[INFO] fetching crate get_mnv 1.1.5...
[INFO] testing get_mnv-1.1.5 against 1.99.0-beta.8+cargoflags=--release for beta-release-1.100-2
[INFO] extracting crate get_mnv 1.1.5 into /workspace/builds/worker-3-tc1/source
[INFO] started tweaking crates.io crate get_mnv 1.1.5
[INFO] finished tweaking crates.io crate get_mnv 1.1.5
[INFO] tweaked toml for crates.io crate get_mnv 1.1.5 written to /workspace/builds/worker-3-tc1/source/Cargo.toml
[INFO] validating manifest of crates.io crate get_mnv 1.1.5 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 crates.io crate get_mnv 1.1.5 already has a lockfile, it will not be regenerated
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+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 noodles v0.109.0
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[INFO] [stderr]   Downloaded env_logger v0.11.10
[INFO] [stderr]   Downloaded noodles-bcf v0.85.0
[INFO] [stderr]   Downloaded noodles-bam v0.88.0
[INFO] [stderr]   Downloaded noodles-sam v0.84.0
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc1/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-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@sha256:77db811e55d90add9212f6832c23229e3de5f1c1f9905e8cb07319ea15df73ac" "sleep" "infinity", kill_on_drop: false }`
[INFO] [stdout] 57acdbecb8835a0c86bd5724ee9afc3c0a33885e0a5e9df1b7b8463fdec8595d
[INFO] running `Command { std: "docker" "start" "57acdbecb8835a0c86bd5724ee9afc3c0a33885e0a5e9df1b7b8463fdec8595d", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "57acdbecb8835a0c86bd5724ee9afc3c0a33885e0a5e9df1b7b8463fdec8595d", 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" "57acdbecb8835a0c86bd5724ee9afc3c0a33885e0a5e9df1b7b8463fdec8595d" "/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" "57acdbecb8835a0c86bd5724ee9afc3c0a33885e0a5e9df1b7b8463fdec8595d", 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" "57acdbecb8835a0c86bd5724ee9afc3c0a33885e0a5e9df1b7b8463fdec8595d" "/opt/rustwide/cargo-home/bin/cargo" "+1.99.0-beta.8" "build" "--frozen" "--message-format=json" "--release", kill_on_drop: false }`
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[INFO] [stderr]    Compiling get_mnv v1.1.5 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished `release` profile [optimized] target(s) in 3m 08s
[INFO] running `Command { std: "docker" "inspect" "57acdbecb8835a0c86bd5724ee9afc3c0a33885e0a5e9df1b7b8463fdec8595d", 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" "57acdbecb8835a0c86bd5724ee9afc3c0a33885e0a5e9df1b7b8463fdec8595d" "/opt/rustwide/cargo-home/bin/cargo" "+1.99.0-beta.8" "test" "--frozen" "--no-run" "--message-format=json" "--release", kill_on_drop: false }`
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[INFO] [stderr]    Compiling get_mnv v1.1.5 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished `release` profile [optimized] target(s) in 2m 39s
[INFO] running `Command { std: "docker" "inspect" "57acdbecb8835a0c86bd5724ee9afc3c0a33885e0a5e9df1b7b8463fdec8595d", 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" "57acdbecb8835a0c86bd5724ee9afc3c0a33885e0a5e9df1b7b8463fdec8595d" "/opt/rustwide/cargo-home/bin/cargo" "+1.99.0-beta.8" "test" "--frozen" "--release", kill_on_drop: false }`
[INFO] [stderr]     Finished `release` profile [optimized] target(s) in 0.19s
[INFO] [stderr]      Running unittests src/lib.rs (/opt/rustwide/target/release/deps/get_mnv-95567b0c9aee1d04)
[INFO] [stdout] 
[INFO] [stdout] running 420 tests
[INFO] [stdout] test cli::tests::test_custom_gff_features ... ok
[INFO] [stdout] test cli::tests::test_frequency_filters_parse ... ok
[INFO] [stdout] test cli::tests::test_convert_and_both_conflict ... ok
[INFO] [stdout] test cli::tests::test_genes_file_accessor ... ok
[INFO] [stdout] test cli::tests::test_genes_or_gff_required ... ok
[INFO] [stdout] test cli::tests::test_translation_table_default ... ok
[INFO] [stdout] test cli::tests::test_tsv_option_selects_tsv_input ... ok
[INFO] [stdout] test cli::tests::test_translation_table_custom ... ok
[INFO] [stdout] test cli::tests::test_default_gff_features ... ok
[INFO] [stdout] test cli::tests::test_vcf_and_tsv_conflict ... ok
[INFO] [stdout] test error::tests::test_all_error_codes_unique ... ok
[INFO] [stdout] test cli::tests::test_mapq_alias ... ok
[INFO] [stdout] test cli::tests::test_input_format_tsv ... ok
[INFO] [stdout] test error::tests::test_context_wraps_original ... ok
[INFO] [stdout] test error::tests::test_error_code_formatting ... ok
[INFO] [stdout] test error::tests::test_chain_format ... ok
[INFO] [stdout] test error::tests::test_from_parse_float_error ... ok
[INFO] [stdout] test error::tests::test_error_json_omits_cause_when_none ... ok
[INFO] [stdout] test error::tests::test_from_serde_json_error ... ok
[INFO] [stdout] test error::tests::test_result_ext_context ... ok
[INFO] [stdout] test genetic_code::tests::test_all_supported_tables_construct ... ok
[INFO] [stdout] test error::tests::test_error_json_includes_cause ... ok
[INFO] [stdout] test error::tests::test_error_message_includes_code ... ok
[INFO] [stdout] test genetic_code::tests::test_standard_codons_shared ... ok
[INFO] [stdout] test genetic_code::tests::test_table12_alt_yeast ... ok
[INFO] [stdout] test genetic_code::tests::test_table25_sr1 ... ok
[INFO] [stdout] test error::tests::test_io_result_ext_with_path ... ok
[INFO] [stdout] test error::tests::test_new_error_codes ... ok
[INFO] [stdout] test error::tests::test_with_source_preserves_chain ... ok
[INFO] [stdout] test genetic_code::tests::test_default_is_table_11 ... ok
[INFO] [stdout] test genetic_code::tests::test_display ... ok
[INFO] [stdout] test genetic_code::tests::test_translate_seq ... ok
[INFO] [stdout] test genetic_code::tests::test_table4_mold_mito ... ok
[INFO] [stdout] test genetic_code::tests::test_table5_invertebrate_mito ... ok
[INFO] [stdout] test genetic_code::tests::test_table2_vertebrate_mito ... ok
[INFO] [stdout] test genetic_code::tests::test_table3_yeast_mito ... ok
[INFO] [stdout] test genetic_code::tests::test_table6_ciliate ... ok
[INFO] [stdout] test genetic_code::tests::test_unsupported_table ... ok
[INFO] [stdout] test io::annotation::tests::test_assign_protein_offsets_gnaq_minus_strand ... ok
[INFO] [stdout] test io::annotation::tests::test_build_transcript_cds_records_collapses_exons ... ok
[INFO] [stdout] test io::annotation::tests::test_count_multi_exon_cds_transcripts ... ok
[INFO] [stdout] test io::annotation::tests::test_decode_percent_invalid_hex ... ok
[INFO] [stdout] test io::annotation::tests::test_decode_percent_multiple ... ok
[INFO] [stdout] test io::annotation::tests::test_assign_protein_offsets_gnaq_q209l_hotspot ... ok
[INFO] [stdout] test io::annotation::tests::test_decode_percent_plain ... ok
[INFO] [stdout] test io::annotation::tests::test_assign_protein_offsets_non_cds_untouched ... ok
[INFO] [stdout] test io::annotation::tests::test_decode_percent_space ... ok
[INFO] [stdout] test io::annotation::tests::test_filter_genes_with_snps ... ok
[INFO] [stdout] test io::annotation::tests::test_gene_name_from_gff_empty ... ok
[INFO] [stdout] test io::annotation::tests::test_gene_name_from_gff_empty_locus_tag_no_trailing_underscore ... ok
[INFO] [stdout] test io::annotation::tests::test_gene_name_from_gff_full ... ok
[INFO] [stdout] test io::annotation::tests::test_decode_percent_trailing_incomplete ... ok
[INFO] [stdout] test io::annotation::tests::test_duplicate_cds_rows_are_counted_once ... ok
[INFO] [stdout] test io::annotation::tests::test_gene_name_from_gff_no_gene_uses_name ... ok
[INFO] [stdout] test io::annotation::cds_model::tests::a_multi_valued_parent_belongs_to_every_transcript_it_names ... ok
[INFO] [stdout] test io::annotation::tests::test_gene_name_from_gff_prefers_gene_name_over_id ... ok
[INFO] [stdout] test cli::tests::test_input_format_ivar_alias ... ok
[INFO] [stdout] test io::annotation::tests::test_assign_protein_offsets_plus_strand_two_exons ... ok
[INFO] [stdout] test io::annotation::tests::test_gene_name_from_gff_uses_gene_id_when_no_name ... ok
[INFO] [stdout] test io::annotation::tests::test_gene_name_from_gff_locus_tag_equal_to_primary_not_duplicated ... ok
[INFO] [stdout] test io::annotation::tests::test_a_quote_inside_a_value_does_not_swallow_the_column ... ok
[INFO] [stdout] test io::annotation::tests::test_has_snp_in_interval_not_found ... ok
[INFO] [stdout] test io::annotation::tests::test_mixed_strand_transcript_is_not_aggregated ... ok
[INFO] [stdout] test io::annotation::tests::test_parse_gff_key_value ... ok
[INFO] [stdout] test io::annotation::tests::test_a_gff_feature_says_what_kind_of_gene_it_is ... ok
[INFO] [stdout] test io::annotation::tests::test_parse_gff_percent_encoded ... ok
[INFO] [stdout] test io::annotation::tests::test_parse_gff_space_separated ... ok
[INFO] [stdout] test io::annotation::tests::test_single_strand_transcript_still_aggregates ... ok
[INFO] [stdout] test io::annotation::tests::test_split_quoted_semicolon ... ok
[INFO] [stdout] test io::annotation::tests::test_split_empty ... ok
[INFO] [stdout] test io::annotation::tests::test_transcript_gene_filter_keeps_intronic_variants ... ok
[INFO] [stdout] test io::fasta::tests::test_load_duplicate_contig_rejected ... ok
[INFO] [stdout] test io::annotation::tests::test_has_snp_in_interval_empty ... ok
[INFO] [stdout] test io::annotation::tests::test_has_snp_in_interval_found ... ok
[INFO] [stdout] test io::annotation::tests::test_split_simple ... ok
[INFO] [stdout] test io::annotation::tests::test_split_trailing_semicolon ... ok
[INFO] [stdout] test io::fasta::tests::test_load_header_description_stripped ... ok
[INFO] [stdout] test io::fasta::tests::a_reference_call_is_not_a_variant ... ok
[INFO] [stdout] test io::fasta::tests::test_load_empty_file_rejected ... ok
[INFO] [stdout] test io::fasta::tests::test_load_multi_contig ... ok
[INFO] [stdout] test io::fasta::tests::test_load_invalid_base_rejected ... ok
[INFO] [stdout] test io::fasta::tests::test_load_only_contig_filter ... ok
[INFO] [stdout] test io::fasta::tests::test_load_iupac_ambiguity ... ok
[INFO] [stdout] test io::fasta::tests::test_load_single_contig ... ok
[INFO] [stdout] test io::fasta::tests::test_load_only_contig_not_found_errors ... ok
[INFO] [stdout] test io::fasta::tests::test_reference_for_chrom_found ... ok
[INFO] [stdout] test io::fasta::tests::test_load_lowercase_uppercased ... ok
[INFO] [stdout] test io::fasta::tests::test_reference_for_chrom_missing ... ok
[INFO] [stdout] test io::fasta::tests::test_validate_vcf_ref_mismatch ... ok
[INFO] [stdout] test io::fasta::tests::test_validate_vcf_ref_alleles_ok ... ok
[INFO] [stdout] test io::fasta::tests::test_validate_vcf_ref_out_of_bounds ... ok
[INFO] [stdout] test io::tests::test_decode_percent_passthrough ... ok
[INFO] [stdout] test io::ivar::tests::test_load_ivar_tsv_converts_deletion_to_vcf_allele ... ok
[INFO] [stdout] test io::ivar::tests::test_load_ivar_tsv_keeps_passing_snvs_and_insertions ... ok
[INFO] [stdout] test io::ivar::tests::test_looks_like_ivar_tsv ... ok
[INFO] [stdout] test io::tests::test_decode_percent_basic_ascii ... ok
[INFO] [stdout] test io::tests::test_decode_percent_truncated_sequence ... ok
[INFO] [stdout] test io::tests::test_gene_name_fallback_chain ... ok
[INFO] [stdout] test io::tests::test_gene_name_from_gff_attributes ... ok
[INFO] [stdout] test io::tests::test_parse_annotation_format_by_extension ... ok
[INFO] [stdout] test io::tests::test_parse_gff_attributes_handles_encoded_and_gtf_styles ... ok
[INFO] [stdout] test io::tests::test_load_references_multiple_contigs ... ok
[INFO] [stdout] test io::tests::test_decode_percent_invalid_hex ... ok
[INFO] [stdout] test io::tests::test_decode_percent_multibyte_utf8 ... ok
[INFO] [stdout] test io::tests::test_parse_optional_depth_handles_integer_and_float_strings ... ok
[INFO] [stdout] test io::tests::test_parse_gff_gene_records_filters_by_feature_type ... ok
[INFO] [stdout] test io::tests::test_load_genes_from_gff_filters_contigs ... ok
[INFO] [stdout] test io::tests::test_split_attribute_fields_quoted_semicolon ... ok
[INFO] [stdout] test io::tests::test_load_vcf_positions_multiallelic_split_mode ... ok
[INFO] [stdout] test io::tests::test_parse_annotation_format_by_content ... ok
[INFO] [stdout] test io::tests::test_parse_gff_attributes_property_randomized_input ... ok
[INFO] [stdout] test io::tests::test_validate_iupac_sequence_rejects_invalid_base ... ok
[INFO] [stdout] test io::tests::test_validate_vcf_reference_alleles_detects_mismatch ... ok
[INFO] [stdout] test io::validation::tests::test_base_name_no_extension ... ok
[INFO] [stdout] test io::tests::test_preload_gff_genes_groups_by_contig ... ok
[INFO] [stdout] test io::validation::tests::test_base_name_other_extension ... ok
[INFO] [stdout] test io::tests::test_split_attribute_fields_basic ... ok
[INFO] [stdout] test io::tests::test_split_attribute_fields_empty_and_trailing ... ok
[INFO] [stdout] test io::validation::tests::test_base_name_vcf_gz ... ok
[INFO] [stdout] test io::validation::tests::test_iupac_empty_rejected ... ok
[INFO] [stdout] test io::validation::tests::test_iupac_invalid_base ... ok
[INFO] [stdout] test io::validation::tests::test_iupac_valid ... ok
[INFO] [stdout] test io::validation::tests::test_iupac_lowercase_valid ... ok
[INFO] [stdout] test io::validation::tests::test_vcf_allele_star_rejected ... ok
[INFO] [stdout] test io::validation::tests::test_base_name_plain_gz ... ok
[INFO] [stdout] test io::validation::tests::test_base_name_vcf ... ok
[INFO] [stdout] test io::vcf::tests::anchored_deletion_overlaps_deleted_reference_span ... ok
[INFO] [stdout] test io::validation::tests::test_vcf_allele_valid_snp ... ok
[INFO] [stdout] test io::vcf::tests::insertion_overlaps_only_between_interval_bases ... ok
[INFO] [stdout] test io::validation::tests::test_vcf_allele_symbolic_alt_ok ... ok
[INFO] [stdout] test io::vcf::tests::test_list_vcf_samples_accepts_lowercase_chrom_header ... ok
[INFO] [stdout] test io::vcf::tests::test_filter_and_subset_original_info_multiallelic ... ok
[INFO] [stdout] test io::vcf::tests::normalising_a_substitution_trims_both_ends ... ok
[INFO] [stdout] test io::validation::tests::test_vcf_allele_symbolic_ref_rejected ... ok
[INFO] [stdout] test io::vcf::tests::normalising_an_indel_keeps_its_anchor ... ok
[INFO] [stdout] test io::vcf_fast::tests::test_derive_freq_from_ad_missing_values ... ok
[INFO] [stdout] test io::vcf::tests::test_filter_and_subset_original_info_biallelic_unchanged ... ok
[INFO] [stdout] test io::vcf::tests::test_load_vcf_accepts_lowercase_chrom_and_skips_preheader_data ... ok
[INFO] [stdout] test io::vcf::tests::test_per_allele_info_numbers_parses_number ... ok
[INFO] [stdout] test io::vcf::tests::test_sample_carries_alt_reads_the_genotype ... ok
[INFO] [stdout] test io::vcf_fast::tests::test_derive_freq_from_ad ... ok
[INFO] [stdout] test io::vcf_fast::tests::test_extract_info_headers_example ... FAILED
[INFO] [stdout] test io::vcf_fast::tests::test_parse_freq_indexed_multiallelic ... ok
[INFO] [stdout] test io::vcf_fast::tests::test_parse_freq_indexed_out_of_bounds_single ... ok
[INFO] [stdout] test io::vcf_fast::tests::test_list_samples_example ... FAILED
[INFO] [stdout] test io::vcf_fast::tests::test_load_vcf_text_example ... FAILED
[INFO] [stdout] test io::vcf_fast::tests::test_parse_freq_token_percent ... ok
[INFO] [stdout] test io::vcf_fast::tests::test_parse_text_metrics_derives_freq_from_format_ao_ro ... ok
[INFO] [stdout] test io::vcf_fast::tests::test_extract_original_info_dot ... ok
[INFO] [stdout] test io::vcf_fast::tests::test_find_info_tag ... ok
[INFO] [stdout] test io::vcf_fast::tests::test_parse_freq_token_missing ... ok
[INFO] [stdout] test io::vcf_fast::tests::test_parse_text_metrics_derives_freq_from_info_ao_ro ... ok
[INFO] [stdout] test io::vcf_fast::tests::test_use_fast_parser_edge_cases ... ok
[INFO] [stdout] test io::vcf_fast::tests::test_derive_freq_from_ad_zero_total ... ok
[INFO] [stdout] test io::vcf_fast::tests::test_extract_original_info_all_filtered ... ok
[INFO] [stdout] test io::vcf_fast::tests::test_extract_original_info_filters_tags ... ok
[INFO] [stdout] test io::vcf_fast::tests::test_parse_freq_token_decimal ... ok
[INFO] [stdout] test output::common::tests::strand_bias_p_values_far_apart_are_printed_apart ... ok
[INFO] [stdout] test output::common::tests::test_build_alt_region_adjacent_snps ... ok
[INFO] [stdout] test output::common::tests::test_build_alt_region_mismatch_lengths_fails ... ok
[INFO] [stdout] test io::vcf_fast::tests::test_use_fast_parser_not_vcf_gz ... ok
[INFO] [stdout] test output::common::tests::test_build_alt_region_single_snp ... ok
[INFO] [stdout] test output::common::tests::test_encode_info_value_escapes_structural_chars ... ok
[INFO] [stdout] test output::common::tests::test_build_info_string_special_gene_name_does_not_corrupt_info ... ok
[INFO] [stdout] test output::common::tests::test_build_info_string_with_original_info ... ok
[INFO] [stdout] test io::vcf_fast::tests::test_use_fast_parser_vcf ... ok
[INFO] [stdout] test output::common::tests::test_build_alt_region_empty_positions_fails ... ok
[INFO] [stdout] test output::common::tests::test_build_info_string_basic ... ok
[INFO] [stdout] test output::common::tests::test_format_freq_precision ... ok
[INFO] [stdout] test output::common::tests::test_filter_value_pass_when_empty ... ok
[INFO] [stdout] test output::common::tests::test_mnv_phasing_support_does_not_saturate_on_an_even_mixture ... ok
[INFO] [stdout] test output::common::tests::test_mnv_phasing_support_ratio_and_guards ... ok
[INFO] [stdout] test output::common::tests::test_reference_subsequence_out_of_bounds ... ok
[INFO] [stdout] test output::common::tests::test_build_alt_region_two_snps ... ok
[INFO] [stdout] test output::common::tests::test_filter_value_single ... ok
[INFO] [stdout] test output::common::tests::test_build_info_string_skips_reserved_original_keys ... ok
[INFO] [stdout] test output::common::tests::test_filter_value_multiple ... ok
[INFO] [stdout] test output::common::tests::test_mnv_phasing_support_is_unknown_when_no_read_spans_the_codon ... ok
[INFO] [stdout] test output::common::tests::test_validate_variant_shape_mismatched_lengths ... ok
[INFO] [stdout] test output::common::tests::test_reference_subsequence_zero_start ... ok
[INFO] [stdout] test output::common::tests::test_snp_aa_for_index_valid ... ok
[INFO] [stdout] test output::common::tests::test_validate_variant_shape_empty_positions ... ok
[INFO] [stdout] test output::common::tests::test_reference_subsequence_valid ... ok
[INFO] [stdout] test output::common::tests::test_snp_aa_for_index_out_of_range_falls_back ... ok
[INFO] [stdout] test output::report::tests::builder_reads_a_tsv_and_emits_embeddable_json ... ok
[INFO] [stdout] test output::report::tests::compressed_input_is_reported_as_such ... ok
[INFO] [stdout] test output::common::tests::test_validate_variant_shape_ok ... ok
[INFO] [stdout] test output::report::tests::sample_label_strips_mnv_suffixes ... ok
[INFO] [stdout] test output::report::tests::every_input_file_keeps_its_own_sample_row ... ok
[INFO] [stdout] test output::report::tests::sample_labels_disambiguate_identical_file_names ... ok
[INFO] [stdout] test output::report::tests::first_number_takes_the_leading_entry ... ok
[INFO] [stdout] test output::report::tests::json_string_escaping_cannot_break_out_of_the_script_tag ... ok
[INFO] [stdout] test output::report::tests::leading_u32_parses_grantham_cell ... ok
[INFO] [stdout] test output::report::tests::interner_reuses_ids ... ok
[INFO] [stdout] test output::report::tests::optional_treats_dash_as_absent ... ok
[INFO] [stdout] test output::report::tests::sample_labels_keep_the_bare_stem_when_it_is_unique ... ok
[INFO] [stdout] test output::report::tests::sample_labels_qualify_only_the_colliding_group ... ok
[INFO] [stdout] test output::stats::tests::test_fisher_exact_no_bias ... ok
[INFO] [stdout] test output::report::tests::sample_labels_walk_up_until_the_paths_differ ... ok
[INFO] [stdout] test output::stats::tests::a_stronger_bias_never_reports_a_weaker_p_value ... ok
[INFO] [stdout] test output::stats::tests::fisher_matches_an_independent_implementation_on_extreme_tables ... ok
[INFO] [stdout] test output::stats::tests::test_fisher_exact_all_zeros ... ok
[INFO] [stdout] test output::stats::tests::test_fisher_exact_extreme_bias ... ok
[INFO] [stdout] test output::report::tests::sample_labels_number_repeats_of_the_same_path ... ok
[INFO] [stdout] test output::tsv::tests::test_build_tsv_row_uses_mnv_total_depth_for_mnv_metrics ... ok
[INFO] [stdout] test output::tsv::tests::test_intergenic_indel_respects_mnv_filters ... ok
[INFO] [stdout] test output::stats::tests::test_fisher_exact_symmetric ... ok
[INFO] [stdout] test output::stats::tests::test_fisher_exact_p_value_bounded ... ok
[INFO] [stdout] test output::tsv::tests::test_build_tsv_row_emits_local_aa_columns ... ok
[INFO] [stdout] test output::vcf::tests::test_write_sorted_vcf_entries_orders_by_position ... ok
[INFO] [stdout] test output::vcf::tests::zero_support_records_obey_the_threshold_and_emit_filtered ... ok
[INFO] [stdout] test pipeline::config::tests::no_warning_once_a_snp_threshold_gives_the_or_something_to_fail ... ok
[INFO] [stdout] test output::tsv::tests::test_intergenic_snp_filtered_by_real_read_support ... ok
[INFO] [stdout] test pipeline::config::tests::no_warning_without_a_bam_or_without_an_mnv_threshold ... ok
[INFO] [stdout] test output::tsv::tests::test_tsv_frequency_filters_keep_snp_mnv_when_mnv_component_passes ... ok
[INFO] [stdout] test output::tsv::tests::test_tsv_frequency_filters_use_bam_derived_values ... ok
[INFO] [stdout] test output::tsv::tests::test_tsv_strand_filters_keep_snp_mnv_when_mnv_component_passes ... ok
[INFO] [stdout] test pipeline::config::tests::test_append_sample_suffix_with_and_without ... ok
[INFO] [stdout] test output::vcf::tests::test_low_frequency_filter_marks_snp_when_emit_filtered ... ok
[INFO] [stdout] test pipeline::config::tests::test_validate_contig_inputs_tsv_multi_contig_error ... ok
[INFO] [stdout] test pipeline::config::tests::test_validate_strict_original_metrics_missing_dp ... ok
[INFO] [stdout] test output::vcf::tests::zero_support_records_are_written_when_no_threshold_asks_otherwise ... ok
[INFO] [stdout] test pipeline::config::tests::warns_when_mnv_thresholds_cannot_reach_codon_rows ... ok
[INFO] [stdout] test pipeline::output_paths::tests::test_output_prefix_keeps_the_sample_suffix ... ok
[INFO] [stdout] test pipeline::config::tests::test_sanitize_sample_for_path_special_chars ... ok
[INFO] [stdout] test pipeline::config::tests::test_selected_contigs_from_chrom_arg ... ok
[INFO] [stdout] test pipeline::config::tests::test_validate_strict_disabled_always_ok ... ok
[INFO] [stdout] test pipeline::summary::tests::test_update_global_summary_accumulates ... ok
[INFO] [stdout] test pipeline::tests::test_summary_to_json_contains_expected_keys ... ok
[INFO] [stdout] test read_count::cache::counting_tests::a_read_carrying_every_alternate_supports_the_haplotype ... ok
[INFO] [stdout] test pipeline::summary::tests::test_summarize_contig_variants_counts ... ok
[INFO] [stdout] test read_count::cache::counting_tests::a_read_covering_one_position_is_not_informative_about_linkage ... ok
[INFO] [stdout] test read_count::cache::counting_tests::a_base_below_the_quality_floor_is_not_observed ... ok
[INFO] [stdout] test read_count::cache::counting_tests::a_base_exactly_at_the_quality_floor_is_observed ... ok
[INFO] [stdout] test read_count::cache::counting_tests::a_single_position_request_counts_only_that_position ... ok
[INFO] [stdout] test read_count::cache::counting_tests::a_spanning_read_with_one_alternate_argues_against_linkage ... ok
[INFO] [stdout] test read_count::cache::counting_tests::agreeing_mates_keep_the_better_quality ... ok
[INFO] [stdout] test read_count::cache::counting_tests::an_overlapping_pair_counts_on_both_strands ... ok
[INFO] [stdout] test read_count::cache::counting_tests::counting_mates_separately_gives_two_observations ... ok
[INFO] [stdout] test pipeline::config::tests::test_configure_threads_none_is_ok ... ok
[INFO] [stdout] test pipeline::config::tests::test_configure_threads_zero_is_error ... ok
[INFO] [stdout] test pipeline::config::tests::test_selected_contigs_empty_is_error ... ok
[INFO] [stdout] test read_count::cache::counting_tests::mates_that_disagree_observe_nothing_at_that_position ... ok
[INFO] [stdout] test read_count::observation::component_tests::a_symbolic_component_can_never_be_supported_by_a_read ... ok
[INFO] [stdout] test read_count::observation::component_tests::an_insertion_must_match_the_sequence_after_the_anchor ... ok
[INFO] [stdout] test read_count::observation::component_tests::every_component_must_hold_at_once ... ok
[INFO] [stdout] test read_count::cache::counting_tests::strand_does_not_travel_between_positions_of_a_fragment ... ok
[INFO] [stdout] test read_count::cache::counting_tests::molecules_carrying_neither_alternate_are_still_counted ... ok
[INFO] [stdout] test read_count::observation::component_tests::a_deletion_needs_every_one_of_its_bases_gone ... ok
[INFO] [stdout] test read_count::cache::tests::test_normalize_positions_deduplicates_and_sorts ... ok
[INFO] [stdout] test read_count::observation::component_tests::a_substitution_is_supported_only_by_that_base ... ok
[INFO] [stdout] test read_count::observation::tests::test_a_molecule_seen_on_both_strands_counts_on_both ... ok
[INFO] [stdout] test read_count::cache::counting_tests::overlapping_mates_are_one_molecule ... ok
[INFO] [stdout] test read_count::observation::component_tests::no_components_at_all_is_vacuously_supported ... ok
[INFO] [stdout] test read_count::phasing::tests::no_molecule_carrying_the_indel_is_trans ... ok
[INFO] [stdout] test read_count::phasing::tests::a_handful_of_cis_molecules_is_tolerated_as_sequencing_error ... ok
[INFO] [stdout] test test_support::tests::joined_gene_builds_a_slippage_join ... ok
[INFO] [stdout] test read_count::phasing::tests::molecules_that_mostly_carry_both_are_not_trans ... ok
[INFO] [stdout] test test_support::tests::joined_gene_rejects_a_real_intron - should panic ... ok
[INFO] [stdout] test test_support::tests::phase_is_carried_through_to_the_gene ... ok
[INFO] [stdout] test test_support::tests::single_exon_gene_matches_a_prokaryotic_cds_row ... ok
[INFO] [stdout] test test_support::tests::spliced_gene_computes_protein_offsets_from_the_segment_lengths ... ok
[INFO] [stdout] test read_count::observation::tests::test_increment_directional_count_single_strand ... ok
[INFO] [stdout] test test_support::tests::spliced_gene_keeps_transcript_order_on_the_minus_strand ... ok
[INFO] [stdout] test test_support::tests::spliced_gene_rejects_abutting_segments - should panic ... ok
[INFO] [stdout] test read_count::phasing::tests::nothing_spanning_both_loci_says_nothing ... ok
[INFO] [stdout] test read_count::phasing::tests::one_molecule_settles_nothing ... ok
[INFO] [stdout] test test_support::tests::spliced_gene_segments_are_separated_by_real_introns ... ok
[INFO] [stdout] test utils::tests::test_dbs_class_canonical_collapsing ... ok
[INFO] [stdout] test utils::tests::test_dbs_class_palindromic_reference_tiebreak ... ok
[INFO] [stdout] test utils::tests::test_dbs_class_rejects_non_doublets ... ok
[INFO] [stdout] test utils::tests::test_determine_change_type_start_lost ... ok
[INFO] [stdout] test utils::tests::test_grantham_distance_and_category ... ok
[INFO] [stdout] test utils::tests::test_determine_change_type ... ok
[INFO] [stdout] test utils::tests::test_determine_change_type_ambiguous_x ... ok
[INFO] [stdout] test utils::tests::test_iupac_aa_expansion ... ok
[INFO] [stdout] test utils::tests::test_process_translate ... ok
[INFO] [stdout] test variants::codon::gene_path::annotation_tests::test_consequence_shift_single_snv_not_applicable ... ok
[INFO] [stdout] test utils::tests::test_reverse_complement ... ok
[INFO] [stdout] test variants::codon::gene_path::annotation_tests::test_dbs_class_for_adjacent_pair_is_order_independent ... ok
[INFO] [stdout] test variants::codon::grouping::tests::test_merge_original_info_shared_value ... ok
[INFO] [stdout] test variants::codon::nmd::tests::junction_is_the_last_real_intron_not_the_last_segment ... ok
[INFO] [stdout] test variants::codon::nmd::tests::ptc_far_upstream_of_last_junction_triggers_nmd ... ok
[INFO] [stdout] test variants::codon::gene_path::annotation_tests::test_consequence_shift_masked_when_mnv_retains_stop ... ok
[INFO] [stdout] test variants::codon::grouping::tests::test_merge_original_info_none_when_absent ... ok
[INFO] [stdout] test variants::codon::nmd::tests::ptc_in_last_exon_escapes ... ok
[INFO] [stdout] test variants::codon::nmd::tests::single_exon_transcript_has_no_prediction ... ok
[INFO] [stdout] test variants::codon::protein::tests::c_terminal_insertion_falls_back_to_bare_positions ... ok
[INFO] [stdout] test variants::codon::protein::tests::inframe_deletion_and_delins_keep_residue_aware_hgvs ... ok
[INFO] [stdout] test variants::codon::protein::tests::inframe_insertion_applies_protein_offset_to_positions_only ... ok
[INFO] [stdout] test variants::codon::protein::tests::multi_residue_insertion_names_flanks_once ... ok
[INFO] [stdout] test variants::codon::tests::test_both_codon_paths_describe_a_minus_strand_mnv_identically ... ok
[INFO] [stdout] test variants::codon::tests::test_build_intergenic_variant_indel ... ok
[INFO] [stdout] test variants::codon::gene_path::annotation_tests::test_aa_severity_retained_stop_is_synonymous ... ok
[INFO] [stdout] test variants::codon::protein::tests::inframe_insertion_names_both_flanking_residues ... ok
[INFO] [stdout] test variants::codon::gene_path::annotation_tests::test_consequence_shift_gained_two_synonymous ... ok
[INFO] [stdout] test variants::codon::tests::test_build_phased_indel_haplotype_combines_nearby_snv ... ok
[INFO] [stdout] test variants::codon::tests::test_build_phased_indel_haplotype_preserves_deletion_component_coordinate ... ok
[INFO] [stdout] test variants::codon::tests::test_change_type_from_label_roundtrip ... ok
[INFO] [stdout] test variants::codon::tests::test_change_type_from_label_unknown_fallback ... ok
[INFO] [stdout] test variants::codon::gene_path::annotation_tests::test_dbs_class_none_for_non_adjacent_or_single ... ok
[INFO] [stdout] test variants::codon::nmd::tests::ptc_within_50nt_of_last_junction_escapes ... ok
[INFO] [stdout] test variants::codon::tests::test_build_phased_indel_haplotype_combines_two_indels ... ok
[INFO] [stdout] test variants::codon::grouping::tests::test_merge_original_info_divergent_keeps_first_without_pipe ... ok
[INFO] [stdout] test variants::codon::nmd::tests::ribosomal_slippage_join_has_no_junction ... ok
[INFO] [stdout] test variants::codon::tests::test_build_phased_indel_haplotype_ignores_distant_snv ... ok
[INFO] [stdout] test variants::codon::tests::test_build_intergenic_variant_snp ... ok
[INFO] [stdout] test variants::codon::tests::test_codon_bounds_minus_strand_phase_1_gnaq_regression ... ok
[INFO] [stdout] test variants::codon::tests::test_codon_bounds_outside_gene_returns_none ... ok
[INFO] [stdout] test variants::codon::tests::test_codon_bounds_phase_skipped_position_returns_none ... ok
[INFO] [stdout] test variants::codon::tests::test_codon_bounds_plus_strand_with_phase_1 ... ok
[INFO] [stdout] test variants::codon::tests::test_frameshift_frequency_gate_skips_low_freq_upstream_indel ... ok
[INFO] [stdout] test variants::codon::tests::test_insertion_above_the_gene_is_not_coding_on_either_strand ... ok
[INFO] [stdout] test variants::codon::tests::test_insertion_after_cds_end_is_not_coding ... ok
[INFO] [stdout] test variants::codon::tests::test_construct_codon_uppercase_alt ... ok
[INFO] [stdout] test variants::codon::tests::test_deletion_anchored_before_cds_keeps_protein_effect ... ok
[INFO] [stdout] test variants::codon::tests::test_exonic_variant_near_junction_is_splice_region ... ok
[INFO] [stdout] test variants::codon::tests::test_indel_reports_event_components_and_frameshift_protein_effect ... ok
[INFO] [stdout] test variants::codon::tests::test_insertion_after_codon_end_does_not_mask_that_codon_snp ... ok
[INFO] [stdout] test variants::codon::tests::test_inframe_insertion_creating_stop_is_stop_gained ... ok
[INFO] [stdout] test variants::codon::tests::test_local_haplotype_components_group_without_enumerating_subsets ... ok
[INFO] [stdout] test variants::codon::tests::test_minus_strand_inframe_insertion_is_inframe ... ok
[INFO] [stdout] test variants::codon::tests::test_minus_strand_insertion_at_internal_exon_junction_is_coding ... ok
[INFO] [stdout] test variants::codon::tests::test_plus_strand_insertion_at_internal_exon_junction_is_coding ... ok
[INFO] [stdout] test variants::codon::tests::test_process_codon_emits_expected_variant_type_for_single_snp ... ok
[INFO] [stdout] test variants::codon::tests::test_minus_strand_insertion_is_complemented_and_placed_between_the_right_residues ... ok
[INFO] [stdout] test variants::codon::tests::test_nonsense_snv_far_upstream_of_last_junction_is_nmd_triggering ... ok
[INFO] [stdout] test variants::codon::tests::test_process_codon_mnv_two_snps_in_codon ... ok
[INFO] [stdout] test variants::codon::tests::test_get_mnv_variants_for_gene_mixed_snps_and_indels ... ok
[INFO] [stdout] test variants::codon::tests::test_property_codon_bounds_minus_strand_cover_position ... ok
[INFO] [stdout] test variants::codon::tests::test_hgvs_coding_descriptor_plus_and_minus_strand ... ok
[INFO] [stdout] test variants::codon::tests::test_property_codon_bounds_plus_strand_cover_position ... ok
[INFO] [stdout] test variants::codon::tests::test_minus_strand_legacy_deletion_reports_consistent_codons ... ok
[INFO] [stdout] test variants::codon::tests::test_multiallelic_position_emits_one_row_per_alt ... ok
[INFO] [stdout] test variants::codon::tests::test_property_reverse_complement_involution_for_random_sequences ... ok
[INFO] [stdout] test variants::codon::tests::test_spliced_indel_marks_only_the_codon_it_overlaps ... ok
[INFO] [stdout] test variants::codon::tests::test_spliced_in_frame_upstream_indel_does_not_frameshift_downstream ... ok
[INFO] [stdout] test variants::codon::tests::test_spliced_upstream_frameshift_indel_propagates_to_a_downstream_codon ... ok
[INFO] [stdout] test variants::codon::tests::test_transcript_model_groups_mnv_across_exon_junction ... ok
[INFO] [stdout] test variants::codon::tests::test_spliced_downstream_indel_does_not_reach_an_upstream_codon ... ok
[INFO] [stdout] test variants::codon::tests::test_transcript_model_restored_frame_does_not_mark_downstream_snp_frameshift ... ok
[INFO] [stdout] test variants::codon::tests::test_spliced_frameshift_gate_suppresses_a_low_frequency_indel ... ok
[INFO] [stdout] test variants::codon::tests::test_strand_from_str ... ok
[INFO] [stdout] test variants::codon::tests::test_variant_type_display ... ok
[INFO] [stdout] test variants::consequence::tests::a_stop_at_position_one_is_a_stop_gained_on_both_paths ... ok
[INFO] [stdout] test variants::consequence::tests::both_paths_agree_on_the_initiator_rule ... ok
[INFO] [stdout] test variants::codon::tests::test_vcf_mnv_record_is_decomposed_into_codon_haplotype ... ok
[INFO] [stdout] test variants::consequence::tests::indels_detect_stop_changes_and_leave_the_rest_alone ... ok
[INFO] [stdout] test variants::codon::tests::test_with_frameshift_idempotent ... ok
[INFO] [stdout] test variants::consequence::tests::a_cds_model_without_an_initiator_is_left_alone ... ok
[INFO] [stdout] test variants::consequence::tests::the_initiator_rule_only_applies_at_position_one ... ok
[INFO] [stdout] test variants::codon::tests::test_true_duplicate_position_still_dedup ... ok
[INFO] [stdout] test variants::declared_phase::tests::an_unphased_genotype_declares_nothing ... ok
[INFO] [stdout] test variants::declared_phase::tests::a_row_whose_other_position_was_never_phased_claims_nothing ... ok
[INFO] [stdout] test variants::declared_phase::tests::a_split_multiallelic_site_does_not_lend_its_claim_to_the_other_allele ... ok
[INFO] [stdout] test variants::declared_phase::tests::different_phase_sets_say_nothing_about_each_other ... ok
[INFO] [stdout] test variants::declared_phase::tests::only_the_extremes_count_as_a_contradiction ... ok
[INFO] [stdout] test variants::consequence::tests::indels_keep_the_frameshift_label ... ok
[INFO] [stdout] test variants::codon::tests::test_transcript_synonymous_snp_is_synonymous ... ok
[INFO] [stdout] test variants::consequence::tests::substitutions_classify_the_ordinary_cases ... ok
[INFO] [stdout] test variants::codon::tests::test_transcript_start_lost_snp_is_start_lost ... ok
[INFO] [stdout] test variants::declared_phase::tests::phased_without_a_phase_set_is_not_comparable_across_records ... ok
[INFO] [stdout] test variants::event::tests::decomposes_anchored_deletion ... ok
[INFO] [stdout] test variants::declared_phase::tests::same_haplotype_in_one_phase_set_is_cis ... ok
[INFO] [stdout] test variants::declared_phase::tests::opposite_haplotypes_in_one_phase_set_are_trans ... ok
[INFO] [stdout] test variants::event::tests::decomposes_anchored_insertion ... ok
[INFO] [stdout] test variants::hgvs::tests::a_multi_base_substitution_never_uses_the_single_base_form ... ok
[INFO] [stdout] test variants::event::tests::parses_component_labels_roundtrip ... ok
[INFO] [stdout] test variants::hgvs::tests::genomic_indels ... ok
[INFO] [stdout] test variants::hgvs::tests::coding_substitution_single_and_bracket ... ok
[INFO] [stdout] test variants::event::tests::decomposes_complex_indel_with_substitution ... ok
[INFO] [stdout] test variants::hgvs::tests::genomic_mnv_uses_allele_bracket_sorted_by_position ... ok
[INFO] [stdout] test variants::event::tests::decomposes_mnv ... ok
[INFO] [stdout] test variants::event::tests::a_right_anchored_insertion_anchors_on_the_base_before_it ... ok
[INFO] [stdout] test variants::hgvs::tests::genomic_snv ... ok
[INFO] [stdout] test variants::linkage::tests::a_haplotype_inside_another_is_still_perfectly_linked ... ok
[INFO] [stdout] test variants::linkage::tests::a_single_position_row_has_no_pair ... ok
[INFO] [stdout] test variants::linkage::tests::an_asymmetric_deficit_pins_the_other_branch ... ok
[INFO] [stdout] test variants::linkage::tests::a_two_position_codon_is_its_only_pair ... ok
[INFO] [stdout] test variants::linkage::tests::alleles_that_never_share_a_molecule_are_complete_repulsion ... ok
[INFO] [stdout] test variants::linkage::tests::the_other_half_of_the_deficit_maximum_decides_too ... ok
[INFO] [stdout] test variants::linkage::tests::an_asymmetric_table_pins_the_arithmetic ... ok
[INFO] [stdout] test variants::linkage::tests::a_locus_carried_by_every_molecule_has_no_linkage_to_report ... ok
[INFO] [stdout] test variants::linkage::tests::no_molecule_spanning_the_pair_yields_nothing ... ok
[INFO] [stdout] test variants::linkage::tests::perfect_co_occurrence_is_complete_linkage ... ok
[INFO] [stdout] test variants::linkage::tests::a_rare_allele_riding_inside_a_common_one_is_completely_linked ... ok
[INFO] [stdout] test variants::linkage::tests::restricting_merges_the_combinations_that_become_identical ... ok
[INFO] [stdout] test variants::linkage::tests::the_other_half_of_the_maximum_decides_when_it_is_the_smaller ... ok
[INFO] [stdout] test variants::linkage::tests::the_weakest_pair_decides_a_three_position_codon ... ok
[INFO] [stdout] test variants::linkage::tests::two_common_alleles_that_merely_coincide_are_not_linked ... ok
[INFO] [stdout] test variants::splice::tests::a_real_intron_beside_a_slippage_join_still_yields_splice_sites ... ok
[INFO] [stdout] test variants::splice::tests::abutting_segments_are_not_a_junction ... ok
[INFO] [stdout] test variants::property_tests::codon_bounds_cover_every_position_inside_a_gene ... ok
[INFO] [stdout] test variants::property_tests::components_rebuild_the_alternate_allele ... ok
[INFO] [stdout] test variants::splice::tests::minus_strand_flips_donor_and_acceptor ... ok
[INFO] [stdout] test variants::splice::tests::intronic_positions_are_inside_a_real_intron ... ok
[INFO] [stdout] test variants::splice::tests::minus_strand_slippage_join_is_not_a_junction ... ok
[INFO] [stdout] test variants::splice::tests::plus_strand_donor_acceptor_and_regions ... ok
[INFO] [stdout] test variants::types::biotype_tests::an_unknown_biotype_is_an_error_rather_than_a_guess ... ok
[INFO] [stdout] test variants::types::biotype_tests::coding_and_non_coding_vocabularies_are_recognised ... ok
[INFO] [stdout] test variants::types::biotype_tests::the_default_is_coding_so_existing_annotations_are_unchanged ... ok
[INFO] [stdout] test variants::types::intron_tests::a_spliced_transcript_yields_its_introns_in_transcript_order ... ok
[INFO] [stdout] test variants::types::intron_tests::a_slippage_join_after_a_real_intron_does_not_move_the_junction ... ok
[INFO] [stdout] test variants::property_tests::normalising_preserves_the_decomposed_event ... ok
[INFO] [stdout] test variants::property_tests::reverse_complement_is_an_involution ... ok
[INFO] [stdout] test variants::splice::tests::ribosomal_slippage_join_is_not_a_junction ... ok
[INFO] [stdout] test variants::splice::tests::an_unspliced_transcript_has_no_intronic_positions ... ok
[INFO] [stdout] test variants::types::intron_tests::an_unspliced_transcript_has_no_introns ... ok
[INFO] [stdout] test variants::splice::tests::single_exon_has_no_splice_sites ... ok
[INFO] [stdout] test variants::types::intron_tests::junction_offsets_accumulate_across_several_exons ... ok
[INFO] [stdout] test variants::types::tests::test_variant_type_as_str ... ok
[INFO] [stdout] test variants::types::tests::test_change_type_display_roundtrip ... ok
[INFO] [stdout] test variants::types::intron_tests::minus_strand_introns_keep_transcript_orientation ... ok
[INFO] [stdout] test variants::types::tests::test_change_type_from_unknown_label ... ok
[INFO] [stdout] test variants::types::tests::test_change_type_ord ... ok
[INFO] [stdout] test variants::types::tests::test_strand_from_str ... ok
[INFO] [stdout] test variants::types::tests::test_variant_type_display ... ok
[INFO] [stdout] test variants::types::tests::test_variant_type_ord ... ok
[INFO] [stdout] test variants::types::tests::test_with_frameshift ... ok
[INFO] [stdout] test variants::property_tests::strand_symmetry_of_codon_annotation ... ok
[INFO] [stdout] 
[INFO] [stdout] failures:
[INFO] [stdout] 
[INFO] [stdout] ---- io::vcf_fast::tests::test_extract_info_headers_example stdout ----
[INFO] [stdout] 
[INFO] [stdout] thread 'io::vcf_fast::tests::test_extract_info_headers_example' (2079) panicked at src/io/vcf_fast.rs:569:54:
[INFO] [stdout] called `Result::unwrap()` on an `Err` value: AppError { code: Generic, message: "Cannot open VCF file '/opt/rustwide/workdir/example/G35894.var.snp.vcf': No such file or directory (os error 2)", source: None }
[INFO] [stdout] stack backtrace:
[INFO] [stdout]    0:     0x63436ee82176 - <<std[70759c8f55707aa4]::sys::backtrace::BacktraceLock>::print::DisplayBacktrace as core[df12db4294e9bfd3]::fmt::Display>::fmt
[INFO] [stdout]    1:     0x63436ec8a74a - core[df12db4294e9bfd3]::fmt::write
[INFO] [stdout]    2:     0x63436ee88cec - <alloc[2182bb758b4b3781]::vec::Vec<u8> as core[df12db4294e9bfd3]::io::write::Write>::write_fmt
[INFO] [stdout]    3:     0x63436ee59ac2 - std[70759c8f55707aa4]::panicking::default_hook::{closure#0}
[INFO] [stdout]    4:     0x63436ee7a211 - std[70759c8f55707aa4]::panicking::default_hook
[INFO] [stdout]    5:     0x63436ee7a3f2 - std[70759c8f55707aa4]::panicking::panic_with_hook
[INFO] [stdout]    6:     0x63436ee59b72 - std[70759c8f55707aa4]::panicking::panic_handler::{closure#0}
[INFO] [stdout]    7:     0x63436ee528d9 - std[70759c8f55707aa4]::sys::backtrace::__rust_end_short_backtrace::<std[70759c8f55707aa4]::panicking::panic_handler::{closure#0}, !>
[INFO] [stdout]    8:     0x63436ee5ea6d - __rustc[8fa7c3cbc660c2b3]::rust_begin_unwind
[INFO] [stdout]    9:     0x63436ec8ae6c - core[df12db4294e9bfd3]::panicking::panic_fmt
[INFO] [stdout]   10:     0x63436ec8ac42 - core[df12db4294e9bfd3]::result::unwrap_failed
[INFO] [stdout]   11:     0x63436edc043a - <get_mnv[fae8fac0f241cfa2]::io::vcf_fast::tests::test_extract_info_headers_example::{closure#0} as core[df12db4294e9bfd3]::ops::function::FnOnce<()>>::call_once
[INFO] [stdout]   12:     0x63436ee8d25b - test[9d35eded1c95d3be]::__rust_begin_short_backtrace::<core[df12db4294e9bfd3]::result::Result<(), alloc[2182bb758b4b3781]::string::String>, fn() -> core[df12db4294e9bfd3]::result::Result<(), alloc[2182bb758b4b3781]::string::String>>
[INFO] [stdout]   13:     0x63436ee9b3b1 - test[9d35eded1c95d3be]::run_test::{closure#0}
[INFO] [stdout]   14:     0x63436ee94ac4 - std[70759c8f55707aa4]::sys::backtrace::__rust_begin_short_backtrace::<test[9d35eded1c95d3be]::run_test::{closure#1}, ()>
[INFO] [stdout]   15:     0x63436ee9f1d2 - <std[70759c8f55707aa4]::thread::lifecycle::spawn_unchecked<test[9d35eded1c95d3be]::run_test::{closure#1}, ()>::{closure#1} as core[df12db4294e9bfd3]::ops::function::FnOnce<()>>::call_once::{shim:vtable#0}
[INFO] [stdout]   16:     0x63436ee817be - <std[70759c8f55707aa4]::sys::thread::unix::Thread>::new::thread_start
[INFO] [stdout]   17:     0x7c2f8d347dfa - <unknown>
[INFO] [stdout]   18:     0x7c2f8d3db3d4 - clone
[INFO] [stdout]   19:                0x0 - <unknown>
[INFO] [stdout] 
[INFO] [stdout] ---- io::vcf_fast::tests::test_list_samples_example stdout ----
[INFO] [stdout] 
[INFO] [stdout] thread 'io::vcf_fast::tests::test_list_samples_example' (2084) panicked at src/io/vcf_fast.rs:561:50:
[INFO] [stdout] called `Result::unwrap()` on an `Err` value: AppError { code: Generic, message: "Cannot open VCF file '/opt/rustwide/workdir/example/G35894.var.snp.vcf': No such file or directory (os error 2)", source: None }
[INFO] [stdout] stack backtrace:
[INFO] [stdout]    0:     0x63436ee82176 - <<std[70759c8f55707aa4]::sys::backtrace::BacktraceLock>::print::DisplayBacktrace as core[df12db4294e9bfd3]::fmt::Display>::fmt
[INFO] [stdout]    1:     0x63436ec8a74a - core[df12db4294e9bfd3]::fmt::write
[INFO] [stdout]    2:     0x63436ee88cec - <alloc[2182bb758b4b3781]::vec::Vec<u8> as core[df12db4294e9bfd3]::io::write::Write>::write_fmt
[INFO] [stdout]    3:     0x63436ee59ac2 - std[70759c8f55707aa4]::panicking::default_hook::{closure#0}
[INFO] [stdout]    4:     0x63436ee7a211 - std[70759c8f55707aa4]::panicking::default_hook
[INFO] [stdout]    5:     0x63436ee7a3f2 - std[70759c8f55707aa4]::panicking::panic_with_hook
[INFO] [stdout]    6:     0x63436ee59b72 - std[70759c8f55707aa4]::panicking::panic_handler::{closure#0}
[INFO] [stdout]    7:     0x63436ee528d9 - std[70759c8f55707aa4]::sys::backtrace::__rust_end_short_backtrace::<std[70759c8f55707aa4]::panicking::panic_handler::{closure#0}, !>
[INFO] [stdout]    8:     0x63436ee5ea6d - __rustc[8fa7c3cbc660c2b3]::rust_begin_unwind
[INFO] [stdout]    9:     0x63436ec8ae6c - core[df12db4294e9bfd3]::panicking::panic_fmt
[INFO] [stdout]   10:     0x63436ec8ac42 - core[df12db4294e9bfd3]::result::unwrap_failed
[INFO] [stdout]   11:     0x63436edbce8b - <get_mnv[fae8fac0f241cfa2]::io::vcf_fast::tests::test_list_samples_example::{closure#0} as core[df12db4294e9bfd3]::ops::function::FnOnce<()>>::call_once
[INFO] [stdout]   12:     0x63436ee8d25b - test[9d35eded1c95d3be]::__rust_begin_short_backtrace::<core[df12db4294e9bfd3]::result::Result<(), alloc[2182bb758b4b3781]::string::String>, fn() -> core[df12db4294e9bfd3]::result::Result<(), alloc[2182bb758b4b3781]::string::String>>
[INFO] [stdout]   13:     0x63436ee9b3b1 - test[9d35eded1c95d3be]::run_test::{closure#0}
[INFO] [stdout]   14:     0x63436ee94ac4 - std[70759c8f55707aa4]::sys::backtrace::__rust_begin_short_backtrace::<test[9d35eded1c95d3be]::run_test::{closure#1}, ()>
[INFO] [stdout]   15:     0x63436ee9f1d2 - <std[70759c8f55707aa4]::thread::lifecycle::spawn_unchecked<test[9d35eded1c95d3be]::run_test::{closure#1}, ()>::{closure#1} as core[df12db4294e9bfd3]::ops::function::FnOnce<()>>::call_once::{shim:vtable#0}
[INFO] [stderr] error: test failed, to rerun pass `--lib`
[INFO] [stdout]   16:     0x63436ee817be - <std[70759c8f55707aa4]::sys::thread::unix::Thread>::new::thread_start
[INFO] [stdout]   17:     0x7c2f8d347dfa - <unknown>
[INFO] [stdout]   18:     0x7c2f8d3db3d4 - clone
[INFO] [stdout]   19:                0x0 - <unknown>
[INFO] [stdout] 
[INFO] [stdout] ---- io::vcf_fast::tests::test_load_vcf_text_example stdout ----
[INFO] [stdout] 
[INFO] [stdout] thread 'io::vcf_fast::tests::test_load_vcf_text_example' (2085) panicked at src/io/vcf_fast.rs:550:68:
[INFO] [stdout] called `Result::unwrap()` on an `Err` value: AppError { code: Generic, message: "Cannot open VCF file '/opt/rustwide/workdir/example/G35894.var.snp.vcf': No such file or directory (os error 2)", source: None }
[INFO] [stdout] stack backtrace:
[INFO] [stdout]    0:     0x63436ee82176 - <<std[70759c8f55707aa4]::sys::backtrace::BacktraceLock>::print::DisplayBacktrace as core[df12db4294e9bfd3]::fmt::Display>::fmt
[INFO] [stdout]    1:     0x63436ec8a74a - core[df12db4294e9bfd3]::fmt::write
[INFO] [stdout]    2:     0x63436ee88cec - <alloc[2182bb758b4b3781]::vec::Vec<u8> as core[df12db4294e9bfd3]::io::write::Write>::write_fmt
[INFO] [stdout]    3:     0x63436ee59ac2 - std[70759c8f55707aa4]::panicking::default_hook::{closure#0}
[INFO] [stdout]    4:     0x63436ee7a211 - std[70759c8f55707aa4]::panicking::default_hook
[INFO] [stdout]    5:     0x63436ee7a3f2 - std[70759c8f55707aa4]::panicking::panic_with_hook
[INFO] [stdout]    6:     0x63436ee59b72 - std[70759c8f55707aa4]::panicking::panic_handler::{closure#0}
[INFO] [stdout]    7:     0x63436ee528d9 - std[70759c8f55707aa4]::sys::backtrace::__rust_end_short_backtrace::<std[70759c8f55707aa4]::panicking::panic_handler::{closure#0}, !>
[INFO] [stdout]    8:     0x63436ee5ea6d - __rustc[8fa7c3cbc660c2b3]::rust_begin_unwind
[INFO] [stdout]    9:     0x63436ec8ae6c - core[df12db4294e9bfd3]::panicking::panic_fmt
[INFO] [stdout]   10:     0x63436ec8ac42 - core[df12db4294e9bfd3]::result::unwrap_failed
[INFO] [stdout]   11:     0x63436edbef8e - <get_mnv[fae8fac0f241cfa2]::io::vcf_fast::tests::test_load_vcf_text_example::{closure#0} as core[df12db4294e9bfd3]::ops::function::FnOnce<()>>::call_once
[INFO] [stdout]   12:     0x63436ee8d25b - test[9d35eded1c95d3be]::__rust_begin_short_backtrace::<core[df12db4294e9bfd3]::result::Result<(), alloc[2182bb758b4b3781]::string::String>, fn() -> core[df12db4294e9bfd3]::result::Result<(), alloc[2182bb758b4b3781]::string::String>>
[INFO] [stdout]   13:     0x63436ee9b3b1 - test[9d35eded1c95d3be]::run_test::{closure#0}
[INFO] [stdout]   14:     0x63436ee94ac4 - std[70759c8f55707aa4]::sys::backtrace::__rust_begin_short_backtrace::<test[9d35eded1c95d3be]::run_test::{closure#1}, ()>
[INFO] [stdout]   15:     0x63436ee9f1d2 - <std[70759c8f55707aa4]::thread::lifecycle::spawn_unchecked<test[9d35eded1c95d3be]::run_test::{closure#1}, ()>::{closure#1} as core[df12db4294e9bfd3]::ops::function::FnOnce<()>>::call_once::{shim:vtable#0}
[INFO] [stdout]   16:     0x63436ee817be - <std[70759c8f55707aa4]::sys::thread::unix::Thread>::new::thread_start
[INFO] [stdout]   17:     0x7c2f8d347dfa - <unknown>
[INFO] [stdout]   18:     0x7c2f8d3db3d4 - clone
[INFO] [stdout]   19:                0x0 - <unknown>
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] failures:
[INFO] [stdout]     io::vcf_fast::tests::test_extract_info_headers_example
[INFO] [stdout]     io::vcf_fast::tests::test_list_samples_example
[INFO] [stdout]     io::vcf_fast::tests::test_load_vcf_text_example
[INFO] [stdout] 
[INFO] [stdout] test result: FAILED. 417 passed; 3 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.17s
[INFO] [stdout] 
[INFO] running `Command { std: "docker" "inspect" "57acdbecb8835a0c86bd5724ee9afc3c0a33885e0a5e9df1b7b8463fdec8595d", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "57acdbecb8835a0c86bd5724ee9afc3c0a33885e0a5e9df1b7b8463fdec8595d", kill_on_drop: false }`
[INFO] [stdout] 57acdbecb8835a0c86bd5724ee9afc3c0a33885e0a5e9df1b7b8463fdec8595d
