[INFO] fetching crate riker-ngs 0.1.0... [INFO] testing riker-ngs-0.1.0 against beta-2026-04-21 for beta-1.96-1 [INFO] extracting crate riker-ngs 0.1.0 into /workspace/builds/worker-1-tc2/source [INFO] removed /workspace/builds/worker-1-tc2/source/.cargo/config.toml [INFO] removed /workspace/builds/worker-1-tc2/source/rust-toolchain.toml [INFO] started tweaking crates.io crate riker-ngs 0.1.0 [INFO] removed 0 missing tests [INFO] finished tweaking crates.io crate riker-ngs 0.1.0 [INFO] tweaked toml for crates.io crate riker-ngs 0.1.0 written to /workspace/builds/worker-1-tc2/source/Cargo.toml [INFO] validating manifest of crates.io crate riker-ngs 0.1.0 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 riker-ngs 0.1.0 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-1-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-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] 51a0c457db35a231a4fa765dd21252c6ef6a6eb15b72967119f694b14873a4c0 [INFO] running `Command { std: "docker" "start" "-a" "51a0c457db35a231a4fa765dd21252c6ef6a6eb15b72967119f694b14873a4c0", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "51a0c457db35a231a4fa765dd21252c6ef6a6eb15b72967119f694b14873a4c0", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "51a0c457db35a231a4fa765dd21252c6ef6a6eb15b72967119f694b14873a4c0", kill_on_drop: false }` [INFO] [stdout] 51a0c457db35a231a4fa765dd21252c6ef6a6eb15b72967119f694b14873a4c0 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-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] 72b04c6b826aec1d0981b206af8e2d7c56291c90e39673ef280851bdca463747 [INFO] running `Command { std: "docker" "start" "-a" "72b04c6b826aec1d0981b206af8e2d7c56291c90e39673ef280851bdca463747", kill_on_drop: false }` [INFO] [stderr] Compiling simd-adler32 v0.3.8 [INFO] [stderr] Compiling zlib-rs v0.6.2 [INFO] [stderr] Compiling bitflags v2.11.0 [INFO] [stderr] Compiling regex-syntax v0.8.10 [INFO] [stderr] Compiling crossbeam-utils v0.8.21 [INFO] [stderr] Compiling libdeflate-sys v1.25.2 [INFO] [stderr] Compiling log v0.4.29 [INFO] [stderr] Compiling libm v0.2.11 [INFO] [stderr] Compiling miniz_oxide v0.8.9 [INFO] [stderr] Compiling quote v1.0.44 [INFO] [stderr] Compiling bytemuck v1.25.0 [INFO] [stderr] Compiling lexical-util v1.0.7 [INFO] [stderr] Compiling num-traits v0.2.19 [INFO] [stderr] Compiling syn v2.0.117 [INFO] [stderr] Compiling generic-array v0.14.7 [INFO] [stderr] Compiling crossbeam-channel v0.5.15 [INFO] [stderr] Compiling fdeflate v0.3.7 [INFO] [stderr] Compiling slotmap v1.1.1 [INFO] [stderr] Compiling regex-automata v0.4.14 [INFO] [stderr] Compiling core_maths v0.1.1 [INFO] [stderr] Compiling smallvec v1.14.0 [INFO] [stderr] Compiling float-cmp v0.9.0 [INFO] [stderr] Compiling arrayvec v0.7.6 [INFO] [stderr] Compiling strict-num v0.1.1 [INFO] [stderr] Compiling ttf-parser v0.25.1 [INFO] [stderr] Compiling crypto-common v0.1.7 [INFO] [stderr] Compiling block-buffer v0.10.4 [INFO] [stderr] Compiling lexical-write-integer v1.0.6 [INFO] [stderr] Compiling lexical-parse-integer v1.0.6 [INFO] [stderr] Compiling roxmltree v0.20.0 [INFO] [stderr] Compiling weezl v0.1.12 [INFO] [stderr] Compiling arrayref v0.3.9 [INFO] [stderr] Compiling color_quant v1.1.0 [INFO] [stderr] Compiling tinyvec v1.9.0 [INFO] [stderr] Compiling tiny-skia-path v0.11.4 [INFO] [stderr] Compiling fontconfig-parser v0.5.8 [INFO] [stderr] Compiling lexical-parse-float v1.0.6 [INFO] [stderr] Compiling lexical-write-float v1.0.6 [INFO] [stderr] Compiling libdeflater v1.25.2 [INFO] [stderr] Compiling digest v0.10.7 [INFO] [stderr] Compiling kurbo v0.11.1 [INFO] [stderr] Compiling memmap2 v0.9.5 [INFO] [stderr] Compiling bstr v1.12.1 [INFO] [stderr] Compiling unicode-script v0.5.8 [INFO] [stderr] Compiling unicode-bidi-mirroring v0.4.0 [INFO] [stderr] Compiling unicode-ccc v0.4.0 [INFO] [stderr] Compiling rustix v1.1.4 [INFO] [stderr] Compiling flate2 v1.1.9 [INFO] [stderr] Compiling byteorder-lite v0.1.0 [INFO] [stderr] Compiling unicode-properties v0.1.4 [INFO] [stderr] Compiling noodles-bgzf v0.46.0 [INFO] [stderr] Compiling noodles-core v0.19.0 [INFO] [stderr] Compiling rustybuzz v0.20.1 [INFO] [stderr] Compiling png v0.17.16 [INFO] [stderr] Compiling svgtypes v0.15.3 [INFO] [stderr] Compiling fontdb v0.23.0 [INFO] [stderr] Compiling lexical-core v1.0.6 [INFO] [stderr] Compiling simplecss v0.2.2 [INFO] [stderr] Compiling noodles-csi v0.54.0 [INFO] [stderr] Compiling linux-raw-sys v0.12.1 [INFO] [stderr] Compiling zune-core v0.5.1 [INFO] [stderr] Compiling zune-core v0.4.12 [INFO] [stderr] Compiling data-url v0.3.2 [INFO] [stderr] Compiling xmlwriter v0.1.0 [INFO] [stderr] Compiling unicode-bidi v0.3.18 [INFO] [stderr] Compiling pico-args v0.5.0 [INFO] [stderr] Compiling imagesize v0.13.0 [INFO] [stderr] Compiling quick-error v2.0.1 [INFO] [stderr] Compiling unicode-vo v0.1.0 [INFO] [stderr] Compiling pxfm v0.1.28 [INFO] [stderr] Compiling sha2 v0.10.9 [INFO] [stderr] Compiling image-webp v0.2.4 [INFO] [stderr] Compiling noodles-tabix v0.60.0 [INFO] [stderr] Compiling noodles-sam v0.82.0 [INFO] [stderr] Compiling zune-jpeg v0.4.21 [INFO] [stderr] Compiling tiny-skia v0.11.4 [INFO] [stderr] Compiling zune-jpeg v0.5.12 [INFO] [stderr] Compiling usvg v0.45.1 [INFO] [stderr] Compiling rpmalloc-sys v0.2.3+b097fd0 [INFO] [stderr] Compiling png v0.18.1 [INFO] [stderr] Compiling moxcms v0.7.11 [INFO] [stderr] Compiling gif v0.13.3 [INFO] [stderr] Compiling gif v0.14.1 [INFO] [stderr] Compiling rgb v0.8.53 [INFO] [stderr] Compiling rustc-hash v2.1.1 [INFO] [stderr] Compiling libbz2-rs-sys v0.2.2 [INFO] [stderr] Compiling radium v0.7.0 [INFO] [stderr] Compiling noodles-vcf v0.85.0 [INFO] [stderr] Compiling subsetter v0.2.2 [INFO] [stderr] Compiling noodles-bam v0.86.0 [INFO] [stderr] Compiling resvg v0.45.1 [INFO] [stderr] Compiling bzip2 v0.6.1 [INFO] [stderr] Compiling terminal_size v0.4.3 [INFO] [stderr] Compiling lzma-rust2 v0.16.2 [INFO] [stderr] Compiling pdf-writer v0.12.1 [INFO] [stderr] Compiling noodles-fasta v0.60.0 [INFO] [stderr] Compiling regex v1.12.3 [INFO] [stderr] Compiling md-5 v0.10.6 [INFO] [stderr] Compiling unicase v2.9.0 [INFO] [stderr] Compiling kuva v0.1.6 [INFO] [stderr] Compiling tap v1.0.1 [INFO] [stderr] Compiling built v0.8.0 [INFO] [stderr] Compiling wyz v0.5.1 [INFO] [stderr] Compiling env_filter v1.0.0 [INFO] [stderr] Compiling clap_builder v4.5.60 [INFO] [stderr] Compiling chrono v0.4.44 [INFO] [stderr] Compiling riker-ngs v0.1.0 (/opt/rustwide/workdir) [INFO] [stderr] Compiling noodles-bcf v0.83.0 [INFO] [stderr] Compiling noodles-cram v0.90.0 [INFO] [stderr] Compiling strum_macros v0.27.2 [INFO] [stderr] Compiling image v0.25.9 [INFO] [stderr] Compiling clap_derive v4.5.55 [INFO] [stderr] Compiling serde_derive v1.0.228 [INFO] [stderr] Compiling csv-core v0.1.13 [INFO] [stderr] Compiling funty v2.0.0 [INFO] [stderr] Compiling jiff v0.2.21 [INFO] [stderr] Compiling colorous v1.0.16 [INFO] [stderr] Compiling clap v4.5.60 [INFO] [stderr] Compiling noodles v0.107.0 [INFO] [stderr] Compiling bitvec v1.0.1 [INFO] [stderr] Compiling strum v0.27.2 [INFO] [stderr] Compiling csv v1.4.0 [INFO] [stderr] Compiling svg2pdf v0.13.0 [INFO] [stderr] Compiling serde v1.0.228 [INFO] [stderr] Compiling env_logger v0.11.9 [INFO] [stderr] Compiling rpmalloc v0.2.2 [INFO] [stderr] Compiling enum_dispatch v0.3.13 [INFO] [stderr] Compiling riker-ngs-derive v0.1.0 [INFO] [stderr] Compiling rust-lapper v1.2.0 [INFO] [stderr] Finished `dev` profile [unoptimized + debuginfo] target(s) in 2m 33s [INFO] running `Command { std: "docker" "inspect" "72b04c6b826aec1d0981b206af8e2d7c56291c90e39673ef280851bdca463747", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "72b04c6b826aec1d0981b206af8e2d7c56291c90e39673ef280851bdca463747", kill_on_drop: false }` [INFO] [stdout] 72b04c6b826aec1d0981b206af8e2d7c56291c90e39673ef280851bdca463747 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-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] 36cfc7c958d1e3debd351d06b7617b77c380a70b9e1e9ff8fd7c5cd4ca22f922 [INFO] running `Command { std: "docker" "start" "-a" "36cfc7c958d1e3debd351d06b7617b77c380a70b9e1e9ff8fd7c5cd4ca22f922", kill_on_drop: false }` [INFO] [stderr] Compiling rustix v1.1.4 [INFO] [stderr] Compiling approx v0.5.1 [INFO] [stderr] Compiling terminal_size v0.4.3 [INFO] [stderr] Compiling tempfile v3.26.0 [INFO] [stderr] Compiling clap_builder v4.5.60 [INFO] [stderr] Compiling clap v4.5.60 [INFO] [stderr] Compiling riker-ngs v0.1.0 (/opt/rustwide/workdir) [INFO] [stderr] Finished `test` profile [unoptimized + debuginfo] target(s) in 44.40s [INFO] running `Command { std: "docker" "inspect" "36cfc7c958d1e3debd351d06b7617b77c380a70b9e1e9ff8fd7c5cd4ca22f922", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "36cfc7c958d1e3debd351d06b7617b77c380a70b9e1e9ff8fd7c5cd4ca22f922", kill_on_drop: false }` [INFO] [stdout] 36cfc7c958d1e3debd351d06b7617b77c380a70b9e1e9ff8fd7c5cd4ca22f922 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-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] 02b18adf9f34c73063b2e85eaa08255b6aa823961f4684f6a558c16396b37db0 [INFO] running `Command { std: "docker" "start" "-a" "02b18adf9f34c73063b2e85eaa08255b6aa823961f4684f6a558c16396b37db0", kill_on_drop: false }` [INFO] [stderr] Finished `test` profile [unoptimized + debuginfo] target(s) in 0.26s [INFO] [stderr] Running unittests src/lib.rs (/opt/rustwide/target/debug/deps/riker_lib-32239216aab0af01) [INFO] [stdout] [INFO] [stdout] running 262 tests [INFO] [stdout] test commands::alignment::tests::test_chimeric_different_contigs ... ok [INFO] [stdout] test commands::alignment::tests::test_3prime_soft_clip_reverse_leading ... ok [INFO] [stdout] test commands::alignment::tests::test_bad_cycles_forward ... ok [INFO] [stdout] test commands::alignment::tests::test_3prime_soft_clip_forward_trailing ... ok [INFO] [stdout] test commands::alignment::tests::test_chimeric_sa_tag ... ok [INFO] [stdout] test commands::alignment::tests::test_cigar_stats_with_deletion ... ok [INFO] [stdout] test commands::alignment::tests::test_cigar_stats_with_hard_clip ... ok [INFO] [stdout] test commands::alignment::tests::test_cigar_stats_with_insertion ... ok [INFO] [stdout] test commands::alignment::tests::test_cigar_stats_with_soft_clip ... ok [INFO] [stdout] test commands::alignment::tests::test_compute_metric_bad_cycles_threshold ... ok [INFO] [stdout] test commands::alignment::tests::test_compute_metric_basic ... ok [INFO] [stdout] test commands::alignment::tests::test_compute_metric_zero_reads ... ok [INFO] [stdout] test commands::alignment::tests::test_count_bad_cycles_at_threshold ... ok [INFO] [stdout] test commands::alignment::tests::test_count_bad_cycles_below_threshold ... ok [INFO] [stdout] test commands::alignment::tests::test_count_bad_cycles_multiple ... ok [INFO] [stdout] test commands::alignment::tests::test_count_bad_cycles_zero_reads ... ok [INFO] [stdout] test commands::alignment::tests::test_3prime_soft_clip_none ... ok [INFO] [stdout] test commands::alignment::tests::test_cigar_stats_match_only ... ok [INFO] [stdout] test commands::alignment::tests::test_not_chimeric_normal_fr ... ok [INFO] [stdout] test commands::alignment::tests::test_chimeric_large_insert ... ok [INFO] [stdout] test commands::alignment::tests::test_chimeric_non_fr_orientation ... ok [INFO] [stdout] test commands::alignment::tests::test_merge_basic ... ok [INFO] [stdout] test commands::alignment::tests::test_chimeric_exact_max_insert ... ok [INFO] [stdout] test commands::alignment::tests::test_bad_cycles_reverse ... ok [INFO] [stdout] test commands::alignment::tests::test_sum_cigar_op_soft_clip ... ok [INFO] [stdout] test commands::basic::tests::test_base_index_lowercase ... ok [INFO] [stdout] test commands::error::tests::test_stratifier_count_and_indices ... ok [INFO] [stdout] test commands::gcbias::tests::test_base_flags_gc ... ok [INFO] [stdout] test commands::gcbias::tests::test_base_flags_n ... ok [INFO] [stdout] test commands::gcbias::tests::test_compute_dropout_empty ... ok [INFO] [stdout] test commands::gcbias::tests::test_compute_dropout_gc_deficit ... ok [INFO] [stdout] test commands::gcbias::tests::test_compute_dropout_uniform ... ok [INFO] [stdout] test commands::alignment::tests::test_process_cigar_q20_bases ... ok [INFO] [stdout] test commands::gcbias::tests::test_compute_dropout_at_deficit ... ok [INFO] [stdout] test commands::gcbias::tests::test_nc_normal ... ok [INFO] [stdout] test commands::gcbias::tests::test_nc_zero_mean ... ok [INFO] [stdout] test commands::alignment::tests::test_process_cigar_indels_counted ... ok [INFO] [stdout] test commands::gcbias::tests::test_scan_contig_gc_boundary_n_count ... ok [INFO] [stdout] test commands::gcbias::tests::test_scan_contig_gc_case_insensitive ... ok [INFO] [stdout] test commands::basic::tests::test_base_index_standard_bases ... ok [INFO] [stdout] test commands::gcbias::tests::test_scan_contig_gc_mixed ... ok [INFO] [stdout] test commands::basic::tests::test_base_index_unknown ... ok [INFO] [stdout] test commands::gcbias::tests::test_nc_zero_windows ... ok [INFO] [stdout] test commands::gcbias::tests::test_scan_contig_gc_all_gc ... ok [INFO] [stdout] test commands::gcbias::tests::test_scan_contig_gc_window_size_1 ... ok [INFO] [stdout] test commands::gcbias::tests::test_scan_contig_gc_with_ns ... ok [INFO] [stdout] test commands::gcbias::tests::test_dropout_calculation ... ok [INFO] [stdout] test commands::hybcap::tests::test_compute_median_empty ... ok [INFO] [stdout] test commands::gcbias::tests::test_scan_contig_gc_short_seq ... ok [INFO] [stdout] test commands::gcbias::tests::test_phred_quality_calculation ... ok [INFO] [stdout] test commands::gcbias::tests::test_scan_contig_gc_too_many_ns ... ok [INFO] [stdout] test commands::hybcap::tests::test_compute_bases_at_or_above ... ok [INFO] [stdout] test commands::gcbias::tests::test_scan_contig_gc_simple ... ok [INFO] [stdout] test commands::hybcap::tests::test_compute_percentile ... ok [INFO] [stdout] test commands::hybcap::tests::test_estimate_library_size ... ok [INFO] [stdout] test commands::isize::tests::test_below_min_frac_at_threshold ... ok [INFO] [stdout] test commands::isize::tests::test_below_min_frac_zero_total ... ok [INFO] [stdout] test commands::wgs::tests::test_depth_buffer_basic_push_and_flush ... ok [INFO] [stdout] test commands::isize::tests::test_below_min_frac_above ... ok [INFO] [stdout] test commands::wgs::tests::test_depth_buffer_circular_wrap ... ok [INFO] [stdout] test commands::hybcap::tests::test_estimate_roi ... ok [INFO] [stdout] test commands::hybcap::tests::test_compute_median_simple ... ok [INFO] [stdout] test commands::isize::tests::test_below_min_frac_below ... ok [INFO] [stdout] test commands::wgs::tests::test_depth_buffer_excess_counting ... ok [INFO] [stdout] test commands::wgs::tests::test_depth_buffer_hashes_at ... ok [INFO] [stdout] test commands::wgs::tests::test_depth_buffer_coverage_cap ... ok [INFO] [stdout] test commands::wgs::tests::test_percentile_empty_histogram ... ok [INFO] [stdout] test commands::wgs::tests::test_depth_buffer_overlap_detection ... ok [INFO] [stdout] test commands::hybcap::tests::test_hs_penalty_basic ... ok [INFO] [stdout] test commands::hybcap::tests::test_hs_penalty_no_library_size ... ok [INFO] [stdout] test commands::wgs::tests::test_depth_buffer_clear_position ... ok [INFO] [stdout] test commands::wgs::tests::test_percentile_frac_one ... ok [INFO] [stdout] test commands::wgs::tests::test_percentile_frac_zero ... ok [INFO] [stdout] test commands::wgs::tests::test_percentile_from_hist_80pct ... ok [INFO] [stdout] test commands::wgs::tests::test_percentile_two_bins ... ok [INFO] [stdout] test commands::wgs::tests::test_percentile_from_hist_basic ... ok [INFO] [stdout] test counter::tests::test_count_single ... ok [INFO] [stdout] test counter::tests::test_from_iterator ... ok [INFO] [stdout] test commands::wgs::tests::test_percentile_single_bin ... ok [INFO] [stdout] test counter::tests::test_count_n ... ok [INFO] [stdout] test counter::tests::test_count_multiple ... ok [INFO] [stdout] test counter::tests::test_count_of_absent ... ok [INFO] [stdout] test counter::tests::test_default ... ok [INFO] [stdout] test counter::tests::test_index_absent ... ok [INFO] [stdout] test counter::tests::test_into_iter_owned ... ok [INFO] [stdout] test counter::tests::test_i32_counter ... ok [INFO] [stdout] test counter::tests::test_add_assign ... ok [INFO] [stdout] test counter::tests::test_into_iter_borrowed ... ok [INFO] [stdout] test counter::tests::test_mad_single_element ... ok [INFO] [stdout] test counter::tests::test_mad_constant ... ok [INFO] [stdout] test counter::tests::test_index_present ... ok [INFO] [stdout] test counter::tests::test_mad_empty ... ok [INFO] [stdout] test counter::tests::test_iter ... ok [INFO] [stdout] test counter::tests::test_keys ... ok [INFO] [stdout] test counter::tests::test_mean_and_stddev_empty ... ok [INFO] [stdout] test counter::tests::test_mad_symmetric ... ok [INFO] [stdout] test counter::tests::test_mean_and_stddev_symmetric ... ok [INFO] [stdout] test counter::tests::test_mean_empty ... ok [INFO] [stdout] test counter::tests::test_mean_single ... ok [INFO] [stdout] test counter::tests::test_mean_weighted ... ok [INFO] [stdout] test counter::tests::test_median_empty ... ok [INFO] [stdout] test counter::tests::test_median_even_adjacent_bins ... ok [INFO] [stdout] test counter::tests::test_median_even_same_bin ... ok [INFO] [stdout] test counter::tests::test_median_heavily_weighted ... ok [INFO] [stdout] test counter::tests::test_median_large_counts ... ok [INFO] [stdout] test counter::tests::test_median_odd_uniform ... ok [INFO] [stdout] test counter::tests::test_median_with_counts ... ok [INFO] [stdout] test counter::tests::test_min_max ... ok [INFO] [stdout] test counter::tests::test_mode_single_peak ... ok [INFO] [stdout] test counter::tests::test_new_is_empty ... ok [INFO] [stdout] test counter::tests::test_median_single_value ... ok [INFO] [stdout] test counter::tests::test_stddev_constant ... ok [INFO] [stdout] test counter::tests::test_mode_tie_returns_largest ... ok [INFO] [stdout] test counter::tests::test_sorted ... ok [INFO] [stdout] test counter::tests::test_trimmed_all_excluded ... ok [INFO] [stdout] test counter::tests::test_string_counter_sorted ... ok [INFO] [stdout] test counter::tests::test_merge ... ok [INFO] [stdout] test counter::tests::test_trimmed_mean_constant ... ok [INFO] [stdout] test counter::tests::test_trimmed_mean_empty ... ok [INFO] [stdout] test counter::tests::test_trimmed_excludes_outliers ... ok [INFO] [stdout] test counter::tests::test_u16_counter ... ok [INFO] [stdout] test counter::tests::test_u64_counter ... ok [INFO] [stdout] test counter::tests::test_u8_counter ... ok [INFO] [stdout] test counter::tests::test_min_max_empty ... ok [INFO] [stdout] test counter::tests::test_mode_empty ... ok [INFO] [stdout] test counter::tests::test_values ... ok [INFO] [stdout] test intervals::tests::test_contains_pos_empty ... ok [INFO] [stdout] test intervals::tests::test_contains_pos_hit ... ok [INFO] [stdout] test intervals::tests::test_contains_pos_bad_ref_id ... ok [INFO] [stdout] test intervals::tests::test_contig_bitvec_clamped_to_length ... ok [INFO] [stdout] test intervals::tests::test_contig_bitvec_empty ... ok [INFO] [stdout] test intervals::tests::test_contains_pos_miss ... ok [INFO] [stdout] test intervals::tests::test_contig_bitvec_basic ... ok [INFO] [stdout] test intervals::tests::test_contig_bitvec_multiple_intervals ... ok [INFO] [stdout] test intervals::tests::test_contig_bitvec_out_of_range ... ok [INFO] [stdout] test intervals::tests::test_has_contig ... ok [INFO] [stdout] test intervals::tests::test_get_contig ... ok [INFO] [stdout] test intervals::tests::test_bed_unknown_contig_is_warning_not_error ... ok [INFO] [stdout] test intervals::tests::test_detect_format_skips_leading_blank_lines_for_bed ... ok [INFO] [stdout] test intervals::tests::test_detect_bed_format ... ok [INFO] [stdout] test intervals::tests::test_header_exact_match ... ok [INFO] [stdout] test intervals::tests::test_detect_interval_list_format ... ok [INFO] [stdout] test intervals::tests::test_header_only_no_intervals ... ok [INFO] [stdout] test intervals::tests::test_interval_empty ... ok [INFO] [stdout] test intervals::tests::test_header_valid_prefix ... ok [INFO] [stdout] test intervals::tests::test_interval_end_at_contig_length ... ok [INFO] [stdout] test intervals::tests::test_interval_len ... ok [INFO] [stdout] test intervals::tests::test_interval_list_blank_lines_between_data ... ok [INFO] [stdout] test intervals::tests::test_header_no_sq_lines ... ok [INFO] [stdout] test intervals::tests::test_header_length_mismatch ... ok [INFO] [stdout] test intervals::tests::test_interval_name ... ok [INFO] [stdout] test intervals::tests::test_interval_with_contig_name ... ok [INFO] [stdout] test intervals::tests::test_iter ... ok [INFO] [stdout] test intervals::tests::test_header_multiple_mismatches_reported ... ok [INFO] [stdout] test intervals::tests::test_header_more_contigs_than_bam ... ok [INFO] [stdout] test intervals::tests::test_merged_abutting ... ok [INFO] [stdout] test intervals::tests::test_header_name_mismatch ... ok [INFO] [stdout] test intervals::tests::test_interval_unknown_contig_in_interval_list ... ok [INFO] [stdout] test intervals::tests::test_interval_end_exceeds_contig_length ... ok [INFO] [stdout] test intervals::tests::test_load_gzipped_bed ... ok [INFO] [stdout] test intervals::tests::test_merged_no_overlap ... ok [INFO] [stdout] test intervals::tests::test_merged_with_overlap ... ok [INFO] [stdout] test intervals::tests::test_padded_clamped ... ok [INFO] [stdout] test intervals::tests::test_parse_bed_line_bad_number ... ok [INFO] [stdout] test intervals::tests::test_parse_bed_line_dot_name ... ok [INFO] [stdout] test intervals::tests::test_parse_bed_line_valid ... ok [INFO] [stdout] test intervals::tests::test_multiple_interval_errors_reported ... ok [INFO] [stdout] test intervals::tests::test_parse_interval_list_line_missing_end ... ok [INFO] [stdout] test intervals::tests::test_parse_interval_list_line_bad_number ... ok [INFO] [stdout] test intervals::tests::test_parse_bed_line_no_name ... ok [INFO] [stdout] test intervals::tests::test_parse_bed_line_missing_end ... ok [INFO] [stdout] test intervals::tests::test_parse_interval_list_line_no_name ... ok [INFO] [stdout] test intervals::tests::test_load_gzipped_interval_list ... ok [INFO] [stdout] test intervals::tests::test_padded ... ok [INFO] [stdout] test intervals::tests::test_raw_count ... ok [INFO] [stdout] test intervals::tests::test_territory ... ok [INFO] [stdout] test math::tests::test_safe_div_f_inf_denom ... ok [INFO] [stdout] test math::tests::test_safe_div_f_nan_denom ... ok [INFO] [stdout] test math::tests::test_safe_div_f_normal ... ok [INFO] [stdout] test math::tests::test_safe_div_f_zero_denom ... ok [INFO] [stdout] test intervals::tests::test_bed_with_blank_lines ... ok [INFO] [stdout] test math::tests::test_safe_div_normal ... ok [INFO] [stdout] test math::tests::test_safe_div_zero_both ... ok [INFO] [stdout] test math::tests::test_safe_div_zero_denom ... ok [INFO] [stdout] test metrics::tests::test_metric_docs_field_names_and_descs ... ok [INFO] [stdout] test metrics::tests::test_metric_docs_multi_line ... ok [INFO] [stdout] test metrics::tests::test_render_markdown ... ok [INFO] [stdout] test metrics::tests::test_render_metric_docs_text_no_fields ... ok [INFO] [stdout] test metrics::tests::test_render_text ... ok [INFO] [stdout] test metrics::tests::test_metric_docs_empty_doc ... ok [INFO] [stdout] test metrics::tests::test_metric_docs_description ... ok [INFO] [stdout] test metrics::tests::test_serialize_f64_6dp ... ok [INFO] [stdout] test metrics::tests::test_metric_docs_field_count ... ok [INFO] [stdout] test metrics::tests::test_serialize_f64_2dp ... ok [INFO] [stdout] test metrics::tests::test_serialize_opt_f64_5dp_none ... ok [INFO] [stdout] test metrics::tests::test_write_tsv_empty_rows ... ok [INFO] [stdout] test overlapper::tests::test_basic_overlap ... ok [INFO] [stdout] test overlapper::tests::test_contains_position ... ok [INFO] [stdout] test overlapper::tests::test_empty_overlapper ... ok [INFO] [stdout] test overlapper::tests::test_overlaps_any ... ok [INFO] [stdout] test overlapper::tests::test_sparse_contigs ... ok [INFO] [stdout] test metrics::tests::test_write_tsv_roundtrip ... ok [INFO] [stdout] test progress::tests::test_extract_chrom_pos_mapped ... ok [INFO] [stdout] test progress::tests::test_format_count_millions ... ok [INFO] [stdout] test progress::tests::test_extract_chrom_pos_unmapped ... ok [INFO] [stdout] test progress::tests::test_format_count_small ... ok [INFO] [stdout] test progress::tests::test_format_count_thousands ... ok [INFO] [stdout] test progress::tests::test_format_elapsed_exact_minute ... ok [INFO] [stdout] test progress::tests::test_format_elapsed_minutes_and_seconds ... ok [INFO] [stdout] test intervals::tests::test_parse_interval_list_line_valid ... ok [INFO] [stdout] test metrics::tests::test_serialize_f64_5dp ... ok [INFO] [stdout] test intervals::tests::test_parse_interval_list_line_start_zero ... ok [INFO] [stdout] test metrics::tests::test_write_tsv_headers_lowercase ... ok [INFO] [stdout] test progress::tests::test_format_position_small ... ok [INFO] [stdout] test progress::tests::test_format_elapsed_seconds_only ... ok [INFO] [stdout] test metrics::tests::test_serialize_opt_f64_5dp_some ... ok [INFO] [stdout] test progress::tests::test_format_position_large ... ok [INFO] [stdout] test progress::tests::test_record_n_crosses_milestones ... ok [INFO] [stdout] test progress::tests::test_record_n_zero_is_noop ... ok [INFO] [stdout] test progress::tests::test_format_position_zero ... ok [INFO] [stdout] test progress::tests::test_record_no_panic ... ok [INFO] [stdout] test sam::overlap_clipper::tests::test_right_most_read_not_clipped ... ok [INFO] [stdout] test progress::tests::test_record_with_position_no_panic ... ok [INFO] [stdout] test sam::overlap_clipper::tests::test_full_overlap ... ok [INFO] [stdout] test sam::overlap_clipper::tests::test_overlap_with_deletion ... ok [INFO] [stdout] test sam::overlap_clipper::tests::test_no_overlap ... ok [INFO] [stdout] test sam::overlap_clipper::tests::test_first_of_pair_tie_not_clipped ... ok [INFO] [stdout] test sam::overlap_clipper::tests::test_overlap_with_insertion ... ok [INFO] [stdout] test sam::overlap_clipper::tests::test_simple_overlap ... ok [INFO] [stdout] test sam::overlap_clipper::tests::test_unpaired_not_clipped ... ok [INFO] [stdout] test sam::pair_orientation::tests::test_fr_rf_boundary ... ok [INFO] [stdout] test sam::pair_orientation::tests::test_mate_different_contig ... ok [INFO] [stdout] test sam::pair_orientation::tests::test_mate_unmapped ... ok [INFO] [stdout] test sam::pair_orientation::tests::test_record_unmapped ... ok [INFO] [stdout] test sam::pair_orientation::tests::test_tandem_both_forward ... ok [INFO] [stdout] test sam::pair_orientation::tests::test_rf_orientation ... ok [INFO] [stdout] test sam::pair_orientation::tests::test_fr_orientation ... ok [INFO] [stdout] test sam::pair_orientation::tests::test_tandem_both_reverse ... ok [INFO] [stdout] test sam::record_utils::tests::test_derive_sample_fallback_to_filename ... ok [INFO] [stdout] test sam::record_utils::tests::test_derive_sample_from_read_group ... ok [INFO] [stdout] test sam::record_utils::tests::test_derive_sample_no_read_groups ... ok [INFO] [stdout] test sam::record_utils::tests::test_get_integer_tag_int16_negative_clamped ... ok [INFO] [stdout] test sam::record_utils::tests::test_get_integer_tag_int32_negative_clamped ... ok [INFO] [stdout] test sam::record_utils::tests::test_get_integer_tag_int8_negative_clamped ... ok [INFO] [stdout] test sam::pair_orientation::tests::test_unpaired_returns_none ... ok [INFO] [stdout] test sam::record_utils::tests::test_derive_sample_unknown_fallback ... ok [INFO] [stdout] test sam::record_utils::tests::test_get_integer_tag_int8_positive ... ok [INFO] [stdout] test sam::record_utils::tests::test_get_integer_tag_missing ... ok [INFO] [stdout] test sam::record_utils::tests::test_get_integer_tag_uint32 ... ok [INFO] [stdout] test sam::record_utils::tests::test_get_integer_tag_uint8 ... ok [INFO] [stdout] test sequence_dict::tests::test_get_by_index ... ok [INFO] [stdout] test sequence_dict::tests::test_from_header ... ok [INFO] [stdout] test sequence_dict::tests::test_get_by_name ... ok [INFO] [stdout] test sequence_dict::tests::test_from_empty_header ... ok [INFO] [stdout] test sam::record_utils::tests::test_get_integer_tag_uint16 ... ok [INFO] [stdout] test sequence_dict::tests::test_index_by_str ... ok [INFO] [stdout] test sam::record_utils::tests::test_get_integer_tag_non_integer ... ok [INFO] [stdout] test sequence_dict::tests::test_iter ... ok [INFO] [stdout] test sequence_dict::tests::test_index_by_usize ... ok [INFO] [stdout] test sequence_dict::tests::test_names ... ok [INFO] [stdout] test sequence_dict::tests::test_index_by_usize_out_of_bounds - should panic ... ok [INFO] [stdout] test sequence_dict::tests::test_index_by_str_unknown - should panic ... ok [INFO] [stdout] [INFO] [stdout] test result: ok. 262 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.58s [INFO] [stdout] [INFO] [stderr] Running unittests src/main.rs (/opt/rustwide/target/debug/deps/riker-bd41eada1c88cf19) [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/test_alignment.rs (/opt/rustwide/target/debug/deps/test_alignment-15a41c76bf552588) [INFO] [stdout] [INFO] [stdout] running 17 tests [INFO] [stdout] test test_improper_pairs_counted ... ok [INFO] [stdout] test test_chimera_different_contigs ... ok [INFO] [stdout] test test_hq_threshold_filters_low_mapq ... ok [INFO] [stdout] test test_indel_rate_from_cigar ... ok [INFO] [stdout] test test_no_paired_data_produces_unpaired_row ... ok [INFO] [stdout] test test_output_file_created_with_correct_suffix ... ok [INFO] [stdout] test test_pair_bad_cycles_is_sum_of_first_and_second ... ok [INFO] [stdout] test test_chimera_large_insert ... ok [INFO] [stdout] test test_bad_cycles_all_n_at_same_position ... ok [INFO] [stdout] test test_mismatch_rate_from_nm_tag ... ok [INFO] [stdout] test test_hq_median_mismatches ... ok [INFO] [stdout] test test_bad_cycles_below_threshold_not_counted ... ok [INFO] [stdout] test test_basic_paired_reads_first_and_second ... ok [INFO] [stdout] test test_reference_validation_missing_contig_errors ... ok [INFO] [stdout] test test_softclip_fraction ... ok [INFO] [stdout] test test_qc_fail_counted_in_total_not_stats ... ok [INFO] [stdout] test test_unpaired_reads_category ... ok [INFO] [stdout] [INFO] [stdout] test result: ok. 17 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.03s [INFO] [stdout] [INFO] [stderr] Running tests/test_bam_reader.rs (/opt/rustwide/target/debug/deps/test_bam_reader-f733e6a67eaa4ea2) [INFO] [stdout] [INFO] [stdout] running 2 tests [INFO] [stdout] test test_open_invalid_bam ... ok [INFO] [stdout] test test_open_nonexistent_file ... ok [INFO] [stdout] [INFO] [stdout] test result: ok. 2 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s [INFO] [stdout] [INFO] [stderr] Running tests/test_basic.rs (/opt/rustwide/target/debug/deps/test_basic-4ec0b3b22aa2bce9) [INFO] [stdout] [INFO] [stdout] running 11 tests [INFO] [stdout] test test_empty_bam ... ok [INFO] [stdout] test test_plot_files_created ... ok [INFO] [stdout] test test_secondary_supplementary_skipped ... ok [INFO] [stdout] test test_duplicates_included ... ok [INFO] [stdout] test test_qc_fail_skipped ... ok [INFO] [stdout] test test_mixed_read_lengths ... ok [INFO] [stdout] test test_paired_reads ... ok [INFO] [stdout] test test_multiple_reads_accumulation ... ok [INFO] [stdout] test test_n_bases_in_base_dist_excluded_from_qual_dist ... ok [INFO] [stdout] test test_unpaired_reverse_read ... ok [INFO] [stdout] test test_unpaired_forward_read ... ok [INFO] [stdout] [INFO] [stdout] test result: ok. 11 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 2.35s [INFO] [stdout] [INFO] [stderr] Running tests/test_docs.rs (/opt/rustwide/target/debug/deps/test_docs-629d8702e1f669dd) [INFO] [stdout] [INFO] [stdout] running 4 tests [INFO] [stdout] test test_docs_unknown_format ... ok [INFO] [stdout] test test_docs_text_output ... ok [INFO] [stdout] test test_docs_markdown_output ... ok [INFO] [stdout] Alignment summary metrics per read category (read1, read2, pair). [INFO] [stdout] ----------------------------------------------------------------- [INFO] [stdout] sample Sample name derived from the BAM read group SM tag or filename. [INFO] [stdout] category Read category: read1, read2, or pair. [INFO] [stdout] total_reads Total number of reads (including QC-failed reads). [INFO] [stdout] aligned_reads Number of PF reads that aligned to the reference. [INFO] [stderr] Running tests/test_error.rs (/opt/rustwide/target/debug/deps/test_error-0208316254ff4cb2) [INFO] [stdout] frac_aligned Fraction of PF reads that aligned to the reference. [INFO] [stdout] hq_aligned_reads Number of aligned reads with mapping quality >= min_mapq. [INFO] [stdout] hq_aligned_bases Total aligned bases from high-quality reads. [INFO] [stdout] hq_aligned_q20_bases Number of aligned bases with base quality >= 20 from high-quality reads. [INFO] [stdout] hq_median_mismatches Median number of mismatches per high-quality aligned read. [INFO] [stdout] mismatch_rate Rate of mismatches per aligned base across all PF aligned reads. [INFO] [stdout] hq_mismatch_rate Rate of mismatches per aligned base for high-quality reads only. [INFO] [stdout] indel_rate Rate of insertion and deletion events per aligned base. [INFO] [stdout] mean_read_length Mean read length across all PF reads. [INFO] [stdout] sd_read_length Standard deviation of read length across all PF reads. [INFO] [stdout] median_read_length Median read length across all PF reads. [INFO] [stdout] mad_read_length Median absolute deviation of read length across all PF reads. [INFO] [stdout] min_read_length Minimum read length observed. [INFO] [stdout] max_read_length Maximum read length observed. [INFO] [stdout] mean_aligned_read_length Mean aligned read length (M, I, =, X bases) for reads that aligned. [INFO] [stdout] aligned_reads_in_pairs Number of aligned reads that are part of a mapped pair. [INFO] [stdout] frac_aligned_in_pairs Fraction of aligned reads that are part of a mapped pair. [INFO] [stdout] reads_improperly_paired Number of reads that are aligned and paired but not properly paired. [INFO] [stdout] frac_reads_improperly_paired Fraction of aligned reads that are improperly paired. [INFO] [stdout] bad_cycles Number of sequencing cycles where >= 80% of reads had an N base call. [INFO] [stdout] strand_balance Fraction of aligned reads on the positive strand. [INFO] [stdout] frac_chimeras Fraction of read pairs that are chimeric (different contig, large insert, or unexpected orientation). [INFO] [stdout] frac_softclipped_reads Fraction of total bases that are soft-clipped (mapped reads only). [INFO] [stdout] frac_hardclipped_reads Fraction of total bases that are hard-clipped (all PF reads). [INFO] [stdout] mean_3prime_softclipped_bases Mean number of soft-clipped bases at the 3-prime end of reads. [INFO] [stdout] [INFO] [stdout] Base distribution by cycle, showing the fraction of each base at each sequencing cycle. [INFO] [stdout] --------------------------------------------------------------------------------------- [INFO] [stdout] read_end Read end (1 or 2). [INFO] [stdout] cycle Sequencing cycle number (1-based). [INFO] [stdout] frac_a Fraction of A bases at this cycle. [INFO] [stdout] frac_c Fraction of C bases at this cycle. [INFO] [stdout] frac_g Fraction of G bases at this cycle. [INFO] [stdout] frac_t Fraction of T bases at this cycle. [INFO] [stdout] frac_n Fraction of N bases at this cycle. [INFO] [stdout] [INFO] [stdout] GC bias detail metrics — one row per GC percentage bin (0-100). [INFO] [stdout] ----------------------------------------------------------------- [INFO] [stdout] sample Sample name derived from the BAM read group SM tag or filename. [INFO] [stdout] gc GC content percentage (0-100). [INFO] [stdout] windows Number of reference windows at this GC percentage. [INFO] [stdout] read_starts Number of reads starting at positions with this GC percentage. [INFO] [stdout] reported_base_quality Mean of actual base quality scores from reads in this bin. [INFO] [stdout] empirical_base_quality Phred-scaled error rate derived from the NM tag (mismatches + indels). [INFO] [stdout] normalized_coverage Normalized coverage: (reads/windows) / mean_reads_per_window. [INFO] [stdout] error_bar_width Error bar width: sqrt(reads)/windows / mean_reads_per_window. [INFO] [stdout] [INFO] [stdout] GC bias summary metrics — one row per sample. [INFO] [stdout] ----------------------------------------------- [INFO] [stdout] sample Sample name derived from the BAM read group SM tag or filename. [INFO] [stdout] window_size Sliding window size used for GC content calculation. [INFO] [stdout] total_clusters Total clusters (first-of-pair or unpaired mapped reads). [INFO] [stdout] aligned_reads Total aligned reads counted. [INFO] [stdout] at_dropout AT dropout: deficit at GC 0-50%. [INFO] [stdout] gc_dropout GC dropout: deficit at GC 51-100%. [INFO] [stdout] gc_0_19_normcov Aggregate normalized coverage for GC 0-19%. [INFO] [stdout] gc_20_39_normcov Aggregate normalized coverage for GC 20-39%. [INFO] [stdout] gc_40_59_normcov Aggregate normalized coverage for GC 40-59%. [INFO] [stdout] gc_60_79_normcov Aggregate normalized coverage for GC 60-79%. [INFO] [stdout] gc_80_100_normcov Aggregate normalized coverage for GC 80-100%. [INFO] [stdout] [INFO] [stdout] Hybrid capture (HS) sequencing metrics. [INFO] [stdout] --------------------------------------- [INFO] [stdout] sample Sample name derived from the BAM read group SM tag or filename. [INFO] [stdout] panel_name Name of the bait/target panel. [INFO] [stdout] genome_size Total number of bases in the reference genome. [INFO] [stdout] bait_territory Total number of unique bases covered by bait intervals. [INFO] [stdout] target_territory Total number of unique bases covered by target intervals. [INFO] [stdout] bait_design_efficiency Ratio of target territory to bait territory. [INFO] [stdout] total_reads Total primary reads in the BAM file (excludes non-PF reads). [INFO] [stdout] deduped_reads Non-duplicate reads. [INFO] [stdout] deduped_reads_aligned Non-duplicate aligned reads. [INFO] [stdout] total_bases Total bases (read length × primary reads). [INFO] [stdout] bases_aligned Total aligned bases (from primary + supplementary). [INFO] [stdout] deduped_bases_aligned Non-duplicate aligned bases. [INFO] [stdout] on_bait_bases Aligned bases falling on bait intervals (includes duplicates). [INFO] [stdout] near_bait_bases Aligned bases near but not on baits (includes duplicates). [INFO] [stdout] off_bait_bases Aligned bases not near any bait (includes duplicates). [INFO] [stdout] on_target_bases High-quality non-duplicate bases on target intervals. [INFO] [stdout] on_target_bases_from_pairs High-quality non-duplicate bases on target from mapped pairs. [INFO] [stdout] selected_pairs First-of-pair reads overlapping any bait (both ends mapped). [INFO] [stdout] selected_unique_pairs Same as selected_pairs but excluding duplicates. [INFO] [stdout] frac_deduped_reads Fraction of total reads that are non-duplicate. [INFO] [stdout] frac_deduped_reads_aligned Fraction of non-duplicate reads that are aligned. [INFO] [stdout] frac_selected_bases Fraction of aligned bases that are on or near a bait. [INFO] [stdout] frac_off_bait Fraction of aligned bases that are off-bait. [INFO] [stdout] on_bait_vs_selected Fraction of selected bases that are strictly on (not near) bait. [INFO] [stdout] mean_bait_coverage Mean coverage depth across bait bases (from aligned bases incl. duplicates). [INFO] [stdout] mean_target_coverage Mean coverage depth across target bases (from HQ non-dup bases). [INFO] [stdout] median_target_coverage Median per-base coverage depth across target bases. [INFO] [stdout] max_target_coverage Maximum per-base coverage depth across target bases. [INFO] [stdout] min_target_coverage Minimum per-base coverage depth across target bases. [INFO] [stdout] frac_uncovered_targets Fraction of raw (pre-merge) targets with zero coverage. [INFO] [stdout] fold_enrichment Fold enrichment of on-bait bases vs. random genomic distribution. [INFO] [stdout] fold_80_base_penalty Mean / 20th-percentile coverage depth (uniformity penalty). [INFO] [stdout] frac_exc_dupe Fraction of aligned bases excluded because the read was a duplicate. [INFO] [stdout] frac_exc_mapq Fraction of aligned bases excluded due to low mapping quality. [INFO] [stdout] frac_exc_overlap Fraction of aligned bases excluded due to read-pair overlap clipping. [INFO] [stdout] frac_exc_baseq Fraction of aligned bases excluded due to low base quality. [INFO] [stdout] frac_exc_off_target Fraction of aligned bases excluded because they were off-target (but high quality). [INFO] [stdout] frac_target_bases_1x Fraction of target bases with coverage >= 1x. [INFO] [stdout] frac_target_bases_10x Fraction of target bases with coverage >= 10x. [INFO] [stdout] frac_target_bases_20x Fraction of target bases with coverage >= 20x. [INFO] [stdout] frac_target_bases_30x Fraction of target bases with coverage >= 30x. [INFO] [stdout] frac_target_bases_50x Fraction of target bases with coverage >= 50x. [INFO] [stdout] frac_target_bases_100x Fraction of target bases with coverage >= 100x. [INFO] [stdout] frac_target_bases_250x Fraction of target bases with coverage >= 250x. [INFO] [stdout] frac_target_bases_500x Fraction of target bases with coverage >= 500x. [INFO] [stdout] frac_target_bases_1000x Fraction of target bases with coverage >= 1000x. [INFO] [stdout] at_dropout AT dropout: under-representation of AT-rich targets. [INFO] [stdout] gc_dropout GC dropout: under-representation of GC-rich targets. [INFO] [stdout] frac_usable_bases_on_bait Fraction of total bases that are on-bait (including duplicates in denominator). [INFO] [stdout] frac_usable_bases_on_target Fraction of total bases that are on-target (HQ, non-dup numerator, all bases denominator). [INFO] [stdout] hs_library_size Estimated library size using Lander-Waterman model on selected pairs. [INFO] [stdout] hs_penalty_10x Fold sequencing needed to reach 80% of targets at 10x. [INFO] [stdout] hs_penalty_20x Fold sequencing needed to reach 80% of targets at 20x. [INFO] [stdout] hs_penalty_30x Fold sequencing needed to reach 80% of targets at 30x. [INFO] [stdout] hs_penalty_40x Fold sequencing needed to reach 80% of targets at 40x. [INFO] [stdout] hs_penalty_50x Fold sequencing needed to reach 80% of targets at 50x. [INFO] [stdout] hs_penalty_100x Fold sequencing needed to reach 80% of targets at 100x. [INFO] [stdout] [INFO] [stdout] Per-target coverage metrics (one row per merged target interval). [INFO] [stdout] ----------------------------------------------------------------- [INFO] [stdout] chrom Contig name. [INFO] [stdout] start 1-based start position. [INFO] [stdout] end 1-based inclusive end position. [INFO] [stdout] length Interval length in bases. [INFO] [stdout] name Interval name. [INFO] [stdout] gc_frac GC fraction of the target region (0.0 if no reference provided). [INFO] [stdout] mean_coverage Mean high-quality coverage depth. [INFO] [stdout] normalized_coverage Mean coverage normalized by overall mean target coverage. [INFO] [stdout] min_coverage Minimum per-base coverage. [INFO] [stdout] max_coverage Maximum per-base coverage. [INFO] [stdout] frac_0x Fraction of bases with zero coverage. [INFO] [stdout] read_count Number of reads overlapping this target. [INFO] [stdout] [INFO] [stdout] Per-base coverage (one row per target base position). [INFO] [stdout] ----------------------------------------------------- [INFO] [stdout] chrom Contig name. [INFO] [stdout] pos 1-based position. [INFO] [stdout] target Name of the target interval containing this position. [INFO] [stdout] coverage High-quality coverage depth at this position. [INFO] [stdout] [INFO] [stdout] Insert size distribution metrics, one row per pair orientation. [INFO] [stdout] --------------------------------------------------------------- [INFO] [stdout] pair_orientation Pair orientation (FR, RF, or TANDEM). [INFO] [stdout] read_pairs Number of read pairs in this orientation. [INFO] [stdout] mean_insert_size Mean insert size after trimming outliers. [INFO] [stdout] standard_deviation Standard deviation of insert size after trimming outliers. [INFO] [stdout] median_insert_size Median insert size across all pairs in this orientation. [INFO] [stdout] median_absolute_deviation Median absolute deviation of insert size. [INFO] [stdout] mode_insert_size Most frequent insert size. [INFO] [stdout] min_insert_size Smallest insert size observed. [INFO] [stdout] max_insert_size Largest insert size observed. [INFO] [stdout] [INFO] [stdout] Insert size histogram with counts per orientation at each size. [INFO] [stdout] --------------------------------------------------------------- [INFO] [stdout] insert_size Insert size in base pairs. [INFO] [stdout] fr_count Number of FR (forward-reverse) pairs at this insert size. [INFO] [stdout] rf_count Number of RF (reverse-forward) pairs at this insert size. [INFO] [stdout] tandem_count Number of tandem (FF/RR) pairs at this insert size. [INFO] [stdout] [INFO] [stdout] Mean base quality by sequencing cycle. [INFO] [stdout] -------------------------------------- [INFO] [stdout] cycle Sequencing cycle number (1-based). [INFO] [stdout] mean_quality Mean base quality score at this cycle. [INFO] [stdout] [INFO] [stdout] Quality score distribution across all bases. [INFO] [stdout] -------------------------------------------- [INFO] [stdout] quality Base quality score. [INFO] [stdout] count Number of bases with this quality score. [INFO] [stdout] frac_bases Fraction of all bases with this quality score. [INFO] [stdout] [INFO] [stdout] Whole-genome sequencing coverage summary metrics. [INFO] [stdout] ------------------------------------------------- [INFO] [stdout] sample Sample name derived from the BAM read group SM tag or filename. [INFO] [stdout] genome_territory Number of non-N reference bases in the genome territory (or interval set). [INFO] [stdout] mean_coverage Mean coverage depth across all genome territory positions. [INFO] [stdout] sd_coverage Standard deviation of coverage depth. [INFO] [stdout] median_coverage Median coverage depth. [INFO] [stdout] mad_coverage Median absolute deviation of coverage depth. [INFO] [stdout] frac_excluded_mapq Fraction of bases excluded due to low mapping quality. [INFO] [stdout] frac_excluded_dupe Fraction of bases excluded because the read was marked as a duplicate. [INFO] [stdout] frac_excluded_unpaired Fraction of bases excluded because the read was unpaired or had an unmapped mate. [INFO] [stdout] frac_excluded_baseq Fraction of bases excluded due to low base quality. [INFO] [stdout] frac_excluded_overlap Fraction of bases excluded due to read-pair overlap (second occurrence of a read name). [INFO] [stdout] frac_excluded_capped Fraction of bases excluded because the coverage cap was exceeded. [INFO] [stdout] frac_excluded_truncated Fraction of bases excluded because the read's reference span exceeded --max-read-ref-len. [INFO] [stdout] frac_excluded_total Total fraction of bases excluded for any reason. [INFO] [stdout] frac_bases_at_1x Fraction of genome territory positions with coverage ≥ 1×. [INFO] [stdout] frac_bases_at_5x Fraction of genome territory positions with coverage ≥ 5×. [INFO] [stdout] frac_bases_at_10x Fraction of genome territory positions with coverage ≥ 10×. [INFO] [stdout] frac_bases_at_15x Fraction of genome territory positions with coverage ≥ 15×. [INFO] [stdout] frac_bases_at_20x Fraction of genome territory positions with coverage ≥ 20×. [INFO] [stdout] frac_bases_at_25x Fraction of genome territory positions with coverage ≥ 25×. [INFO] [stdout] frac_bases_at_30x Fraction of genome territory positions with coverage ≥ 30×. [INFO] [stdout] frac_bases_at_40x Fraction of genome territory positions with coverage ≥ 40×. [INFO] [stdout] frac_bases_at_50x Fraction of genome territory positions with coverage ≥ 50×. [INFO] [stdout] frac_bases_at_60x Fraction of genome territory positions with coverage ≥ 60×. [INFO] [stdout] frac_bases_at_100x Fraction of genome territory positions with coverage ≥ 100×. [INFO] [stdout] fold_80_base_penalty Mean coverage divided by the 20th-percentile coverage (80% of bases are at/above that level). [INFO] [stdout] fold_90_base_penalty Mean coverage divided by the 10th-percentile coverage. [INFO] [stdout] fold_95_base_penalty Mean coverage divided by the 5th-percentile coverage. [INFO] [stdout] [INFO] [stdout] One row of the per-depth coverage histogram. [INFO] [stdout] -------------------------------------------- [INFO] [stdout] depth Coverage depth (number of reads covering a position). [INFO] [stdout] bases Number of reference positions with exactly this depth. [INFO] [stdout] frac_bases Fraction of genome territory with exactly this depth. [INFO] [stdout] bases_at_or_above Number of reference positions with depth ≥ this depth. [INFO] [stdout] frac_bases_at_or_above Fraction of genome territory with depth ≥ this depth. [INFO] [stdout] [INFO] [stdout] Mismatch error metrics — one row per stratifier group + covariate combination. Each row reports the total bases examined and the number that mismatched the reference, along with the error rate and phred-scaled Q-score. [INFO] [stdout] ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- [INFO] [stdout] stratifier The stratification group (e.g. "read_num,cycle"). [INFO] [stdout] covariate The covariate value(s) for this row. [INFO] [stdout] total_bases Total bases passing quality and variant-site filters. [INFO] [stdout] error_bases Number of bases mismatching the reference. [INFO] [stdout] frac_error Fraction of bases that are errors (error_bases / total_bases). [INFO] [stdout] q_score Phred-scaled error rate: -10 * log10(error_rate). [INFO] [stdout] [INFO] [stdout] Overlapping-read mismatch metrics — one row per stratifier + covariate. For overlapping paired-end reads, classifies each overlapping base into one of three disagreement categories to distinguish sequencing errors from pre-sequencing (e.g. PCR or DNA damage) errors. [INFO] [stdout] ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- [INFO] [stdout] stratifier The stratification group. [INFO] [stdout] covariate The covariate value(s) for this row. [INFO] [stdout] overlapping_read_bases Number of bases from reads overlapping their mate at this position. [INFO] [stdout] bases_mismatching_ref_and_mate Bases where read disagrees with both reference and mate (mate agrees with ref). Likely sequencing errors. [INFO] [stdout] bases_matching_mate_but_not_ref Bases where read and mate agree with each other but both disagree with reference. Likely pre-sequencing errors. [INFO] [stdout] bases_in_three_way_disagreement Bases where read, mate, and reference all differ from each other. [INFO] [stdout] q_mismatching_ref_and_mate Q-score for bases mismatching ref and mate (likely sequencing errors). [INFO] [stdout] q_matching_mate_but_not_ref Q-score for bases matching mate but not ref (likely pre-sequencing errors). [INFO] [stdout] q_three_way_disagreement Q-score for three-way disagreements. [INFO] [stdout] [INFO] [stdout] Indel error metrics — one row per stratifier + covariate. Counts insertion and deletion events from CIGAR strings. The "anchor base" (base immediately before the indel in sequencing order) is used for per-base stratifiers like base quality and read base. [INFO] [stdout] ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- [INFO] [stdout] stratifier The stratification group. [INFO] [stdout] covariate The covariate value(s) for this row. [INFO] [stdout] total_bases Total bases considered (alignment-consuming bases). [INFO] [stdout] num_insertions Number of insertion events. [INFO] [stdout] num_inserted_bases Total bases inserted across all insertion events. [INFO] [stdout] num_deletions Number of deletion events. [INFO] [stdout] num_deleted_bases Total bases deleted across all deletion events. [INFO] [stdout] frac_indel_error Fraction of indel events relative to total bases. [INFO] [stdout] q_score Phred-scaled indel error rate. [INFO] [stdout] test test_docs_stdout_default ... ok [INFO] [stdout] [INFO] [stdout] test result: ok. 4 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.01s [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] running 39 tests [INFO] [stdout] test test_all_group_always_present ... ok [INFO] [stdout] test test_composite_stratifier ... ok [INFO] [stdout] test test_gc_stratification ... ok [INFO] [stdout] test test_insertion_at_read_start ... ok [INFO] [stdout] test test_deletion_at_read_start ... ok [INFO] [stdout] test test_duplicate_exclusion ... ok [INFO] [stdout] test test_deletion_detection ... ok [INFO] [stdout] test test_context_3bp_stratification ... ok [INFO] [stdout] test test_multi_contig ... ok [INFO] [stdout] test test_min_mapq_filter ... ok [INFO] [stdout] test test_min_bq_filter ... ok [INFO] [stdout] test test_insertion_detection ... ok [INFO] [stdout] test test_max_isize_exclusion ... ok [INFO] [stdout] test test_no_errors ... ok [INFO] [stdout] test test_insertion_low_bq_first_base_excluded ... ok [INFO] [stdout] test test_mixed_insertion_and_deletion ... ok [INFO] [stdout] test test_insertion_at_read_start_no_anchor ... ok [INFO] [stdout] test test_n_bases_excluded ... ok [INFO] [stdout] test test_orphaned_buffered_read_still_counted ... ok [INFO] [stdout] test test_overlap_double_counted ... ok [INFO] [stdout] test test_overlapping_reads_all_agree ... ok [INFO] [stdout] test test_overlapping_reads_mismatching_ref_and_mate_exact ... ok [INFO] [stdout] test test_non_overlapping_pair_no_overlap_metrics ... ok [INFO] [stdout] test test_overlapping_reads_mismatching_ref_and_mate ... ok [INFO] [stdout] test test_soft_clip_excluded ... ok [INFO] [stdout] test test_stratifier_parse_error ... ok [INFO] [stdout] test test_overlapping_reads_three_way ... ok [INFO] [stdout] test test_simple_mismatches ... ok [INFO] [stdout] test test_secondary_supplementary_excluded ... ok [INFO] [stdout] test test_stratify_by_hp_len ... ok [INFO] [stdout] test test_stratify_by_indel_len ... ok [INFO] [stdout] test test_stratify_by_ref_base ... ok [INFO] [stdout] test test_stratify_by_cycle ... ok [INFO] [stdout] test test_pre_dinuc_stratification ... ok [INFO] [stdout] test test_overlapping_reads_matching_mate_but_not_ref ... ok [INFO] [stdout] test test_three_output_files_always_created ... ok [INFO] [stdout] test test_q_score_calculation ... ok [INFO] [stdout] test test_stratify_by_read_num ... ok [INFO] [stdout] test test_stratify_by_strand ... ok [INFO] [stdout] [INFO] [stdout] test result: ok. 39 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.24s [INFO] [stdout] [INFO] [stderr] Running tests/test_fasta.rs (/opt/rustwide/target/debug/deps/test_fasta-69f6e94339977079) [INFO] [stdout] [INFO] [stdout] running 7 tests [INFO] [stdout] test test_contig_length ... ok [INFO] [stdout] test test_load_contig_ok ... ok [INFO] [stdout] test test_validate_bam_header_mismatch ... ok [INFO] [stdout] test test_contig_names ... ok [INFO] [stdout] test test_validate_bam_header_ok ... ok [INFO] [stdout] test test_from_path_nonexistent ... ok [INFO] [stdout] test test_load_contig_unknown ... ok [INFO] [stdout] [INFO] [stdout] test result: ok. 7 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.01s [INFO] [stdout] [INFO] [stderr] Running tests/test_gcbias.rs (/opt/rustwide/target/debug/deps/test_gcbias-20f71af4ad2292af) [INFO] [stdout] [INFO] [stdout] running 13 tests [INFO] [stdout] test test_empty_bam ... ok [INFO] [stdout] test test_at_dropout ... ok [INFO] [stdout] test test_exclude_supplementary ... ok [INFO] [stdout] test test_mixed_gc_regions ... ok [INFO] [stdout] test test_gc_dropout ... ok [INFO] [stdout] test test_forward_vs_reverse_strand ... ok [INFO] [stdout] test test_multiple_contigs ... ok [INFO] [stdout] test test_duplicate_handling ... ok [INFO] [stdout] test test_n_bases_exclude_windows ... ok [INFO] [stdout] test test_uniform_zero_gc ... ok [INFO] [stdout] test test_quintile_nc_uniform ... ok [INFO] [stdout] test test_paired_reads_cluster_counting ... ok [INFO] [stdout] test test_read_filtering ... ok [INFO] [stdout] [INFO] [stdout] test result: ok. 13 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 1.26s [INFO] [stdout] [INFO] [stderr] Running tests/test_hybcap.rs (/opt/rustwide/target/debug/deps/test_hybcap-c8eb1216c413b176) [INFO] [stdout] [INFO] [stdout] running 42 tests [INFO] [stdout] test test_bait_classification ... ok [INFO] [stdout] test test_duplicate_exclusion ... ok [INFO] [stdout] test test_coverage_fractions_at_thresholds ... ok [INFO] [stdout] test test_empty_bam ... ok [INFO] [stdout] test test_fraction_computations ... ok [INFO] [stdout] test test_gc_dropout_with_reference ... ok [INFO] [stdout] test test_all_reads_filtered_by_mapq ... ok [INFO] [stdout] test test_include_duplicates ... ok [INFO] [stdout] test test_genome_size ... ok [INFO] [stdout] test test_hs_library_size_no_duplicates ... ok [INFO] [stdout] test test_fold_enrichment ... ok [INFO] [stdout] test test_insertion_with_include_indels ... ok [INFO] [stdout] test test_fold_80_uniform_coverage ... ok [INFO] [stdout] test test_multiple_overlapping_targets ... ok [INFO] [stdout] test test_low_base_quality_exclusion ... ok [INFO] [stdout] test test_low_mapq_filtering ... ok [INFO] [stdout] test test_mixed_base_quality_in_read ... ok [INFO] [stdout] test test_off_bait_classification ... ok [INFO] [stdout] test test_deletion_without_include_indels ... ok [INFO] [stdout] test test_deletion_with_include_indels ... ok [INFO] [stdout] test test_insertion_without_include_indels ... ok [INFO] [stdout] test test_off_target_exclusion ... ok [INFO] [stdout] test test_overlap_clipping_with_leading_and_trailing_soft_clips ... ok [INFO] [stdout] test test_overlap_clipping_with_trailing_soft_clips ... ok [INFO] [stdout] test test_panel_name_custom ... ok [INFO] [stdout] test test_overlap_clipping_trailing_soft_clip_with_hard_clip ... ok [INFO] [stdout] test test_overlap_clipping_trailing_soft_clip_fully_clips_read ... ok [INFO] [stdout] test test_overlapping_reads_with_clipping ... ok [INFO] [stdout] test test_panel_name_default ... ok [INFO] [stdout] test test_per_base_coverage_output ... ok [INFO] [stdout] test test_qc_fail_excluded ... ok [INFO] [stdout] test test_per_target_coverage_output ... ok [INFO] [stdout] test test_overlapping_reads_without_clipping ... ok [INFO] [stdout] test test_per_target_coordinates_are_one_based ... ok [INFO] [stdout] test test_partial_overlap_clipping ... ok [INFO] [stdout] test test_secondary_skipped ... ok [INFO] [stdout] test test_short_read_partial_target ... ok [INFO] [stdout] test test_selected_pairs ... ok [INFO] [stdout] test test_territory_computation ... ok [INFO] [stdout] test test_soft_clip_excluded ... ok [INFO] [stdout] test test_zero_coverage_targets ... ok [INFO] [stdout] test test_high_coverage_u64_safety ... ok [INFO] [stdout] [INFO] [stdout] test result: ok. 42 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.12s [INFO] [stdout] [INFO] [stderr] Running tests/test_isize.rs (/opt/rustwide/target/debug/deps/test_isize-807595dc9dc51658) [INFO] [stdout] [INFO] [stdout] running 8 tests [INFO] [stdout] test test_varied_insert_sizes ... ok [INFO] [stdout] test test_basic_fr_five_pairs ... ok [INFO] [stdout] test test_plot_output_created ... ok [INFO] [stdout] test test_min_frac_excludes_minority_orientation ... ok [INFO] [stdout] test test_histogram_output ... ok [INFO] [stdout] test test_min_frac_zero_includes_all_orientations ... ok [INFO] [stdout] test test_qc_fail_filter ... ok [INFO] [stdout] test test_duplicate_filter ... ok [INFO] [stdout] [INFO] [stdout] test result: ok. 8 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.74s [INFO] [stdout] [INFO] [stderr] Running tests/test_multi.rs (/opt/rustwide/target/debug/deps/test_multi-4cb36c7c593b4dc0) [INFO] [stdout] [INFO] [stdout] running 19 tests [INFO] [stdout] test test_hybcap_requires_targets_and_baits ... ok [INFO] [stdout] test test_empty_bam ... ok [INFO] [stdout] test test_alignment_only ... ok [INFO] [stdout] test test_gcbias_requires_reference ... ok [INFO] [stdout] test test_hybcap_via_multi ... ok [INFO] [stdout] test test_gcbias_collector ... ok [INFO] [stdout] test test_both_collectors ... ok [INFO] [stdout] test test_parallel_empty_bam ... ok [INFO] [stdout] test test_duplicate_collectors_deduplicated ... ok [INFO] [stdout] test test_validate_roundtrip_preserves_defaults ... ok [INFO] [stdout] test test_hybcap_targets_not_required_when_not_selected ... ok [INFO] [stdout] test test_wgs_requires_reference ... ok [INFO] [stdout] test test_isize_only ... ok [INFO] [stdout] test test_matches_standalone_isize ... ok [INFO] [stdout] test test_wgs_collector ... ok [INFO] [stdout] test test_all_collectors ... ok [INFO] [stdout] test test_matches_standalone_wgs ... ok [INFO] [stdout] test test_parallel_matches_single_threaded_isize_alignment ... ok [INFO] [stdout] test test_parallel_all_collectors ... ok [INFO] [stdout] [INFO] [stdout] test result: ok. 19 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 1.75s [INFO] [stdout] [INFO] [stderr] Running tests/test_wgs.rs (/opt/rustwide/target/debug/deps/test_wgs-8bdc0a60c591d9ea) [INFO] [stdout] [INFO] [stdout] running 13 tests [INFO] [stdout] test test_dup_exclusion ... ok [INFO] [stdout] test test_coverage_histogram_file ... ok [INFO] [stdout] test test_exclude_unpaired ... ok [INFO] [stdout] test test_coverage_cap ... ok [INFO] [stdout] test test_baseq_exclusion ... ok [INFO] [stdout] test test_frac_bases_at_nx ... ok [INFO] [stdout] test test_basic_coverage ... ok [INFO] [stdout] test test_fold_penalty ... ok [INFO] [stdout] test test_overlap_detection ... ok [INFO] [stdout] test test_mapq_exclusion ... ok [INFO] [stdout] test test_n_bases_excluded ... ok [INFO] [stdout] test test_sd_coverage_uses_capped_depth ... ok [INFO] [stdout] test test_with_intervals ... ok [INFO] [stdout] [INFO] [stdout] test result: ok. 13 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 1.23s [INFO] [stdout] [INFO] [stderr] Doc-tests riker_lib [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] running `Command { std: "docker" "inspect" "02b18adf9f34c73063b2e85eaa08255b6aa823961f4684f6a558c16396b37db0", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "02b18adf9f34c73063b2e85eaa08255b6aa823961f4684f6a558c16396b37db0", kill_on_drop: false }` [INFO] [stdout] 02b18adf9f34c73063b2e85eaa08255b6aa823961f4684f6a558c16396b37db0