [INFO] [stdout] test introns::tests::skips_single_exon_transcripts ... ok [INFO] [stdout] test introns::tests::merges_overlapping_exons_before_introns ... ok [INFO] [stdout] test cnloh::tests::normalizes_chr_prefix_case_insensitive ... 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 tests::derives_introns_output_path_from_gtf_gz ... ok [INFO] [stdout] test tests::derives_introns_output_path_from_plain_gtf ... ok [INFO] [stdout] test merge_bam::tests::bed_all_mode_does_not_duplicate_records_across_overlapping_regions ... 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 merge_bam::tests::filters_by_read_group ... ok [INFO] [stdout] test merge_bam::tests::merges_inputs_in_coordinate_order ... ok [INFO] [stdout] test tests::parses_pod5_inspect_subcommand ... ok [INFO] [stdout] test merge_bam::tests::writes_index_when_requested ... ok [INFO] [stdout] test split_bam::tests::applies_min_overlap_fraction_filter ... ok [INFO] [stdout] test split_bam::tests::splits_records_into_region_outputs ... ok [INFO] [stdout] test tests::parses_cnloh_detect_with_log_output ... ok [INFO] [stdout] test fasta_prep::tests::prepares_sorted_and_indexed_reference_when_unindexed ... ok [INFO] [stdout] test split_bam::tests::writes_unassigned_output_for_non_overlapping_reads ... ok [INFO] [stdout] test tests::parses_vcf_diff_multisample_args ... ok [INFO] [stdout] test tests::parses_pod5_subsample_with_repeated_input_flags ... ok [INFO] [stdout] test tests::parses_call_targets_gpu_with_tuning_overrides ... ok [INFO] [stdout] test tests::rejects_split_bam_min_overlap_fraction_above_one ... ok [INFO] [stdout] test vcf::tests::validates_multisample_mode_with_two_sets ... ok [INFO] [stdout] test tests::rejects_pod5_subsample_percent_above_hundred ... ok [INFO] [stdout] test vcf::tests::validates_multi_file_mode_with_unique_basenames ... ok [INFO] [stdout] test vcf::tests::rejects_ambiguous_multi_file_basename ... ok [INFO] [stdout] test vcf::tests::rejects_duplicate_member_across_sets ... ok [INFO] [stdout] test vcf::tests::rejects_single_set ... ok [INFO] [stdout] test tests::parses_pod5_subsample_with_multiple_inputs ... ok [INFO] [stdout] test fasta_prep::tests::prepares_from_gz_reference ... ok [INFO] [stdout] test tests::parses_cnloh_detect_with_include_noncanonical ... ok [INFO] [stdout] test tests::rejects_call_targets_gpu_wgpu_upload_utilization_over_100 ... ok [INFO] [stdout] test tests::rejects_call_targets_min_alt_fraction_above_one ... 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 2.14s [INFO] [stdout] [INFO] [stderr] Running tests/cnloh_parity_baseline.rs (/opt/rustwide/target/debug/deps/cnloh_parity_baseline-6a5d0c58853ae807) [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=76.88µs [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=16) [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 [2/24] chr2 done rows_seen=1 parsed=1 added=1 dup_skipped=0 cumulative_targets=1 elapsed=92.18µs progress=4.2% path=tests/data/cnloh_fixture/markers/chr2 [INFO] [stderr] cnloh detect: marker load [1/24] chr1 done rows_seen=1 parsed=1 added=1 dup_skipped=0 cumulative_targets=2 elapsed=171.81µs progress=8.3% path=tests/data/cnloh_fixture/markers/chr1 [INFO] [stderr] cnloh detect: marker load [4/24] chr4 done rows_seen=1 parsed=1 added=1 dup_skipped=0 cumulative_targets=4 elapsed=192.68µs progress=12.5% 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=4 elapsed=134.44µs progress=16.7% path=tests/data/cnloh_fixture/markers/chr5 [INFO] [stderr] cnloh detect: marker load [3/24] chr3 done rows_seen=1 parsed=1 added=1 dup_skipped=0 cumulative_targets=5 elapsed=217.84µs progress=20.8% path=tests/data/cnloh_fixture/markers/chr3 [INFO] [stderr] cnloh detect: marker load [7/24] chr7 done rows_seen=1 parsed=1 added=1 dup_skipped=0 cumulative_targets=6 elapsed=62.74µs progress=25.0% 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=7 elapsed=79.24µs progress=29.2% path=tests/data/cnloh_fixture/markers/chr8 [INFO] [stderr] cnloh detect: marker load [10/24] chr10 done rows_seen=1 parsed=1 added=1 dup_skipped=0 cumulative_targets=8 elapsed=48.41µs progress=33.3% path=tests/data/cnloh_fixture/markers/chr10 [INFO] [stderr] cnloh detect: marker load [11/24] chr11 done rows_seen=1 parsed=1 added=1 dup_skipped=0 cumulative_targets=10 elapsed=295.49µs progress=37.5% path=tests/data/cnloh_fixture/markers/chr11 [INFO] [stderr] cnloh detect: marker load [6/24] chr6 done rows_seen=1 parsed=1 added=1 dup_skipped=0 cumulative_targets=11 elapsed=392.42µs progress=41.7% path=tests/data/cnloh_fixture/markers/chr6 [INFO] [stderr] cnloh detect: marker load [13/24] chr13 done rows_seen=1 parsed=1 added=1 dup_skipped=0 cumulative_targets=11 elapsed=196.29µs progress=45.8% path=tests/data/cnloh_fixture/markers/chr13 [INFO] [stderr] cnloh detect: marker load [9/24] chr9 done rows_seen=1 parsed=1 added=1 dup_skipped=0 cumulative_targets=15 elapsed=933.15µs progress=50.0% path=tests/data/cnloh_fixture/markers/chr9 [INFO] [stderr] cnloh detect: marker load [19/24] chr19 done rows_seen=1 parsed=1 added=1 dup_skipped=0 cumulative_targets=17 elapsed=53.59µs progress=54.2% path=tests/data/cnloh_fixture/markers/chr19 [INFO] [stderr] cnloh detect: marker load [15/24] chr15 done rows_seen=1 parsed=1 added=1 dup_skipped=0 cumulative_targets=20 elapsed=274.03µs progress=58.3% path=tests/data/cnloh_fixture/markers/chr15 [INFO] [stderr] cnloh detect: marker load [20/24] chr20 done rows_seen=1 parsed=1 added=1 dup_skipped=0 cumulative_targets=20 elapsed=56.94µs progress=62.5% path=tests/data/cnloh_fixture/markers/chr20 [INFO] [stderr] cnloh detect: marker load [16/24] chr16 done rows_seen=1 parsed=1 added=1 dup_skipped=0 cumulative_targets=21 elapsed=128.86µs progress=66.7% path=tests/data/cnloh_fixture/markers/chr16 [INFO] [stderr] cnloh detect: marker load [14/24] chr14 done rows_seen=1 parsed=1 added=1 dup_skipped=0 cumulative_targets=21 elapsed=820.33µs progress=70.8% path=tests/data/cnloh_fixture/markers/chr14 [INFO] [stderr] cnloh detect: marker load [21/24] chr21 done rows_seen=1 parsed=1 added=1 dup_skipped=0 cumulative_targets=21 elapsed=45.77µs progress=75.0% path=tests/data/cnloh_fixture/markers/chr21 [INFO] [stderr] cnloh detect: marker load [12/24] chr12 done rows_seen=1 parsed=1 added=1 dup_skipped=0 cumulative_targets=22 elapsed=1.04ms progress=79.2% path=tests/data/cnloh_fixture/markers/chr12 [INFO] [stderr] cnloh detect: marker load [22/24] chr22 done rows_seen=1 parsed=1 added=1 dup_skipped=0 cumulative_targets=22 elapsed=67.75µs progress=83.3% path=tests/data/cnloh_fixture/markers/chr22 [INFO] [stderr] cnloh detect: marker load [18/24] chr18 done rows_seen=1 parsed=1 added=1 dup_skipped=0 cumulative_targets=22 elapsed=611.49µs progress=87.5% path=tests/data/cnloh_fixture/markers/chr18 [INFO] [stderr] cnloh detect: marker load [23/24] chrX done rows_seen=1 parsed=1 added=1 dup_skipped=0 cumulative_targets=23 elapsed=325.39µs progress=91.7% path=tests/data/cnloh_fixture/markers/chrX [INFO] [stderr] cnloh detect: marker load [17/24] chr17 done rows_seen=1 parsed=1 added=1 dup_skipped=0 cumulative_targets=24 elapsed=1.18ms progress=95.8% path=tests/data/cnloh_fixture/markers/chr17 [INFO] [stderr] cnloh detect: marker load [24/24] chrY done rows_seen=1 parsed=1 added=1 dup_skipped=0 cumulative_targets=24 elapsed=76.03µs progress=100.0% path=tests/data/cnloh_fixture/markers/chrY [INFO] [stderr] cnloh detect: marker database loaded targets=24 elapsed=2.75ms [INFO] [stderr] cnloh detect: output directory=/tmp/.tmpyUtZJa [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=404.55µs [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=547.25µs [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=623.19µs [INFO] [stderr] cnloh detect: parallel scan stats workers=2 wall=1.37ms summed_bam=1.17ms est_speedup=0.85x [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=47.43µs [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=1.46ms workers=2 wall=1.37ms summed_bam=1.17ms 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=6.98µs [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/.tmpyUtZJa/parity_tiny.WGS.variant_evidence.tsv vaf_preprocessed=/tmp/.tmpyUtZJa/parity_tiny.WGS.vaf_preprocessed.tsv maf=/tmp/.tmpyUtZJa/parity_tiny.WGS.maf.tsv vaf_segments=/tmp/.tmpyUtZJa/parity_tiny.WGS.vaf_segments.tsv roh_segments=/tmp/.tmpyUtZJa/parity_tiny.WGS.roh_segments.tsv vaf_roh_segments=/tmp/.tmpyUtZJa/parity_tiny.WGS.vaf_roh_segments.tsv marker_chrom_stats=/tmp/.tmpyUtZJa/parity_tiny.WGS.marker_chrom_stats.tsv coverage=/tmp/.tmpyUtZJa/parity_tiny.WGS.coverage_summary.tsv coverage_bins=/tmp/.tmpyUtZJa/parity_tiny.WGS.coverage_bins.tsv coverage_segments=/tmp/.tmpyUtZJa/parity_tiny.WGS.coverage_segments.tsv coverage_vaf_segments=/tmp/.tmpyUtZJa/parity_tiny.WGS.coverage_vaf_segments.tsv events=/tmp/.tmpyUtZJa/parity_tiny.WGS.events.tsv summary=/tmp/.tmpyUtZJa/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=572.32µs coverage=316.91µs coverage_bins=246.19µs marker_chrom_stats=256.79µs vaf_preprocessed=206.99µs variant=266.71µs [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=1.43µs [INFO] [stderr] cnloh detect: derived step complete vaf_segments=1 elapsed=3.32µs [INFO] [stderr] cnloh detect: derived step complete roh_segments=0 elapsed=1.64µs [INFO] [stderr] cnloh detect: derived step complete merged_vaf_roh_segments=1 elapsed=14.81µs [INFO] [stderr] cnloh detect: derived step complete coverage_segments=2 elapsed=31.49µs [INFO] [stderr] cnloh detect: derived step complete events=2 elapsed=15.75µs [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=108.38µs [INFO] [stderr] cnloh detect: write phase 2/2 (derived outputs) starting [INFO] [stderr] cnloh detect: write phase 2/2 complete files=7 wall=492.33µs coverage_segments=173.02µs coverage_vaf_segments=179.56µs events=192.14µs maf=91.27µs roh_segments=162.37µs vaf_roh_segments=127.18µs vaf_segments=115.69µs [INFO] [stderr] cnloh detect: rendering CNV plot to /tmp/.tmpyUtZJa/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] [stdout] cnloh detect started: sample=parity_tiny [INFO] [stderr] cnloh detect: complete elapsed=2.02s 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=1.37ms summed_bam=1.17ms 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/.tmpyUtZJa/parity_tiny.WGS.CNV.png [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=1.37ms summed_bam=1.17ms 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/.tmpyUtZJa/parity_tiny.WGS.variant_evidence.tsv [INFO] [stdout] /tmp/.tmpyUtZJa/parity_tiny.WGS.vaf_preprocessed.tsv [INFO] [stdout] /tmp/.tmpyUtZJa/parity_tiny.WGS.maf.tsv [INFO] [stdout] /tmp/.tmpyUtZJa/parity_tiny.WGS.vaf_segments.tsv [INFO] [stdout] /tmp/.tmpyUtZJa/parity_tiny.WGS.roh_segments.tsv [INFO] [stdout] /tmp/.tmpyUtZJa/parity_tiny.WGS.vaf_roh_segments.tsv [INFO] [stdout] /tmp/.tmpyUtZJa/parity_tiny.WGS.marker_chrom_stats.tsv [INFO] [stdout] /tmp/.tmpyUtZJa/parity_tiny.WGS.coverage_summary.tsv [INFO] [stdout] /tmp/.tmpyUtZJa/parity_tiny.WGS.coverage_bins.tsv [INFO] [stdout] /tmp/.tmpyUtZJa/parity_tiny.WGS.analysis_start.txt [INFO] [stdout] /tmp/.tmpyUtZJa/parity_tiny.WGS.coverage_segments.tsv [INFO] [stdout] /tmp/.tmpyUtZJa/parity_tiny.WGS.coverage_vaf_segments.tsv [INFO] [stdout] /tmp/.tmpyUtZJa/parity_tiny.WGS.events.tsv [INFO] [stdout] plots: enabled=true cnv_plot=/tmp/.tmpyUtZJa/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 2.03s [INFO] [stdout] [INFO] [stderr] Running tests/gtf_to_introns.rs (/opt/rustwide/target/debug/deps/gtf_to_introns-00e7ef6c8ef7f90c) [INFO] [stdout] [INFO] [stdout] running 2 tests [INFO] [stdout] test writes_expected_introns_for_plain_gtf ... ok [INFO] [stdout] test derives_default_output_for_gzipped_gtf ... ok [INFO] [stdout] [INFO] [stdout] test result: ok. 2 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.01s [INFO] [stdout] [INFO] running `Command { std: "docker" "inspect" "71f8e5a3c47377c0b104e9907d5d0b58cbc84dfce70c095f96e1a38d4718d624", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "71f8e5a3c47377c0b104e9907d5d0b58cbc84dfce70c095f96e1a38d4718d624", kill_on_drop: false }` [INFO] [stdout] 71f8e5a3c47377c0b104e9907d5d0b58cbc84dfce70c095f96e1a38d4718d624