[INFO] cloning repository https://github.com/fg-labs/holodeck [INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/fg-labs/holodeck" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Ffg-labs%2Fholodeck", kill_on_drop: false }` [INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Ffg-labs%2Fholodeck'... [INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }` [INFO] [stdout] ac66f993fd673cc598d8eeddb9c4c76c67c89af7 [INFO] testing fg-labs/holodeck against 1.99.0-beta.8 for beta-1.100-2 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Ffg-labs%2Fholodeck" "/workspace/builds/worker-5-tc1/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-5-tc1/source'... [INFO] [stderr] done. [INFO] removed /workspace/builds/worker-5-tc1/source/.cargo/config.toml [INFO] removed /workspace/builds/worker-5-tc1/source/rust-toolchain.toml [INFO] started tweaking git repo https://github.com/fg-labs/holodeck [INFO] finished tweaking git repo https://github.com/fg-labs/holodeck [INFO] tweaked toml for git repo https://github.com/fg-labs/holodeck written to /workspace/builds/worker-5-tc1/source/Cargo.toml [INFO] validating manifest of git repo https://github.com/fg-labs/holodeck on toolchain 1.99.0-beta.8 [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+1.99.0-beta.8" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] crate git repo https://github.com/fg-labs/holodeck 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" "+1.99.0-beta.8" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Updating crates.io index [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded pin-project-internal v1.1.11 [INFO] [stderr] Downloaded pin-project v1.1.11 [INFO] [stderr] Downloaded wasm-bindgen-macro v0.2.120 [INFO] [stderr] Downloaded noodles-core v0.19.0 [INFO] [stderr] Downloaded mimalloc v0.1.50 [INFO] [stderr] Downloaded wasm-bindgen-shared v0.2.120 [INFO] [stderr] Downloaded bgzf v0.3.0 [INFO] [stderr] Downloaded wasm-bindgen v0.2.120 [INFO] [stderr] Downloaded noodles-tabix v0.61.0 [INFO] [stderr] Downloaded noodles-fasta v0.60.0 [INFO] [stderr] Downloaded enum_dispatch v0.3.13 [INFO] [stderr] Downloaded pooled-writer v0.4.0 [INFO] [stderr] Downloaded noodles v0.109.0 [INFO] [stderr] Downloaded coitrees v0.4.0 [INFO] [stderr] Downloaded noodles-csi v0.55.0 [INFO] [stderr] Downloaded noodles-bgzf v0.46.0 [INFO] [stderr] Downloaded wasm-bindgen-macro-support v0.2.120 [INFO] [stderr] Downloaded noodles-bam v0.88.0 [INFO] [stderr] Downloaded jiff-static v0.2.24 [INFO] [stderr] Downloaded noodles-vcf v0.87.0 [INFO] [stderr] Downloaded noodles-sam v0.84.0 [INFO] [stderr] Downloaded js-sys v0.3.97 [INFO] [stderr] Downloaded git2 v0.20.4 [INFO] [stderr] Downloaded libmimalloc-sys v0.1.47 [INFO] [stderr] Downloaded libz-ng-sys v1.1.28 [INFO] [stderr] Downloaded jiff v0.2.24 [INFO] [stderr] Downloaded libz-sys v1.1.28 [INFO] [stderr] Downloaded libgit2-sys v0.18.3+1.9.2 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc1/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc1/target:/opt/rustwide/target:rw,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" "-m" "1610612736" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:3111399a4047eeb3a02b7a90e478d715f38a8c6669b5c4b49d30a17385265909" "sleep" "infinity", kill_on_drop: false }` [INFO] [stdout] 814f2f15546f86482530d48defbb161bfdd4fa4acd716884dd66cf26209fb0d8 [INFO] running `Command { std: "docker" "start" "814f2f15546f86482530d48defbb161bfdd4fa4acd716884dd66cf26209fb0d8", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "814f2f15546f86482530d48defbb161bfdd4fa4acd716884dd66cf26209fb0d8", kill_on_drop: false }` [INFO] running `Command { std: "docker" "exec" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-w" "/opt/rustwide/workdir" "--user" "0:0" "814f2f15546f86482530d48defbb161bfdd4fa4acd716884dd66cf26209fb0d8" "/opt/rustwide/cargo-home/bin/cargo" "+1.99.0-beta.8" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "814f2f15546f86482530d48defbb161bfdd4fa4acd716884dd66cf26209fb0d8", kill_on_drop: false }` [INFO] running `Command { std: "docker" "exec" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-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" "-w" "/opt/rustwide/workdir" "--user" "0:0" "814f2f15546f86482530d48defbb161bfdd4fa4acd716884dd66cf26209fb0d8" "/opt/rustwide/cargo-home/bin/cargo" "+1.99.0-beta.8" "build" "--frozen" "--message-format=json", kill_on_drop: false }` [INFO] [stderr] Compiling libc v0.2.186 [INFO] [stderr] Compiling stable_deref_trait v1.2.1 [INFO] [stderr] Compiling regex-syntax v0.8.10 [INFO] [stderr] Compiling litemap v0.8.2 [INFO] [stderr] Compiling writeable v0.6.3 [INFO] [stderr] Compiling aho-corasick v1.1.4 [INFO] [stderr] Compiling bytes v1.11.1 [INFO] [stderr] Compiling utf8_iter v1.0.4 [INFO] [stderr] Compiling icu_properties_data v2.2.0 [INFO] [stderr] Compiling icu_normalizer_data v2.2.0 [INFO] [stderr] Compiling zlib-rs v0.6.3 [INFO] [stderr] Compiling smallvec v1.15.1 [INFO] [stderr] Compiling crossbeam-channel v0.5.15 [INFO] [stderr] Compiling lexical-util v1.0.7 [INFO] [stderr] Compiling syn v2.0.117 [INFO] [stderr] Compiling indexmap v2.14.0 [INFO] [stderr] Compiling getrandom v0.3.4 [INFO] [stderr] Compiling bit-vec v0.9.1 [INFO] [stderr] Compiling percent-encoding v2.3.2 [INFO] [stderr] Compiling zerocopy v0.8.48 [INFO] [stderr] Compiling form_urlencoded v1.2.2 [INFO] [stderr] Compiling num-traits v0.2.19 [INFO] [stderr] Compiling log v0.4.29 [INFO] [stderr] Compiling bitflags v2.11.1 [INFO] [stderr] Compiling spin v0.9.8 [INFO] [stderr] Compiling anyhow v1.0.102 [INFO] [stderr] Compiling thiserror v2.0.18 [INFO] [stderr] Compiling futures-sink v0.3.32 [INFO] [stderr] Compiling futures-core v0.3.32 [INFO] [stderr] Compiling unicase v2.9.0 [INFO] [stderr] Compiling iana-time-zone v0.1.65 [INFO] [stderr] Compiling oneshot v0.2.1 [INFO] [stderr] Compiling jiff v0.2.24 [INFO] [stderr] Compiling lexical-write-integer v1.0.6 [INFO] [stderr] Compiling lexical-parse-integer v1.0.6 [INFO] [stderr] Compiling clap_builder v4.6.0 [INFO] [stderr] Compiling once_cell v1.21.4 [INFO] [stderr] Compiling lexical-write-float v1.0.6 [INFO] [stderr] Compiling coitrees v0.4.0 [INFO] [stderr] Compiling lexical-parse-float v1.0.6 [INFO] [stderr] Compiling jobserver v0.1.34 [INFO] [stderr] Compiling getrandom v0.2.17 [INFO] [stderr] Compiling parking_lot_core v0.9.12 [INFO] [stderr] Compiling chrono v0.4.44 [INFO] [stderr] Compiling nanorand v0.7.0 [INFO] [stderr] Compiling rand_core v0.9.5 [INFO] [stderr] Compiling regex-automata v0.4.14 [INFO] [stderr] Compiling parking_lot v0.12.5 [INFO] [stderr] Compiling cc v1.2.61 [INFO] [stderr] Compiling lexical-core v1.0.6 [INFO] [stderr] Compiling cmake v0.1.58 [INFO] [stderr] Compiling libdeflate-sys v1.25.2 [INFO] [stderr] Compiling libz-ng-sys v1.1.28 [INFO] [stderr] Compiling libz-sys v1.1.28 [INFO] [stderr] Compiling libgit2-sys v0.18.3+1.9.2 [INFO] [stderr] Compiling libmimalloc-sys v0.1.47 [INFO] [stderr] Compiling libdeflater v1.25.2 [INFO] [stderr] Compiling bstr v1.12.1 [INFO] [stderr] Compiling regex v1.12.3 [INFO] [stderr] Compiling mimalloc v0.1.50 [INFO] [stderr] Compiling env_filter v1.0.1 [INFO] [stderr] Compiling synstructure v0.13.2 [INFO] [stderr] Compiling noodles-core v0.19.0 [INFO] [stderr] Compiling ppv-lite86 v0.2.21 [INFO] [stderr] Compiling env_logger v0.11.10 [INFO] [stderr] Compiling rand_chacha v0.9.0 [INFO] [stderr] Compiling zerofrom-derive v0.1.7 [INFO] [stderr] Compiling yoke-derive v0.8.2 [INFO] [stderr] Compiling zerovec-derive v0.11.3 [INFO] [stderr] Compiling displaydoc v0.2.5 [INFO] [stderr] Compiling pin-project-internal v1.1.11 [INFO] [stderr] Compiling thiserror-impl v1.0.69 [INFO] [stderr] Compiling rand v0.9.4 [INFO] [stderr] Compiling thiserror-impl v2.0.18 [INFO] [stderr] Compiling clap_derive v4.6.1 [INFO] [stderr] Compiling enum_dispatch v0.3.13 [INFO] [stderr] Compiling rand_distr v0.5.1 [INFO] [stderr] Compiling pin-project v1.1.11 [INFO] [stderr] Compiling zerofrom v0.1.7 [INFO] [stderr] Compiling flume v0.10.14 [INFO] [stderr] Compiling yoke v0.8.2 [INFO] [stderr] Compiling thiserror v1.0.69 [INFO] [stderr] Compiling zerotrie v0.2.4 [INFO] [stderr] Compiling bgzf v0.3.0 [INFO] [stderr] Compiling zerovec v0.11.6 [INFO] [stderr] Compiling pooled-writer v0.4.0 [INFO] [stderr] Compiling clap v4.6.1 [INFO] [stderr] Compiling tinystr v0.8.3 [INFO] [stderr] Compiling potential_utf v0.1.5 [INFO] [stderr] Compiling icu_locale_core v2.2.0 [INFO] [stderr] Compiling icu_collections v2.2.0 [INFO] [stderr] Compiling icu_provider v2.2.0 [INFO] [stderr] Compiling icu_normalizer v2.2.0 [INFO] [stderr] Compiling icu_properties v2.2.0 [INFO] [stderr] Compiling idna_adapter v1.2.2 [INFO] [stderr] Compiling idna v1.1.0 [INFO] [stderr] Compiling url v2.5.8 [INFO] [stderr] Compiling git2 v0.20.4 [INFO] [stderr] Compiling flate2 v1.1.9 [INFO] [stderr] Compiling built v0.8.0 [INFO] [stderr] Compiling noodles-bgzf v0.46.0 [INFO] [stderr] Compiling holodeck v0.3.0 (/opt/rustwide/workdir) [INFO] [stderr] Compiling noodles-csi v0.55.0 [INFO] [stderr] Compiling noodles-fasta v0.60.0 [INFO] [stderr] Compiling noodles-sam v0.84.0 [INFO] [stderr] Compiling noodles-tabix v0.61.0 [INFO] [stderr] Compiling noodles-vcf v0.87.0 [INFO] [stderr] Compiling noodles-bam v0.88.0 [INFO] [stderr] Compiling noodles v0.109.0 [INFO] [stderr] Finished `dev` profile [unoptimized + debuginfo] target(s) in 1m 29s [INFO] running `Command { std: "docker" "inspect" "814f2f15546f86482530d48defbb161bfdd4fa4acd716884dd66cf26209fb0d8", kill_on_drop: false }` [INFO] running `Command { std: "docker" "exec" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-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" "-w" "/opt/rustwide/workdir" "--user" "0:0" "814f2f15546f86482530d48defbb161bfdd4fa4acd716884dd66cf26209fb0d8" "/opt/rustwide/cargo-home/bin/cargo" "+1.99.0-beta.8" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }` [INFO] [stderr] Compiling rustix v1.1.4 [INFO] [stderr] Compiling getrandom v0.4.2 [INFO] [stderr] Compiling once_cell v1.21.4 [INFO] [stderr] Compiling fastrand v2.4.1 [INFO] [stderr] Compiling approx v0.5.1 [INFO] [stderr] Compiling terminal_size v0.4.4 [INFO] [stderr] Compiling tempfile v3.27.0 [INFO] [stderr] Compiling clap_builder v4.6.0 [INFO] [stderr] Compiling clap v4.6.1 [INFO] [stderr] Compiling holodeck v0.3.0 (/opt/rustwide/workdir) [INFO] [stderr] Finished `test` profile [unoptimized + debuginfo] target(s) in 22.04s [INFO] running `Command { std: "docker" "inspect" "814f2f15546f86482530d48defbb161bfdd4fa4acd716884dd66cf26209fb0d8", kill_on_drop: false }` [INFO] running `Command { std: "docker" "exec" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-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" "-w" "/opt/rustwide/workdir" "--user" "0:0" "814f2f15546f86482530d48defbb161bfdd4fa4acd716884dd66cf26209fb0d8" "/opt/rustwide/cargo-home/bin/cargo" "+1.99.0-beta.8" "test" "--frozen", kill_on_drop: false }` [INFO] [stderr] Finished `test` profile [unoptimized + debuginfo] target(s) in 0.21s [INFO] [stderr] Running unittests src/lib.rs (/opt/rustwide/target/debug/deps/holodeck_lib-63f898d92f51f460) [INFO] [stdout] [INFO] [stdout] running 314 tests [INFO] [stdout] test bed::tests::test_error_unknown_contig ... ok [INFO] [stdout] test bed::tests::test_error_end_exceeds_contig_length ... ok [INFO] [stdout] test bed::tests::test_overlap_hit ... ok [INFO] [stdout] test bed::tests::test_effective_territory_single_target ... ok [INFO] [stdout] test bed::tests::test_load_simple_bed ... ok [INFO] [stdout] test bed::tests::test_contig_effective_territory ... ok [INFO] [stdout] test bed::tests::test_error_start_gte_end ... ok [INFO] [stdout] test bed::tests::test_contig_intervals_empty_contig ... ok [INFO] [stdout] test bed::tests::test_effective_territory_multiple_targets ... ok [INFO] [stdout] test commands::eval::tests::test_format_bin_label ... ok [INFO] [stdout] test bed::tests::test_contig_intervals_returns_sorted_intervals ... ok [INFO] [stdout] test commands::eval::tests::test_mapq_bin ... ok [INFO] [stdout] test commands::eval::tests::test_write_bin_row ... ok [INFO] [stdout] test bed::tests::test_sampler_padding_clamped_to_zero ... ok [INFO] [stdout] test bed::tests::test_overlap_single_base ... ok [INFO] [stdout] test bed::tests::test_overlap_miss ... ok [INFO] [stdout] test bed::tests::test_sampler_single_interval_no_pad ... ok [INFO] [stdout] test bed::tests::test_skips_comments_and_blank_lines ... ok [INFO] [stdout] test commands::command::tests::test_output_path_no_directory ... ok [INFO] [stdout] test bed::tests::test_sampler_merges_overlapping_padded_intervals ... ok [INFO] [stdout] test commands::simulate::tests::test_compute_seed_differs_by_failure_rate ... ok [INFO] [stdout] test commands::mutate::tests::test_generate_indel_deletion ... ok [INFO] [stdout] test commands::mutate::tests::test_generate_indel_insertion ... ok [INFO] [stdout] test bed::tests::test_sampler_keeps_disjoint_padded_intervals_separate ... ok [INFO] [stdout] test commands::mutate::tests::test_generate_genotype_haploid ... ok [INFO] [stdout] test bed::tests::test_sampler_empty_intervals ... ok [INFO] [stdout] test bed::tests::test_sampler_samples_proportional_to_interval_size ... ok [INFO] [stdout] test commands::simulate::tests::test_compute_seed_em_seq_and_taps_differ ... ok [INFO] [stdout] test commands::command::tests::test_output_path_simple ... ok [INFO] [stdout] test commands::mutate::tests::test_generate_snp ... ok [INFO] [stdout] test commands::simulate::tests::test_compute_seed_explicit_seed_unaffected_by_methylation ... ok [INFO] [stdout] test bed::tests::test_sampler_padding_extends_left ... ok [INFO] [stdout] test commands::mutate::tests::test_generate_genotype_diploid_het ... ok [INFO] [stdout] test commands::mutate::tests::test_generate_genotype_triploid ... ok [INFO] [stdout] test commands::simulate::tests::test_compute_seed_no_methylation_matches_legacy ... ok [INFO] [stdout] test commands::mutate::tests::mutate_plain_output_is_text_and_reads_back ... ok [INFO] [stdout] test commands::simulate::tests::test_compute_seed_methylation_differs_from_legacy ... ok [INFO] [stdout] test commands::mutate::tests::test_generate_mnp ... ok [INFO] [stdout] test commands::simulate::tests::test_default_rates_without_mode_accepted ... ok [INFO] [stdout] test commands::simulate::tests::test_methylation_conversion_rate_explicit_one_without_mode_rejected ... ok [INFO] [stdout] test commands::simulate::tests::test_cpg_truth_bedgraph_missing_parent_rejected ... ok [INFO] [stdout] test commands::simulate::tests::test_methylation_conversion_rate_nan_rejected ... ok [INFO] [stdout] test commands::simulate::tests::test_methylation_conversion_rate_out_of_range_rejected ... ok [INFO] [stdout] test commands::simulate::tests::test_methylation_conversion_rate_without_mode_rejected ... ok [INFO] [stdout] test commands::simulate::tests::test_methylation_failure_rate_out_of_range_rejected ... ok [INFO] [stdout] test commands::mutate::tests::mutate_gz_output_is_bgzf_and_reads_back ... ok [INFO] [stdout] test commands::simulate::tests::test_methylation_failure_rate_without_mode_rejected ... ok [INFO] [stdout] test error_model::illumina::tests::test_apply_errors_reproducible ... ok [INFO] [stdout] test error_model::illumina::tests::test_apply_errors_quality_encoding ... ok [INFO] [stdout] test error_model::illumina::tests::test_apply_errors_introduces_errors ... ok [INFO] [stdout] test error_model::illumina::tests::test_error_rate_ramps_to_max ... ok [INFO] [stdout] test error_model::illumina::tests::test_apply_errors_zero_rate ... ok [INFO] [stdout] test error_model::illumina::tests::test_error_rate_at_start ... ok [INFO] [stdout] test error_model::illumina::tests::test_r2_multiplier ... ok [INFO] [stdout] test error_model::tests::test_random_different_base_all_bases ... ok [INFO] [stdout] test fasta::tests::test_from_path_missing_fasta_names_the_fasta ... ok [INFO] [stdout] test error_model::tests::test_random_different_base_never_same ... ok [INFO] [stdout] test fasta::tests::test_from_path_missing_index_quotes_a_path_with_spaces ... ok [INFO] [stdout] test error_model::illumina::tests::test_r2_higher_than_r1 ... ok [INFO] [stdout] test fasta::tests::test_from_path_missing_index_names_the_index ... ok [INFO] [stdout] test error_model::illumina::tests::test_error_rate_flat_before_decay ... ok [INFO] [stdout] test fasta::tests::test_load_contig_iupac_resolved_to_lowercase ... ok [INFO] [stdout] test error_model::illumina::tests::test_error_rate_increases_monotonically ... ok [INFO] [stdout] test fasta::tests::test_load_contig_multiple ... ok [INFO] [stdout] test fasta::tests::test_load_contig_resolution_reproducible ... ok [INFO] [stdout] test fasta::tests::test_load_contig_out_of_order ... ok [INFO] [stdout] test fasta::tests::test_from_path_unreadable_directory_reports_the_os_error ... ok [INFO] [stdout] test fasta::tests::test_load_contig_single ... ok [INFO] [stdout] test fasta::tests::test_load_contig_u_to_t ... ok [INFO] [stdout] test fragment::tests::test_extract_r2_fragment_longer_than_read ... ok [INFO] [stdout] test fragment::tests::test_extract_r2_full_fragment ... ok [INFO] [stdout] test fragment::tests::test_extract_r1_fragment_longer_than_read ... ok [INFO] [stdout] test fragment::tests::test_extract_r1_short_fragment_with_adapter ... ok [INFO] [stdout] test fasta::tests::test_load_contig_uppercases_acgt ... ok [INFO] [stdout] test fasta::tests::test_load_contig_resolution_respects_ambiguity_set ... ok [INFO] [stdout] test fasta::tests::test_shell_quote_escapes_an_embedded_single_quote ... ok [INFO] [stdout] test fragment::tests::test_extract_r1_full_fragment ... ok [INFO] [stdout] test fragment::tests::test_lowercase_fraction_all_upper ... ok [INFO] [stdout] test fragment::tests::test_lowercase_fraction_ignores_non_letters ... ok [INFO] [stdout] test fragment::tests::test_lowercase_fraction_empty ... ok [INFO] [stdout] test fasta::tests::test_shell_quote_leaves_a_safe_path_unquoted ... ok [INFO] [stdout] test fragment::tests::test_extract_empty_fragment_all_adapter ... ok [INFO] [stdout] test fragment::tests::test_lowercase_fraction_mixed ... ok [INFO] [stdout] test fragment::tests::test_extract_r2_short_fragment_with_adapter ... ok [INFO] [stdout] test fragment::tests::test_lowercase_fraction_all_lower ... ok [INFO] [stdout] test fragment::tests::test_uppercase_in_place_empty ... ok [INFO] [stdout] test haplotype::tests::test_extract_fragment_with_deletion ... ok [INFO] [stdout] test fragment::tests::test_reverse_complement_preserves_lowercase ... ok [INFO] [stdout] test haplotype::tests::test_fragment_starts_mid_reference ... ok [INFO] [stdout] test fragment::tests::test_reverse_complement_with_n ... ok [INFO] [stdout] test fragment::tests::test_reverse_complement ... ok [INFO] [stdout] test haplotype::tests::test_fragment_starts_within_deletion ... ok [INFO] [stdout] test haplotype::tests::test_extract_fragment_with_insertion ... ok [INFO] [stdout] test haplotype::tests::test_extract_fragment_with_snp ... ok [INFO] [stdout] test fragment::tests::test_uppercase_in_place ... ok [INFO] [stdout] test haplotype::tests::test_adjacent_variants ... ok [INFO] [stdout] test haplotype::tests::test_extract_fragment_no_variants ... ok [INFO] [stdout] test haplotype::tests::test_extract_fragment_starts_within_deletion_hap_start ... ok [INFO] [stdout] test haplotype::tests::test_phased_allele_assignment ... ok [INFO] [stdout] test haplotype::tests::test_unphased_hom_alt_both_haplotypes ... ok [INFO] [stdout] test meth::tests::test_apply_methylation_conversion_em_seq_zero_meth_full_conversion_forward ... ok [INFO] [stdout] test haplotype::tests::test_variant_at_position_zero ... ok [INFO] [stdout] test meth::tests::test_apply_methylation_conversion_only_converts_c_not_other_bases ... ok [INFO] [stdout] test meth::tests::test_apply_methylation_conversion_taps_methylated_converts ... ok [INFO] [stdout] test meth::tests::test_apply_methylation_conversion_taps_negative_strand ... ok [INFO] [stdout] test meth::tests::test_apply_methylation_conversion_taps_unmethylated_preserved ... ok [INFO] [stdout] test haplotype::tests::test_hap_position_for_with_deletion ... ok [INFO] [stdout] test meth::tests::test_failed_molecule_converts_at_one_minus_conversion_rate ... ok [INFO] [stdout] test meth::tests::test_apply_methylation_conversion_skips_adapter_bases ... ok [INFO] [stdout] test haplotype::tests::test_hap_position_for_with_insertion ... ok [INFO] [stdout] test meth::tests::test_apply_methylation_conversion_with_hap_start_offset ... ok [INFO] [stdout] test haplotype::tests::test_hom_alt_both_haplotypes_affected ... ok [INFO] [stdout] test meth::tests::test_apply_methylation_conversion_em_seq_full_meth_no_conversion ... ok [INFO] [stdout] test meth::tests::test_failed_molecule_retains_all_should_convert_cytosines ... ok [INFO] [stdout] test meth::tests::test_failure_rate_zero_never_flags_failure ... ok [INFO] [stdout] test meth::tests::test_empty_table_returns_false_everywhere ... ok [INFO] [stdout] test meth::tests::test_contig_methylation_per_haplotype_independent ... ok [INFO] [stdout] test meth::tests::test_apply_methylation_conversion_em_seq_zero_conversion_rate_no_change ... ok [INFO] [stdout] test meth::tests::test_from_haplotype_deletion_bridges_cpg ... ok [INFO] [stdout] test meth::tests::test_apply_methylation_conversion_em_seq_partial_conversion_rate_empirical ... ok [INFO] [stdout] test meth::tests::test_find_reference_cpgs_basic ... ok [INFO] [stdout] test meth::tests::test_find_reference_cpgs_empty_and_short ... ok [INFO] [stdout] test meth::tests::test_find_reference_cpgs_case_insensitive ... ok [INFO] [stdout] test meth::tests::test_from_haplotype_case_insensitive ... ok [INFO] [stdout] test meth::tests::test_from_haplotype_empty_and_short ... ok [INFO] [stdout] test meth::tests::test_apply_methylation_conversion_em_seq_negative_strand_uses_reversed_index ... ok [INFO] [stdout] test meth::tests::test_from_haplotype_matches_reference_for_no_variants_haplotype ... ok [INFO] [stdout] test meth::tests::test_from_haplotype_multi_base_insertion_not_truncated ... ok [INFO] [stdout] test meth::tests::test_is_methylated_strand_selection ... ok [INFO] [stdout] test meth::tests::test_from_haplotype_zero_rate_no_methylation ... ok [INFO] [stdout] test meth::tests::test_is_methylated_out_of_range ... ok [INFO] [stdout] test meth::tests::test_from_haplotype_snp_creates_cpg ... ok [INFO] [stdout] test meth::tests::test_island_mask_none_in_at_rich_or_short ... ok [INFO] [stdout] test meth::tests::test_from_haplotype_snp_destroys_cpg ... ok [INFO] [stdout] test meth::tests::test_from_haplotype_symmetric_by_default ... ok [INFO] [stdout] test meth::tests::test_classify_cpg_contexts_island_shore_open_sea ... ok [INFO] [stdout] test meth::tests::test_island_mask_detects_gc_cpg_dense_block ... ok [INFO] [stdout] test meth::tests::test_walk_no_cpg_and_single_cpg_do_not_panic ... ok [INFO] [stdout] test meth::tests::test_failure_rate_observed_fraction_matches ... ok [INFO] [stdout] test meth::tests::test_zero_genomic_bases_is_noop_but_still_draws_failure ... ok [INFO] [stdout] test methylation_tags::tests::test_alignment_offset_into_contig ... ok [INFO] [stdout] test methylation_tags::tests::test_bottom_strand_ga_is_bisulfite_allowed ... ok [INFO] [stdout] test methylation_tags::tests::test_chg_chh_always_lowercase_in_ym ... ok [INFO] [stdout] test meth::tests::test_from_haplotype_inserted_cpg ... ok [INFO] [stdout] test methylation_tags::tests::test_classify_context_bottom_at_pos_zero_returns_none ... ok [INFO] [stdout] test methylation_tags::tests::test_classify_context_bottom_chg ... ok [INFO] [stdout] test methylation_tags::tests::test_classify_context_bottom_chh ... ok [INFO] [stdout] test methylation_tags::tests::test_classify_context_bottom_cpg ... ok [INFO] [stdout] test methylation_tags::tests::test_classify_context_top_chg ... ok [INFO] [stdout] test methylation_tags::tests::test_classify_context_top_cpg ... ok [INFO] [stdout] test methylation_tags::tests::test_classify_context_top_no_lookahead ... ok [INFO] [stdout] test methylation_tags::tests::test_classify_context_top_not_c ... ok [INFO] [stdout] test meth::tests::test_walk_determinism_fixed_seed ... ok [INFO] [stdout] test methylation_tags::tests::test_deletion_increments_nm_and_emits_caret ... ok [INFO] [stdout] test methylation_tags::tests::test_insertion_increments_nm_and_emits_dots ... ok [INFO] [stdout] test methylation_tags::tests::test_classify_context_top_chh ... ok [INFO] [stdout] test methylation_tags::tests::test_real_mismatch_increments_nm ... ok [INFO] [stdout] test methylation_tags::tests::test_simple_match_full_methylation_top ... ok [INFO] [stdout] test methylation_tags::tests::test_simple_match_zero_methylation_with_conversion_top ... ok [INFO] [stdout] test methylation_tags::tests::test_soft_clip_does_not_count ... ok [INFO] [stdout] test methylation_tags::tests::test_taps_bottom_strand_ga_signals_methylation ... ok [INFO] [stdout] test methylation_tags::tests::test_multiple_mismatches_in_md ... ok [INFO] [stdout] test methylation_tags::tests::test_populate_pair_call_tags_clears_stale_r2_when_se ... ok [INFO] [stdout] test methylation_tags::tests::test_taps_methylated_converted_top ... ok [INFO] [stdout] test methylation_tags::tests::test_taps_unmethylated_preserved_top ... ok [INFO] [stdout] test methylation_tags::tests::test_taps_xm_eq_ym_under_zero_errors ... ok [INFO] [stdout] test output::cpg_truth::tests::test_record_mate_aggregates_multiple_calls_at_same_site ... ok [INFO] [stdout] test methylation_tags::tests::test_ym_diverges_from_xm_under_error_at_methylated_cpg ... ok [INFO] [stdout] test output::cpg_truth::tests::test_record_mate_ct_fragment_methylated_top ... ok [INFO] [stdout] test meth::tests::test_walk_shore_rate_is_intermediate_between_island_and_open_sea ... ok [INFO] [stdout] test output::cpg_truth::tests::test_record_mate_ga_fragment_methylated_bottom ... ok [INFO] [stdout] test output::cpg_truth::tests::test_record_mate_only_counts_cpgs_in_span ... ok [INFO] [stdout] test output::cpg_truth::tests::test_write_bedgraph_format ... ok [INFO] [stdout] test meth::tests::test_from_haplotypes_allele_specific_methylation ... ok [INFO] [stdout] test output::methylation_bedgraph::tests::population_fraction_bedgraph_diploid_all_methylated ... ok [INFO] [stdout] test output::fastq::tests::test_fastq_write_and_read_back ... ok [INFO] [stdout] test output::fastq::tests::test_fastq_write_empty_read ... ok [INFO] [stdout] test output::methylation_bedgraph::tests::population_fraction_bedgraph_drops_haplotypes_with_destroyed_cpg ... ok [INFO] [stdout] test output::methylation_bedgraph::tests::population_fraction_bedgraph_multiple_cpgs ... ok [INFO] [stdout] test meth::tests::test_walk_stationary_mean_matches_rate ... ok [INFO] [stdout] test output::methylation_bedgraph::tests::population_fraction_bedgraph_rounds_non_integer_rate ... ok [INFO] [stdout] test meth::tests::test_walk_autocorrelation_present_with_long_l_absent_with_short_l ... ok [INFO] [stdout] test output::methylation_bedgraph::tests::population_fraction_bedgraph_diploid_hemi ... ok [INFO] [stdout] test output::methylation_bedgraph::tests::population_fraction_bedgraph_no_cpg_emits_only_header ... ok [INFO] [stdout] test output::methylation_bedgraph::tests::population_fraction_bedgraph_respects_haplotype_coordinates_for_indel ... ok [INFO] [stdout] test ploidy::tests::test_multiple_contigs_and_ranges ... ok [INFO] [stdout] test ploidy::tests::test_last_writer_wins ... ok [INFO] [stdout] test ploidy::tests::test_default_ploidy ... ok [INFO] [stdout] test output::methylation_bedgraph::tests::population_fraction_bedgraph_skips_cpg_destroyed_on_every_haplotype ... ok [INFO] [stdout] test output::methylation_bedgraph::tests::write_bedgraph_records_streaming_matches_write_bedgraph ... ok [INFO] [stdout] test ploidy::tests::test_range_override ... ok [INFO] [stdout] test read::tests::test_accepts_when_lowercase_below_threshold ... ok [INFO] [stdout] test read::tests::test_adapter_cigar_softclip ... ok [INFO] [stdout] test read::tests::test_cigar_high_positions ... ok [INFO] [stdout] test read::tests::test_cigar_single_base ... ok [INFO] [stdout] test read::tests::test_cigar_with_adapter_and_deletion ... ok [INFO] [stdout] test read::tests::test_cigar_with_adapter_softclip_forward ... ok [INFO] [stdout] test read::tests::test_cigar_with_adapter_softclip_negative_strand ... ok [INFO] [stdout] test meth::tests::test_walk_island_hypomethylated_relative_to_open_sea ... ok [INFO] [stdout] test read::tests::test_cigar_all_adapter ... ok [INFO] [stdout] test read::tests::test_cigar_with_insertion ... ok [INFO] [stdout] test output::cpg_truth::tests::test_record_mate_ga_excludes_site_when_bottom_c_falls_outside_span ... ok [INFO] [stdout] test ploidy::tests::test_whole_contig_override ... ok [INFO] [stdout] test read::tests::test_directional_r2_of_ga_fragment_is_revcomp_of_c2t_bottom ... ok [INFO] [stdout] test read::tests::test_directional_r2_of_ct_fragment_is_revcomp_of_c2t_top ... ok [INFO] [stdout] test read::tests::test_generate_pe_read_pair ... ok [INFO] [stdout] test read::tests::test_generate_read_pair_with_em_seq_converts_forward_r1 ... ok [INFO] [stdout] test read::tests::test_generate_read_pair_with_em_seq_reverse_strand_yields_ga_conversion_type ... ok [INFO] [stdout] test read::tests::test_cigar_all_match ... ok [INFO] [stdout] test read::tests::test_cigar_with_deletion ... ok [INFO] [stdout] test read::tests::test_cigar_with_insertion_and_deletion ... ok [INFO] [stdout] test read::tests::test_generate_se_read ... ok [INFO] [stdout] test read::tests::test_quality_scores_correct_length ... ok [INFO] [stdout] test read::tests::test_rejects_before_applying_errors_to_r1 ... ok [INFO] [stdout] test read_naming::tests::test_cross_format_rejection ... ok [INFO] [stdout] test read_naming::tests::test_encoded_se_name ... ok [INFO] [stdout] test read::tests::test_simple_name_mode ... ok [INFO] [stdout] test read_naming::tests::test_parse_invalid_names ... ok [INFO] [stdout] test read_naming::tests::test_parse_pe_roundtrip ... ok [INFO] [stdout] test read_naming::tests::test_parse_pe_with_colon_in_contig ... ok [INFO] [stdout] test read_naming::tests::test_parse_se_roundtrip ... ok [INFO] [stdout] test read_naming::tests::test_encoded_pe_name ... ok [INFO] [stdout] test read_naming::tests::test_parse_pos_strand ... ok [INFO] [stdout] test read_naming::tests::test_short_fragment_encodes_adapter_boundary ... ok [INFO] [stdout] test read_naming::tests::test_simple_name ... ok [INFO] [stdout] test seed::tests::test_compute_seed_different_inputs ... ok [INFO] [stdout] test seed::tests::test_compute_seed_known_value ... ok [INFO] [stdout] test seed::tests::test_derive_seed_deterministic ... ok [INFO] [stdout] test seed::tests::test_derive_seed_varies_with_namespace ... ok [INFO] [stdout] test seed::tests::test_derive_seed_varies_with_parent ... ok [INFO] [stdout] test seed::tests::test_resolve_seed_derived ... ok [INFO] [stdout] test seed::tests::test_resolve_seed_explicit ... ok [INFO] [stdout] test sequence_dict::tests::test_get_by_index ... ok [INFO] [stdout] test sequence_dict::tests::test_get_by_name ... ok [INFO] [stdout] test sequence_dict::tests::test_index_by_str ... ok [INFO] [stdout] test read::tests::test_rejects_when_r1_exceeds_max_n_frac ... ok [INFO] [stdout] test sequence_dict::tests::test_index_by_usize ... ok [INFO] [stdout] test error_model::illumina::tests::test_min_gt_max_panics - should panic ... ok [INFO] [stdout] test fasta::tests::test_load_contig_rejects_unknown_byte ... ok [INFO] [stdout] test sequence_dict::tests::test_len_and_is_empty ... ok [INFO] [stdout] test fasta::tests::test_load_contig_unknown ... ok [INFO] [stdout] test error_model::illumina::tests::test_zero_read_length_panics - should panic ... ok [INFO] [stdout] test sequence_dict::tests::test_iter ... ok [INFO] [stdout] test meth::tests::test_methylation_model_validate_rejects_bad_fields ... ok [INFO] [stdout] test ploidy::tests::test_parse_errors ... ok [INFO] [stdout] test meth::tests::test_from_haplotype_rejects_rate_above_one - should panic ... ok [INFO] [stdout] test output::methylation_bedgraph::tests::population_fraction_bedgraph_errors_when_haplotypes_len_mismatches_methylation ... ok [INFO] [stdout] test vcf::genotype::tests::test_parse_haploid ... ok [INFO] [stdout] test read_naming::tests::test_formatter_rejects_at_in_contig_se - should panic ... ok [INFO] [stdout] test sequence_dict::tests::test_total_length ... ok [INFO] [stdout] test sequence_dict::tests::test_names ... ok [INFO] [stdout] test vcf::genotype::tests::test_parse_diploid_hom_alt ... ok [INFO] [stdout] test vcf::genotype::tests::test_parse_diploid_hom_ref ... ok [INFO] [stdout] test vcf::genotype::tests::test_parse_diploid_unphased_het ... ok [INFO] [stdout] test vcf::genotype::tests::test_parse_missing_alleles ... ok [INFO] [stdout] test read_naming::tests::test_formatter_rejects_double_colon_in_contig_pe - should panic ... ok [INFO] [stdout] test vcf::methylation::alt_span_cursor_tests::coordinate_after_last_span_is_reference ... ok [INFO] [stdout] test vcf::genotype::tests::test_parse_triploid ... ok [INFO] [stdout] test vcf::genotype::tests::test_parse_diploid_phased_het ... ok [INFO] [stdout] test vcf::methylation::alt_span_cursor_tests::no_spans_is_always_reference ... ok [INFO] [stdout] test vcf::methylation::alt_span_cursor_tests::adjacent_spans_resolve_to_their_own_variants ... ok [INFO] [stdout] test vcf::methylation::alt_span_cursor_tests::coordinate_before_first_span_is_reference ... ok [INFO] [stdout] test vcf::methylation::alt_span_cursor_tests::coordinate_between_spans_is_reference ... ok [INFO] [stdout] test vcf::genotype::tests::test_variant_record_allele_bases ... ok [INFO] [stdout] test vcf::methylation::alt_span_cursor_tests::one_query_can_skip_several_spans ... ok [INFO] [stdout] test sequence_dict::tests::test_index_by_str_unknown - should panic ... ok [INFO] [stdout] test sequence_dict::tests::test_index_by_usize_out_of_bounds - should panic ... ok [INFO] [stdout] test vcf::methylation::alt_span_cursor_tests::repeating_a_coordinate_gives_the_same_source ... ok [INFO] [stdout] test meth::tests::test_from_haplotype_rejects_nan_rate - should panic ... ok [INFO] [stdout] test vcf::genotype::tests::test_parse_empty_errors ... ok [INFO] [stdout] test vcf::genotype::tests::test_parse_invalid_allele_errors ... ok [INFO] [stdout] test vcf::methylation::alt_span_cursor_tests::span_start_is_inclusive_and_end_is_exclusive ... ok [INFO] [stdout] test vcf::methylation::alt_span_cursor_tests::variant_source_reports_the_span_start ... ok [INFO] [stdout] test vcf::methylation::reader_error_tests::variant_record_dot_when_owned_cpgs_expected_is_rejected ... ok [INFO] [stdout] test vcf::methylation::reader_error_tests::standalone_record_with_too_few_mb_entries_is_rejected ... ok [INFO] [stdout] test vcf::methylation::reader_error_tests::standalone_record_with_wrong_mt_entry_count_is_rejected ... ok [INFO] [stdout] test vcf::methylation::fuzz_tests::roundtrip_triploid_with_phased_variants ... ok [INFO] [stdout] test vcf::methylation::reader_error_tests::malformed_record_with_too_few_columns_is_rejected ... ok [INFO] [stdout] test vcf::methylation::reader_error_tests::round_trip_disambiguates_two_variants_sharing_pos ... ok [INFO] [stdout] test vcf::methylation::reader_error_tests::standalone_record_with_pos_zero_is_rejected ... ok [INFO] [stdout] test vcf::methylation::reader_error_tests::haploid_variant_free_contig_writes_single_entry_mt_mb ... ok [INFO] [stdout] test vcf::methylation::reader_error_tests::variant_record_with_too_few_mb_entries_is_rejected ... ok [INFO] [stdout] test vcf::methylation::reader_error_tests::variant_record_with_wrong_mt_entry_count_is_rejected ... ok [INFO] [stdout] test vcf::methylation::fuzz_tests::standalone_cpg_downstream_of_indel_round_trips_per_haplotype ... ok [INFO] [stdout] test vcf::methylation::fuzz_tests::roundtrip_random_bitmap_with_phased_variants ... ok [INFO] [stdout] test vcf::methylation::record_probe_tests::header_only_no_records_returns_false ... ok [INFO] [stdout] test vcf::methylation::reader_error_tests::invalid_mtmb_character_in_standalone_record_is_rejected ... ok [INFO] [stdout] test read_naming::tests::test_parse_se_with_colon_in_contig ... ok [INFO] [stdout] test vcf::methylation::reader_error_tests::variant_record_mtmb_length_mismatch_is_rejected ... ok [INFO] [stdout] test vcf::methylation::record_probe_tests::header_and_record_with_mt_mb_returns_true ... ok [INFO] [stdout] test seed::tests::test_compute_seed_deterministic ... ok [INFO] [stdout] test vcf::methylation::reader_error_tests::invalid_utf8_body_is_rejected ... ok [INFO] [stdout] test vcf::methylation::record_probe_tests::header_with_neither_returns_false ... ok [INFO] [stdout] test vcf::methylation::record_probe_tests::header_with_only_mt_returns_false ... ok [INFO] [stdout] test vcf::methylation::record_probe_tests::no_mt_mb_header_does_not_read_body ... ok [INFO] [stdout] test vcf::methylation::record_probe_tests::header_with_only_mb_returns_false ... ok [INFO] [stdout] test vcf::methylation::writer_tests::writes_variant_record_with_mt_mb_for_alt_cpg ... ok [INFO] [stdout] test vcf::methylation::record_probe_tests::record_without_mt_mb_format_returns_false ... ok [INFO] [stdout] test vcf::tests::parse_variants_by_contig_skips_contigs_with_no_alt_records ... ok [INFO] [stdout] test vcf::tests::parse_variants_by_contig_partitions_and_sorts ... ok [INFO] [stdout] test vcf::tests::validate_vcf_sample_tolerates_duplicate_info_headers ... ok [INFO] [stdout] test vcf::tests::parse_variants_by_contig_resolves_haploid_ploidy_from_homref_only_records ... ok [INFO] [stdout] test vcf::methylation::record_probe_tests::variant_record_with_mt_mb_returns_true ... ok [INFO] [stdout] test vcf::tests::parse_variants_by_contig_tolerates_duplicate_info_headers ... ok [INFO] [stdout] test vcf::methylation::writer_tests::writes_methylation_only_record_for_reference_cpg ... ok [INFO] [stdout] test vcf::writer::tests::gz_path_writes_bgzf_with_eof_block ... ok [INFO] [stdout] test vcf::tests::parse_variants_by_contig_tolerates_duplicate_format_filter_contig ... ok [INFO] [stdout] test vcf::writer::tests::is_bgzf_path_detects_gz_and_bgz_case_insensitively ... ok [INFO] [stdout] test vcf::tests::structured_header_key_extracts_directive_and_id ... ok [INFO] [stdout] test vcf::tests::parse_variants_by_contig_resolves_triploid_ploidy ... ok [INFO] [stdout] test vcf::writer::tests::plain_path_writes_uncompressed_text ... ok [INFO] [stdout] test vcf::methylation::roundtrip_tests::standalone_record_round_trip ... ok [INFO] [stdout] test meth::tests::test_walk_hemi_rate_produces_hemimethylation ... ok [INFO] [stdout] test vcf::methylation::fuzz_tests::roundtrip_random_bitmap_no_variants ... ok [INFO] [stdout] [INFO] [stdout] test result: ok. 314 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.30s [INFO] [stdout] [INFO] [stderr] Running unittests src/main.rs (/opt/rustwide/target/debug/deps/holodeck-3e3ce2482e26145b) [INFO] [stderr] Running tests/test_eval.rs (/opt/rustwide/target/debug/deps/test_eval-f2fd4b49555b3caf) [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] [stdout] [INFO] [stdout] running 4 tests [INFO] [stdout] test test_eval_perfect_alignment_paired_end ... ok [INFO] [stdout] test test_eval_all_unmapped ... ok [INFO] [stdout] test test_eval_wiggle_parameter ... ok [INFO] [stdout] test test_eval_perfect_alignment ... ok [INFO] [stdout] [INFO] [stdout] test result: ok. 4 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.18s [INFO] [stdout] [INFO] [stderr] Running tests/test_methylate.rs (/opt/rustwide/target/debug/deps/test_methylate-a0efb4a6a16e6e07) [INFO] [stdout] [INFO] [stdout] running 13 tests [INFO] [stdout] test methylate_produces_loadable_vcf_with_mt_mb ... ok [INFO] [stdout] test methylate_command_runs_on_empty_reference ... ok [INFO] [stdout] test methylate_writes_bedgraph_when_requested ... ok [INFO] [stdout] test methylate_applies_variants_from_input_vcf ... ok [INFO] [stdout] test methylate_seed_determinism ... ok [INFO] [stdout] test methylate_rejects_methylation_rate_above_one ... ok [INFO] [stdout] test methylate_rejects_nonfinite_methylation_rate ... ok [INFO] [stdout] test methylate_rejects_negative_methylation_rate ... ok [INFO] [stdout] test methylate_rejects_nonpositive_correlation_length ... ok [INFO] [stdout] test methylate_then_simulate_propagates_methylation_to_golden_bam ... ok [INFO] [stdout] test methylate_rejects_sample_without_vcf ... ok [INFO] [stdout] test methylate_context_flags_produce_island_hypomethylation ... ok [INFO] [stdout] test methylate_default_is_no_longer_fully_methylated ... ok [INFO] [stdout] [INFO] [stdout] test result: ok. 13 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.62s [INFO] [stdout] [INFO] [stderr] Running tests/test_methylation_classifier.rs (/opt/rustwide/target/debug/deps/test_methylation_classifier-6e87ec1b862c170b) [INFO] [stdout] [INFO] [stdout] running 20 tests [INFO] [stdout] test case_06_deletion_removes_reference_cpg_hom_alt ... ok [INFO] [stdout] test case_09_multi_allelic_each_haplotype_carries_different_alt ... ok [INFO] [stdout] test case_12_overlapping_variants_rejected ... ok [INFO] [stdout] test case_06_deletion_removes_reference_cpg_het ... ok [INFO] [stdout] test case_01_insertion_creates_cpg_at_downstream_boundary ... ok [INFO] [stdout] test case_13_hemizygous_single_haplotype ... ok [INFO] [stdout] test case_11_unphased_gt_rejected ... ok [INFO] [stdout] test case_03_deletion_juxtaposes_ref_c_and_ref_g ... ok [INFO] [stdout] test case_02_snp_creates_g_at_upstream_boundary_makes_variant_own_cpg ... ok [INFO] [stdout] test case_05_insertion_splits_reference_cpg ... ok [INFO] [stdout] test empty_reference_produces_no_records ... ok [INFO] [stdout] test case_10_homozygous_alt_symmetric_state ... ok [INFO] [stdout] test case_04_snp_destroys_reference_cpg ... ok [INFO] [stdout] test case_08_variant_destroys_then_recreates_cpg ... ok [INFO] [stdout] test phased_ref_span_overlap_on_disjoint_haplotypes_is_allowed ... ok [INFO] [stdout] test phased_ref_span_overlap_sharing_a_haplotype_is_rejected ... ok [INFO] [stdout] test standalone_and_on_variant_at_same_position_both_emitted_in_order ... ok [INFO] [stdout] test non_adjacent_overlap_on_shared_haplotype_is_rejected ... ok [INFO] [stdout] test case_07_adjacent_snps_jointly_form_cpg_upstream_owns ... ok [INFO] [stdout] test reference_cpgs_no_variants_all_standalone ... ok [INFO] [stdout] [INFO] [stdout] test result: ok. 20 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.01s [INFO] [stdout] [INFO] [stderr] Running tests/test_mutate.rs (/opt/rustwide/target/debug/deps/test_mutate-f14ebe899bff3e2e) [INFO] [stdout] [INFO] [stdout] running 7 tests [INFO] [stdout] test test_mutate_with_bed_targets ... ok [INFO] [stdout] test test_mutate_ploidy_override ... ok [INFO] [stdout] test test_mutate_seed_reproducibility ... ok [INFO] [stdout] test test_mutate_basic ... ok [INFO] [stdout] test test_mutate_rates_respected ... ok [INFO] [stdout] test test_mutate_snp_only ... ok [INFO] [stderr] Running tests/test_simulate.rs (/opt/rustwide/target/debug/deps/test_simulate-fd84fe6e78bc477a) [INFO] [stdout] test test_mutate_never_emits_ambiguity_resolved_ref_alleles ... ok [INFO] [stdout] [INFO] [stdout] test result: ok. 7 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.05s [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] running 45 tests [INFO] [stdout] test test_multi_sample_vcf_with_correct_sample_works ... ok [INFO] [stdout] test test_output_directory_does_not_exist_fails ... ok [INFO] [stdout] test test_multi_sample_vcf_without_sample_flag_fails ... ok [INFO] [stdout] test test_adapter_content_short_fragments ... ok [INFO] [stdout] test test_golden_bam_read_group_uses_vcf_sample_name ... ok [INFO] [stdout] test test_sample_without_vcf_fails ... ok [INFO] [stdout] test test_simulate_basic_pe ... ok [INFO] [stdout] test test_simulate_emits_only_acgt_with_iupac_reference ... ok [INFO] [stdout] test test_simulate_golden_bam ... ok [INFO] [stdout] test test_simulate_max_n_frac_zero_avoids_ambiguous_regions ... ok [INFO] [stdout] test test_simulate_reads_overlap_targets ... ok [INFO] [stdout] test test_simulate_rejects_unresolved_ambiguity_bytes ... ok [INFO] [stdout] test test_simulate_reproducible_ambiguity_resolution ... ok [INFO] [stdout] test test_fragment_length_identifies_adapter_boundary ... ok [INFO] [stdout] test test_simulate_seed_reproducibility ... ok [INFO] [stdout] test test_simulate_simple_names ... ok [INFO] [stdout] test test_simulate_single_end ... ok [INFO] [stdout] test test_simulate_sparse_targets_produce_expected_reads ... ok [INFO] [stdout] test test_simulate_then_eval ... ok [INFO] [stdout] test test_simulate_very_short_contig ... ok [INFO] [stdout] test test_simulate_with_bed_targets ... ok [INFO] [stdout] test test_single_sample_vcf_without_sample_flag_works ... ok [INFO] [stdout] test test_simulate_error_rate_introduces_mismatches ... ok [INFO] [stdout] test test_simulate_vcf_plus_bed ... ok [INFO] [stdout] test test_phased_variant_cluster_trans ... ok [INFO] [stdout] test test_multi_contig_read_distribution ... ok [INFO] [stdout] test test_mutate_then_simulate ... ok [INFO] [stdout] test test_phased_variant_cluster_cis ... ok [INFO] [stdout] test test_wrong_sample_name_fails ... ok [INFO] [stdout] test test_phased_snp_and_deletion_cluster ... ok [INFO] [stdout] test test_phased_snp_and_insertion_cluster ... ok [INFO] [stdout] test test_insertion_pileup ... ok [INFO] [stdout] test test_snp_hom_alt_pileup ... ok [INFO] [stdout] test test_multiple_variants_same_contig ... ok [INFO] [stdout] test test_zero_error_rate_reads_match_reference ... ok [INFO] [stdout] test test_wgs_coverage_accuracy ... ok [INFO] [stdout] test test_deletion_pileup ... ok [INFO] [stdout] test test_targeted_coverage_matches_requested ... ok [INFO] [stdout] test test_het_insertion_pileup ... ok [INFO] [stdout] test test_unphased_variant_cluster ... ok [INFO] [stdout] test test_multi_allelic_site ... ok [INFO] [stdout] test test_het_deletion_pileup ... ok [INFO] [stdout] test test_snp_phased_het_pileup ... ok [INFO] [stdout] test test_simulate_multiple_contigs_with_variants ... ok [INFO] [stdout] test test_unphased_het_snp_pileup ... ok [INFO] [stdout] [INFO] [stdout] test result: ok. 45 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 19.38s [INFO] [stdout] [INFO] [stderr] Running tests/test_simulate_meth.rs (/opt/rustwide/target/debug/deps/test_simulate_meth-7b8a157d31a88af5) [INFO] [stdout] [INFO] [stdout] running 39 tests [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Holodeck by Fulcrum Genomics - https://github.com/fg-labs/holodeck [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Executing: /opt/rustwide/target/debug/holodeck methylate --reference /tmp/.tmpcSwPcN/ref.fa --output /tmp/.tmpcSwPcN/meth.vcf.gz --methylation-rate-island 1 --methylation-rate-shore 1 --methylation-rate-open-sea 1 --methylation-correlation-length-island 1 --methylation-correlation-length-shore 1 --methylation-correlation-length-open-sea 1 --hemimethylation-rate 0 --seed 42 [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck_lib::commands::methylate] Using random seed: 42 [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck_lib::commands::methylate] Wrote methylation VCF to /tmp/.tmpcSwPcN/meth.vcf.gz [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Successfully completed execution in 0m:00s. [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Holodeck by Fulcrum Genomics - https://github.com/fg-labs/holodeck [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Executing: /opt/rustwide/target/debug/holodeck methylate --reference /tmp/.tmpToXz3Y/ref.fa --output /tmp/.tmpToXz3Y/meth.vcf.gz --methylation-rate-island 0.5 --methylation-rate-shore 0.5 --methylation-rate-open-sea 0.5 --methylation-correlation-length-island 1 --methylation-correlation-length-shore 1 --methylation-correlation-length-open-sea 1 --hemimethylation-rate 0 --seed 9876 [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck_lib::commands::methylate] Using random seed: 9876 [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Holodeck by Fulcrum Genomics - https://github.com/fg-labs/holodeck [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Executing: /opt/rustwide/target/debug/holodeck methylate --reference /tmp/.tmpV5sx69/ref.fa --output /tmp/.tmpV5sx69/meth.vcf.gz --methylation-rate-island 1 --methylation-rate-shore 1 --methylation-rate-open-sea 1 --methylation-correlation-length-island 1 --methylation-correlation-length-shore 1 --methylation-correlation-length-open-sea 1 --hemimethylation-rate 0 --seed 42 [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck_lib::commands::methylate] Using random seed: 42 [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck_lib::commands::methylate] Wrote methylation VCF to /tmp/.tmpToXz3Y/meth.vcf.gz [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Successfully completed execution in 0m:00s. [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck_lib::commands::methylate] Wrote methylation VCF to /tmp/.tmpV5sx69/meth.vcf.gz [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Successfully completed execution in 0m:00s. [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Holodeck by Fulcrum Genomics - https://github.com/fg-labs/holodeck [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Executing: /opt/rustwide/target/debug/holodeck methylate --reference /tmp/.tmpIeDl5n/ref.fa --output /tmp/.tmpIeDl5n/meth.vcf.gz --methylation-rate-island 1 --methylation-rate-shore 1 --methylation-rate-open-sea 1 --methylation-correlation-length-island 1 --methylation-correlation-length-shore 1 --methylation-correlation-length-open-sea 1 --hemimethylation-rate 0 --seed 42 [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck_lib::commands::methylate] Using random seed: 42 [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Holodeck by Fulcrum Genomics - https://github.com/fg-labs/holodeck [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Executing: /opt/rustwide/target/debug/holodeck methylate --reference /tmp/.tmp1QSzVA/ref.fa --output /tmp/.tmp1QSzVA/meth.vcf.gz --methylation-rate-island 0 --methylation-rate-shore 0 --methylation-rate-open-sea 0 --methylation-correlation-length-island 1 --methylation-correlation-length-shore 1 --methylation-correlation-length-open-sea 1 --hemimethylation-rate 0 --seed 42 [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck_lib::commands::methylate] Using random seed: 42 [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck_lib::commands::methylate] Wrote methylation VCF to /tmp/.tmpIeDl5n/meth.vcf.gz [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Successfully completed execution in 0m:00s. [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Holodeck by Fulcrum Genomics - https://github.com/fg-labs/holodeck [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Holodeck by Fulcrum Genomics - https://github.com/fg-labs/holodeck [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Executing: /opt/rustwide/target/debug/holodeck methylate --reference /tmp/.tmpajS50h/ref.fa --output /tmp/.tmpajS50h/meth.vcf.gz --methylation-rate-island 0 --methylation-rate-shore 0 --methylation-rate-open-sea 0 --methylation-correlation-length-island 1 --methylation-correlation-length-shore 1 --methylation-correlation-length-open-sea 1 --hemimethylation-rate 0 --seed 42 [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck_lib::commands::methylate] Using random seed: 42 [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Executing: /opt/rustwide/target/debug/holodeck methylate --reference /tmp/.tmp5Bu9cj/ref.fa --output /tmp/.tmp5Bu9cj/meth.vcf.gz --methylation-rate-island 0 --methylation-rate-shore 0 --methylation-rate-open-sea 0 --methylation-correlation-length-island 1 --methylation-correlation-length-shore 1 --methylation-correlation-length-open-sea 1 --hemimethylation-rate 0 --seed 42 [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck_lib::commands::methylate] Using random seed: 42 [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Holodeck by Fulcrum Genomics - https://github.com/fg-labs/holodeck [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Executing: /opt/rustwide/target/debug/holodeck methylate --reference /tmp/.tmpaCV2qn/ref.fa --output /tmp/.tmpaCV2qn/meth.vcf.gz --methylation-rate-island 0.5 --methylation-rate-shore 0.5 --methylation-rate-open-sea 0.5 --methylation-correlation-length-island 1 --methylation-correlation-length-shore 1 --methylation-correlation-length-open-sea 1 --hemimethylation-rate 0 --seed 42 [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck_lib::commands::methylate] Wrote methylation VCF to /tmp/.tmp1QSzVA/meth.vcf.gz [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck_lib::commands::methylate] Using random seed: 42 [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Successfully completed execution in 0m:00s. [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Holodeck by Fulcrum Genomics - https://github.com/fg-labs/holodeck [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Executing: /opt/rustwide/target/debug/holodeck methylate --reference /tmp/.tmpsN2iqr/ref.fa --output /tmp/.tmpsN2iqr/meth.vcf.gz --methylation-rate-island 1 --methylation-rate-shore 1 --methylation-rate-open-sea 1 --methylation-correlation-length-island 1 --methylation-correlation-length-shore 1 --methylation-correlation-length-open-sea 1 --hemimethylation-rate 0 --seed 42 [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck_lib::commands::methylate] Using random seed: 42 [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck_lib::commands::methylate] Wrote methylation VCF to /tmp/.tmpajS50h/meth.vcf.gz [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Successfully completed execution in 0m:00s. [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck_lib::commands::methylate] Wrote methylation VCF to /tmp/.tmpaCV2qn/meth.vcf.gz [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Successfully completed execution in 0m:00s. [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck_lib::commands::methylate] Wrote methylation VCF to /tmp/.tmpsN2iqr/meth.vcf.gz [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Successfully completed execution in 0m:00s. [INFO] [stdout] test matrix_no_vcf_no_mode_is_variants_only ... ok [INFO] [stdout] test test_em_seq_full_methylation_preserves_c ... ok [INFO] [stdout] test test_cpg_truth_bedgraph_full_methylation_emits_only_methylated_calls ... ok [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Holodeck by Fulcrum Genomics - https://github.com/fg-labs/holodeck [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Executing: /opt/rustwide/target/debug/holodeck methylate --reference /tmp/.tmpZSsqls/ref.fa --output /tmp/.tmpZSsqls/meth.vcf.gz --methylation-rate-island 1 --methylation-rate-shore 1 --methylation-rate-open-sea 1 --methylation-correlation-length-island 1 --methylation-correlation-length-shore 1 --methylation-correlation-length-open-sea 1 --hemimethylation-rate 0 --seed 42 [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck_lib::commands::methylate] Using random seed: 42 [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck_lib::commands::methylate] Wrote methylation VCF to /tmp/.tmpZSsqls/meth.vcf.gz [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Successfully completed execution in 0m:00s. [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck_lib::commands::methylate] Wrote methylation VCF to /tmp/.tmp5Bu9cj/meth.vcf.gz [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Successfully completed execution in 0m:00s. [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Holodeck by Fulcrum Genomics - https://github.com/fg-labs/holodeck [INFO] [stdout] test test_cpg_truth_bedgraph_zero_methylation_emits_only_unmethylated_calls ... ok [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Executing: /opt/rustwide/target/debug/holodeck methylate --reference /tmp/.tmp1BrP3V/ref.fa --output /tmp/.tmp1BrP3V/meth.vcf.gz --methylation-rate-island 0 --methylation-rate-shore 0 --methylation-rate-open-sea 0 --methylation-correlation-length-island 1 --methylation-correlation-length-shore 1 --methylation-correlation-length-open-sea 1 --hemimethylation-rate 0 --seed 12345 [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Holodeck by Fulcrum Genomics - https://github.com/fg-labs/holodeck [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Executing: /opt/rustwide/target/debug/holodeck methylate --reference /tmp/.tmpWdBKUI/ref.fa --output /tmp/.tmpWdBKUI/meth.vcf.gz --methylation-rate-island 0 --methylation-rate-shore 0 --methylation-rate-open-sea 0 --methylation-correlation-length-island 1 --methylation-correlation-length-shore 1 --methylation-correlation-length-open-sea 1 --hemimethylation-rate 0 --seed 42 [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck_lib::commands::methylate] Using random seed: 42 [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck_lib::commands::methylate] Wrote methylation VCF to /tmp/.tmpWdBKUI/meth.vcf.gz [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Successfully completed execution in 0m:00s. [INFO] [stdout] test cpg_truth_bedgraph_works_with_matrix_true_true_cell ... ok [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck_lib::commands::methylate] Using random seed: 12345 [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Holodeck by Fulcrum Genomics - https://github.com/fg-labs/holodeck [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Executing: /opt/rustwide/target/debug/holodeck methylate --reference /tmp/.tmpx1Dexu/ref.fa --output /tmp/.tmpx1Dexu/meth.vcf.gz --methylation-rate-island 1 --methylation-rate-shore 1 --methylation-rate-open-sea 1 --methylation-correlation-length-island 1 --methylation-correlation-length-shore 1 --methylation-correlation-length-open-sea 1 --hemimethylation-rate 0 --seed 42 --vcf /tmp/.tmpx1Dexu/variants.vcf [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck_lib::commands::methylate] Using random seed: 42 [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck_lib::commands::methylate] Wrote methylation VCF to /tmp/.tmpx1Dexu/meth.vcf.gz [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Successfully completed execution in 0m:00s. [INFO] [stdout] test test_cpg_truth_bedgraph_requires_methylation_mode ... ok [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Holodeck by Fulcrum Genomics - https://github.com/fg-labs/holodeck [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Executing: /opt/rustwide/target/debug/holodeck methylate --reference /tmp/.tmpQmR1Vv/ref.fa --output /tmp/.tmpQmR1Vv/meth.vcf.gz --methylation-rate-island 0 --methylation-rate-shore 0 --methylation-rate-open-sea 0 --methylation-correlation-length-island 1 --methylation-correlation-length-shore 1 --methylation-correlation-length-open-sea 1 --hemimethylation-rate 0 --seed 42 [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck_lib::commands::methylate] Using random seed: 42 [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Holodeck by Fulcrum Genomics - https://github.com/fg-labs/holodeck [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Executing: /opt/rustwide/target/debug/holodeck methylate --reference /tmp/.tmpyn4VBw/ref.fa --output /tmp/.tmpyn4VBw/meth.vcf.gz --methylation-rate-island 0.5 --methylation-rate-shore 0.5 --methylation-rate-open-sea 0.5 --methylation-correlation-length-island 1 --methylation-correlation-length-shore 1 --methylation-correlation-length-open-sea 1 --hemimethylation-rate 0 --seed 42 [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck_lib::commands::methylate] Using random seed: 42 [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck_lib::commands::methylate] Wrote methylation VCF to /tmp/.tmpQmR1Vv/meth.vcf.gz [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Successfully completed execution in 0m:00s. [INFO] [stdout] test test_em_seq_full_conversion_eliminates_c ... ok [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck_lib::commands::methylate] Wrote methylation VCF to /tmp/.tmp1BrP3V/meth.vcf.gz [INFO] [stdout] test matrix_no_vcf_no_mode_is_byte_identical_across_runs ... ok [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Holodeck by Fulcrum Genomics - https://github.com/fg-labs/holodeck [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Holodeck by Fulcrum Genomics - https://github.com/fg-labs/holodeck [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Executing: /opt/rustwide/target/debug/holodeck methylate --reference /tmp/.tmp0ame1C/ref.fa --output /tmp/.tmp0ame1C/meth.vcf.gz --methylation-rate-island 1 --methylation-rate-shore 1 --methylation-rate-open-sea 1 --methylation-correlation-length-island 1 --methylation-correlation-length-shore 1 --methylation-correlation-length-open-sea 1 --hemimethylation-rate 0 --seed 42 [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck_lib::commands::methylate] Using random seed: 42 [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck_lib::commands::methylate] Wrote methylation VCF to /tmp/.tmpyn4VBw/meth.vcf.gz [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Holodeck by Fulcrum Genomics - https://github.com/fg-labs/holodeck [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Successfully completed execution in 0m:00s. [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Successfully completed execution in 0m:00s. [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Executing: /opt/rustwide/target/debug/holodeck methylate --reference /tmp/.tmpPwQ4Xd/ref.fa --output /tmp/.tmpPwQ4Xd/meth.vcf.gz --methylation-rate-island 0.5 --methylation-rate-shore 0.5 --methylation-rate-open-sea 0.5 --methylation-correlation-length-island 1 --methylation-correlation-length-shore 1 --methylation-correlation-length-open-sea 1 --hemimethylation-rate 0 --seed 42 [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck_lib::commands::methylate] Using random seed: 42 [INFO] [stdout] test test_cpg_truth_bedgraph_taps_intermediate_methylation_yields_mixed_rates ... ok [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Executing: /opt/rustwide/target/debug/holodeck methylate --reference /tmp/.tmpRFeurK/ref.fa --output /tmp/.tmpRFeurK/meth.vcf.gz --methylation-rate-island 1 --methylation-rate-shore 1 --methylation-rate-open-sea 1 --methylation-correlation-length-island 1 --methylation-correlation-length-shore 1 --methylation-correlation-length-open-sea 1 --hemimethylation-rate 0 --seed 42 [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck_lib::commands::methylate] Using random seed: 42 [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Holodeck by Fulcrum Genomics - https://github.com/fg-labs/holodeck [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Holodeck by Fulcrum Genomics - https://github.com/fg-labs/holodeck [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Executing: /opt/rustwide/target/debug/holodeck methylate --reference /tmp/.tmpvEpiAU/ref.fa --output /tmp/.tmpvEpiAU/meth.vcf.gz --methylation-rate-island 0 --methylation-rate-shore 0 --methylation-rate-open-sea 0 --methylation-correlation-length-island 1 --methylation-correlation-length-shore 1 --methylation-correlation-length-open-sea 1 --hemimethylation-rate 0 --seed 42 [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck_lib::commands::methylate] Wrote methylation VCF to /tmp/.tmpPwQ4Xd/meth.vcf.gz [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Successfully completed execution in 0m:00s. [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck_lib::commands::methylate] Using random seed: 42 [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck] Executing: /opt/rustwide/target/debug/holodeck methylate --reference /tmp/.tmp3Q7AMi/ref.fa --output /tmp/.tmp3Q7AMi/meth.vcf.gz --methylation-rate-island 0 --methylation-rate-shore 0 --methylation-rate-open-sea 0 --methylation-correlation-length-island 1 --methylation-correlation-length-shore 1 --methylation-correlation-length-open-sea 1 --hemimethylation-rate 0 --seed 42 [INFO] [stderr] [2026-10-06 14:54:09 INFO holodeck_lib::commands::methylate] Using random seed: 42 [INFO] [stdout] test test_em_seq_and_taps_produce_different_output ... ok [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck_lib::commands::methylate] Wrote methylation VCF to /tmp/.tmpvEpiAU/meth.vcf.gz [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck] Successfully completed execution in 0m:00s. [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck_lib::commands::methylate] Wrote methylation VCF to /tmp/.tmp3Q7AMi/meth.vcf.gz [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck] Successfully completed execution in 0m:00s. [INFO] [stdout] test test_em_seq_partial_conversion_rate ... ok [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck_lib::commands::methylate] Wrote methylation VCF to /tmp/.tmpRFeurK/meth.vcf.gz [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck] Holodeck by Fulcrum Genomics - https://github.com/fg-labs/holodeck [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck] Executing: /opt/rustwide/target/debug/holodeck methylate --reference /tmp/.tmpvmGnCE/ref.fa --output /tmp/.tmpvmGnCE/meth.vcf.gz --methylation-rate-island 1 --methylation-rate-shore 1 --methylation-rate-open-sea 1 --methylation-correlation-length-island 1 --methylation-correlation-length-shore 1 --methylation-correlation-length-open-sea 1 --hemimethylation-rate 0 --seed 42 [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck_lib::commands::methylate] Using random seed: 42 [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck] Holodeck by Fulcrum Genomics - https://github.com/fg-labs/holodeck [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck] Executing: /opt/rustwide/target/debug/holodeck methylate --reference /tmp/.tmpbOuFQr/ref.fa --output /tmp/.tmpbOuFQr/meth.vcf.gz --methylation-rate-island 0 --methylation-rate-shore 0 --methylation-rate-open-sea 0 --methylation-correlation-length-island 1 --methylation-correlation-length-shore 1 --methylation-correlation-length-open-sea 1 --hemimethylation-rate 0 --seed 42 [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck_lib::commands::methylate] Using random seed: 42 [INFO] [stdout] test test_em_seq_full_cpg_methylation_still_converts_non_cpg ... ok [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck] Holodeck by Fulcrum Genomics - https://github.com/fg-labs/holodeck [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck] Executing: /opt/rustwide/target/debug/holodeck methylate --reference /tmp/.tmpFReacE/ref.fa --output /tmp/.tmpFReacE/meth.vcf.gz --methylation-rate-island 0 --methylation-rate-shore 0 --methylation-rate-open-sea 0 --methylation-correlation-length-island 1 --methylation-correlation-length-shore 1 --methylation-correlation-length-open-sea 1 --hemimethylation-rate 0 --seed 42 [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck_lib::commands::methylate] Using random seed: 42 [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck_lib::commands::methylate] Wrote methylation VCF to /tmp/.tmpvmGnCE/meth.vcf.gz [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck] Successfully completed execution in 0m:00s. [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck] Successfully completed execution in 0m:00s. [INFO] [stdout] test test_em_seq_intermediate_methylation_preserves_some_c ... ok [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck_lib::commands::methylate] Wrote methylation VCF to /tmp/.tmpFReacE/meth.vcf.gz [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck] Successfully completed execution in 0m:00s. [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck_lib::commands::methylate] Wrote methylation VCF to /tmp/.tmp0ame1C/meth.vcf.gz [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck_lib::commands::methylate] Wrote methylation VCF to /tmp/.tmpbOuFQr/meth.vcf.gz [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck] Successfully completed execution in 0m:00s. [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck] Successfully completed execution in 0m:00s. [INFO] [stdout] test test_golden_bam_omits_xm_ym_nm_md_without_methylation ... ok [INFO] [stdout] test test_em_seq_single_end_emits_xg_ys_and_full_conversion ... ok [INFO] [stdout] test test_golden_bam_emits_xm_ym_nm_md_under_full_methylation_no_errors ... ok [INFO] [stdout] test test_golden_bam_all_failed_sets_cf_one_and_retains_cytosines ... ok [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck] Holodeck by Fulcrum Genomics - https://github.com/fg-labs/holodeck [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck] Executing: /opt/rustwide/target/debug/holodeck methylate --reference /tmp/.tmpE5I7B6/ref.fa --output /tmp/.tmpE5I7B6/meth.vcf.gz --methylation-rate-island 0.7 --methylation-rate-shore 0.7 --methylation-rate-open-sea 0.7 --methylation-correlation-length-island 1 --methylation-correlation-length-shore 1 --methylation-correlation-length-open-sea 1 --hemimethylation-rate 0 --seed 12345 [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck_lib::commands::methylate] Using random seed: 12345 [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck_lib::commands::methylate] Wrote methylation VCF to /tmp/.tmpE5I7B6/meth.vcf.gz [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck] Successfully completed execution in 0m:00s. [INFO] [stdout] test test_golden_bam_omits_methylation_tags_when_methylation_disabled ... ok [INFO] [stdout] test matrix_vcf_with_mtmb_and_mode_runs_chemistry ... ok [INFO] [stdout] test test_golden_bam_em_seq_emits_xg_xr_and_ys_tags_when_enabled ... ok [INFO] [stdout] test matrix_vcf_no_mtmb_with_mode_errors ... ok [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck] Holodeck by Fulcrum Genomics - https://github.com/fg-labs/holodeck [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck] Executing: /opt/rustwide/target/debug/holodeck methylate --reference /tmp/.tmpfvHuL1/ref.fa --output /tmp/.tmpfvHuL1/meth.vcf.gz --methylation-rate-island 1 --methylation-rate-shore 1 --methylation-rate-open-sea 1 --methylation-correlation-length-island 1 --methylation-correlation-length-shore 1 --methylation-correlation-length-open-sea 1 --hemimethylation-rate 0 --seed 42 [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck_lib::commands::methylate] Using random seed: 42 [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck] Holodeck by Fulcrum Genomics - https://github.com/fg-labs/holodeck [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck] Executing: /opt/rustwide/target/debug/holodeck methylate --reference /tmp/.tmpWEBfpz/ref.fa --output /tmp/.tmpWEBfpz/meth.vcf.gz --methylation-rate-island 1 --methylation-rate-shore 1 --methylation-rate-open-sea 1 --methylation-correlation-length-island 1 --methylation-correlation-length-shore 1 --methylation-correlation-length-open-sea 1 --hemimethylation-rate 0 --seed 42 [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck_lib::commands::methylate] Using random seed: 42 [INFO] [stdout] test test_bisulfite_alias_byte_identical_to_em_seq ... ok [INFO] [stdout] test test_golden_bam_no_failure_sets_cf_zero ... ok [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck_lib::commands::methylate] Wrote methylation VCF to /tmp/.tmpfvHuL1/meth.vcf.gz [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck] Holodeck by Fulcrum Genomics - https://github.com/fg-labs/holodeck [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck] Holodeck by Fulcrum Genomics - https://github.com/fg-labs/holodeck [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck_lib::commands::methylate] Wrote methylation VCF to /tmp/.tmpWEBfpz/meth.vcf.gz [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck] Successfully completed execution in 0m:00s. [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck] Executing: /opt/rustwide/target/debug/holodeck methylate --reference /tmp/.tmpPI84lX/ref.fa --output /tmp/.tmpPI84lX/meth.vcf.gz --methylation-rate-island 1 --methylation-rate-shore 1 --methylation-rate-open-sea 1 --methylation-correlation-length-island 1 --methylation-correlation-length-shore 1 --methylation-correlation-length-open-sea 1 --hemimethylation-rate 0 --seed 42 --vcf /tmp/.tmpPI84lX/variants.vcf [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck] Successfully completed execution in 0m:00s. [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck_lib::commands::methylate] Using random seed: 42 [INFO] [stdout] test test_em_seq_with_vcf_handles_haplotype_specific_cpgs ... ok [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck] Executing: /opt/rustwide/target/debug/holodeck methylate --reference /tmp/.tmpn0PNcy/ref.fa --output /tmp/.tmpn0PNcy/meth.vcf.gz --methylation-rate-island 1 --methylation-rate-shore 1 --methylation-rate-open-sea 1 --methylation-correlation-length-island 1 --methylation-correlation-length-shore 1 --methylation-correlation-length-open-sea 1 --hemimethylation-rate 0 --seed 42 [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck_lib::commands::methylate] Using random seed: 42 [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck_lib::commands::methylate] Wrote methylation VCF to /tmp/.tmpPI84lX/meth.vcf.gz [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck] Successfully completed execution in 0m:00s. [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck] Holodeck by Fulcrum Genomics - https://github.com/fg-labs/holodeck [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck] Executing: /opt/rustwide/target/debug/holodeck methylate --reference /tmp/.tmpgrfgUf/ref.fa --output /tmp/.tmpgrfgUf/meth.vcf.gz --methylation-rate-island 0 --methylation-rate-shore 0 --methylation-rate-open-sea 0 --methylation-correlation-length-island 1 --methylation-correlation-length-shore 1 --methylation-correlation-length-open-sea 1 --hemimethylation-rate 0 --seed 42 [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck_lib::commands::methylate] Using random seed: 42 [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck] Holodeck by Fulcrum Genomics - https://github.com/fg-labs/holodeck [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck] Executing: /opt/rustwide/target/debug/holodeck methylate --reference /tmp/.tmpng4P3z/ref.fa --output /tmp/.tmpng4P3z/meth.vcf.gz --methylation-rate-island 1 --methylation-rate-shore 1 --methylation-rate-open-sea 1 --methylation-correlation-length-island 1 --methylation-correlation-length-shore 1 --methylation-correlation-length-open-sea 1 --hemimethylation-rate 0 --seed 42 [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck_lib::commands::methylate] Using random seed: 42 [INFO] [stdout] test test_unknown_methylation_mode_rejected ... ok [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck] Holodeck by Fulcrum Genomics - https://github.com/fg-labs/holodeck [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck] Executing: /opt/rustwide/target/debug/holodeck methylate --reference /tmp/.tmpGntc8T/ref.fa --output /tmp/.tmpGntc8T/meth.vcf.gz --methylation-rate-island 0 --methylation-rate-shore 0 --methylation-rate-open-sea 0 --methylation-correlation-length-island 1 --methylation-correlation-length-shore 1 --methylation-correlation-length-open-sea 1 --hemimethylation-rate 0 --seed 42 [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck_lib::commands::methylate] Using random seed: 42 [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck_lib::commands::methylate] Wrote methylation VCF to /tmp/.tmpgrfgUf/meth.vcf.gz [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck] Successfully completed execution in 0m:00s. [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck_lib::commands::methylate] Wrote methylation VCF to /tmp/.tmpn0PNcy/meth.vcf.gz [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck] Successfully completed execution in 0m:00s. [INFO] [stdout] test test_cf_identical_across_mates_and_mix_present ... ok [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck_lib::commands::methylate] Wrote methylation VCF to /tmp/.tmpng4P3z/meth.vcf.gz [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck] Successfully completed execution in 0m:00s. [INFO] [stdout] test test_header_only_mt_mb_vcf_is_rejected ... ok [INFO] [stdout] test test_taps_full_methylation_full_conversion_eliminates_c_at_cpg ... ok [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck_lib::commands::methylate] Wrote methylation VCF to /tmp/.tmpGntc8T/meth.vcf.gz [INFO] [stderr] [2026-10-06 14:54:10 INFO holodeck] Successfully completed execution in 0m:00s. [INFO] [stdout] test matrix_vcf_with_mtmb_no_mode_warns_and_runs_variants_only ... ok [INFO] [stdout] test test_golden_bam_em_seq_ys_matches_reference_oriented_pre_conversion ... ok [INFO] [stdout] test test_taps_golden_bam_emits_xg_xr_and_ys ... ok [INFO] [stdout] test test_methylation_is_deterministic_with_seed ... ok [INFO] [stdout] test test_em_seq_xg_distribution_covers_all_four_cells ... ok [INFO] [stdout] test test_golden_bam_xm_lowercase_under_full_conversion ... ok [INFO] [stdout] test test_taps_golden_bam_ys_diffs_match_chemistry ... ok [INFO] [stdout] test test_taps_zero_methylation_preserves_all_c ... ok [INFO] [stdout] test test_em_seq_xg_pair_level_consistency ... ok [INFO] [stdout] test test_taps_with_vcf_converts_methylated_haplotype_specific_cpg ... ok [INFO] [stdout] test test_xm_ym_diverge_under_errors_at_methylated_cpg ... ok [INFO] [stdout] [INFO] [stdout] test result: ok. 39 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.52s [INFO] [stdout] [INFO] [stderr] Doc-tests holodeck_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" "814f2f15546f86482530d48defbb161bfdd4fa4acd716884dd66cf26209fb0d8", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "814f2f15546f86482530d48defbb161bfdd4fa4acd716884dd66cf26209fb0d8", kill_on_drop: false }` [INFO] [stdout] 814f2f15546f86482530d48defbb161bfdd4fa4acd716884dd66cf26209fb0d8