[INFO] cloning repository https://github.com/JoseBlanca/join_per_sample_vcfs
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/JoseBlanca/join_per_sample_vcfs" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FJoseBlanca%2Fjoin_per_sample_vcfs", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FJoseBlanca%2Fjoin_per_sample_vcfs'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] b65b0fd2b1c5e659407e7636c058b49577b16af8
[INFO] testing JoseBlanca/join_per_sample_vcfs against master#f9988fefd3add01f414f52b414308e7872622fee for pr-155114
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FJoseBlanca%2Fjoin_per_sample_vcfs" "/workspace/builds/worker-5-tc1/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-5-tc1/source'...
[INFO] [stderr] done.
[INFO] started tweaking git repo https://github.com/JoseBlanca/join_per_sample_vcfs
[INFO] finished tweaking git repo https://github.com/JoseBlanca/join_per_sample_vcfs
[INFO] tweaked toml for git repo https://github.com/JoseBlanca/join_per_sample_vcfs written to /workspace/builds/worker-5-tc1/source/Cargo.toml
[INFO] validating manifest of git repo https://github.com/JoseBlanca/join_per_sample_vcfs on toolchain f9988fefd3add01f414f52b414308e7872622fee
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+f9988fefd3add01f414f52b414308e7872622fee" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate git repo https://github.com/JoseBlanca/join_per_sample_vcfs 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" "+f9988fefd3add01f414f52b414308e7872622fee" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Updating crates.io index
[INFO] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded noodles-csi v0.55.0
[INFO] [stderr]   Downloaded noodles-core v0.19.0
[INFO] [stderr]   Downloaded wasm-bindgen-shared v0.2.111
[INFO] [stderr]   Downloaded wasm-bindgen-macro v0.2.111
[INFO] [stderr]   Downloaded noodles-fasta v0.60.0
[INFO] [stderr]   Downloaded noodles-bgzf v0.46.0
[INFO] [stderr]   Downloaded bit-vec v0.9.1
[INFO] [stderr]   Downloaded bzip2 v0.6.1
[INFO] [stderr]   Downloaded wasm-bindgen-macro-support v0.2.111
[INFO] [stderr]   Downloaded libbz2-rs-sys v0.2.3
[INFO] [stderr]   Downloaded wasm-bindgen v0.2.111
[INFO] [stderr]   Downloaded noodles-bam v0.88.0
[INFO] [stderr]   Downloaded js-sys v0.3.88
[INFO] [stderr]   Downloaded noodles-sam v0.84.0
[INFO] [stderr]   Downloaded syn v2.0.115
[INFO] [stderr]   Downloaded noodles-cram v0.92.0
[INFO] [stderr]   Downloaded lzma-rust2 v0.16.2
[INFO] [stderr]   Downloaded web-sys v0.3.88
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc1/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:d429b63d4308055ea97f60fb1d3dfca48854a00942f1bd2ad806beaf015945ec" "/opt/rustwide/cargo-home/bin/cargo" "+f9988fefd3add01f414f52b414308e7872622fee" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] 76e340178cc36a9fa6e326e64362cbad0950232c23cef7f734acd2b3e27aa997
[INFO] running `Command { std: "docker" "start" "-a" "76e340178cc36a9fa6e326e64362cbad0950232c23cef7f734acd2b3e27aa997", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "76e340178cc36a9fa6e326e64362cbad0950232c23cef7f734acd2b3e27aa997", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "76e340178cc36a9fa6e326e64362cbad0950232c23cef7f734acd2b3e27aa997", kill_on_drop: false }`
[INFO] [stdout] 76e340178cc36a9fa6e326e64362cbad0950232c23cef7f734acd2b3e27aa997
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc1/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "RUSTDOCFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:d429b63d4308055ea97f60fb1d3dfca48854a00942f1bd2ad806beaf015945ec" "/opt/rustwide/cargo-home/bin/cargo" "+f9988fefd3add01f414f52b414308e7872622fee" "build" "--frozen" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 153f79548d0ee5f0cfcfeaa9c2a9905232916886c30710629317ec18fa976148
[INFO] running `Command { std: "docker" "start" "-a" "153f79548d0ee5f0cfcfeaa9c2a9905232916886c30710629317ec18fa976148", kill_on_drop: false }`
[INFO] [stderr]    Compiling lexical-util v1.0.7
[INFO] [stderr]    Compiling typenum v1.20.0
[INFO] [stderr]    Compiling zlib-rs v0.6.3
[INFO] [stderr]    Compiling bstr v1.12.1
[INFO] [stderr]    Compiling libc v0.2.178
[INFO] [stderr]    Compiling bitflags v2.10.0
[INFO] [stderr]    Compiling unicode-ident v1.0.23
[INFO] [stderr]    Compiling bit-vec v0.9.1
[INFO] [stderr]    Compiling proc-macro2 v1.0.106
[INFO] [stderr]    Compiling getrandom v0.3.4
[INFO] [stderr]    Compiling rustix v1.1.2
[INFO] [stderr]    Compiling quote v1.0.44
[INFO] [stderr]    Compiling lexical-write-integer v1.0.6
[INFO] [stderr]    Compiling noodles-core v0.19.0
[INFO] [stderr]    Compiling lexical-parse-integer v1.0.6
[INFO] [stderr]    Compiling zerocopy v0.8.39
[INFO] [stderr]    Compiling syn v2.0.115
[INFO] [stderr]    Compiling lexical-write-float v1.0.6
[INFO] [stderr]    Compiling lexical-parse-float v1.0.6
[INFO] [stderr]    Compiling ahash v0.8.12
[INFO] [stderr]    Compiling generic-array v0.14.7
[INFO] [stderr]    Compiling libbz2-rs-sys v0.2.3
[INFO] [stderr]    Compiling linux-raw-sys v0.11.0
[INFO] [stderr]    Compiling once_cell v1.21.3
[INFO] [stderr]    Compiling lexical-core v1.0.6
[INFO] [stderr]    Compiling bzip2 v0.6.1
[INFO] [stderr]    Compiling block-buffer v0.10.4
[INFO] [stderr]    Compiling crypto-common v0.1.7
[INFO] [stderr]    Compiling digest v0.10.7
[INFO] [stderr]    Compiling sha2 v0.10.9
[INFO] [stderr]    Compiling md-5 v0.10.6
[INFO] [stderr]    Compiling lzma-rust2 v0.16.2
[INFO] [stderr]    Compiling thiserror-impl v2.0.18
[INFO] [stderr]    Compiling tempfile v3.23.0
[INFO] [stderr]    Compiling thiserror v2.0.18
[INFO] [stderr]    Compiling flate2 v1.1.9
[INFO] [stderr]    Compiling noodles-bgzf v0.46.0
[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-bam v0.88.0
[INFO] [stderr]    Compiling noodles-cram v0.92.0
[INFO] [stderr]    Compiling merge_per_sample_vcfs v0.1.0 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 43.18s
[INFO] running `Command { std: "docker" "inspect" "153f79548d0ee5f0cfcfeaa9c2a9905232916886c30710629317ec18fa976148", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "153f79548d0ee5f0cfcfeaa9c2a9905232916886c30710629317ec18fa976148", kill_on_drop: false }`
[INFO] [stdout] 153f79548d0ee5f0cfcfeaa9c2a9905232916886c30710629317ec18fa976148
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc1/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "RUSTDOCFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:d429b63d4308055ea97f60fb1d3dfca48854a00942f1bd2ad806beaf015945ec" "/opt/rustwide/cargo-home/bin/cargo" "+f9988fefd3add01f414f52b414308e7872622fee" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 0fe88e7d363797c97cbbfaa7fbadd308427faaa0f9b0b99530a5b7b9d86546b4
[INFO] running `Command { std: "docker" "start" "-a" "0fe88e7d363797c97cbbfaa7fbadd308427faaa0f9b0b99530a5b7b9d86546b4", kill_on_drop: false }`
[INFO] [stderr]    Compiling regex-syntax v0.8.9
[INFO] [stderr]    Compiling zerocopy v0.8.39
[INFO] [stderr]    Compiling libc v0.2.178
[INFO] [stderr]    Compiling syn v2.0.115
[INFO] [stderr]    Compiling serde v1.0.228
[INFO] [stderr]    Compiling num-traits v0.2.19
[INFO] [stderr]    Compiling rayon v1.11.0
[INFO] [stderr]    Compiling alloca v0.4.0
[INFO] [stderr]    Compiling plotters-backend v0.3.7
[INFO] [stderr]    Compiling ciborium-io v0.2.2
[INFO] [stderr]    Compiling serde_json v1.0.149
[INFO] [stderr]    Compiling clap_builder v4.5.60
[INFO] [stderr]    Compiling plotters-svg v0.3.7
[INFO] [stderr]    Compiling cast v0.3.0
[INFO] [stderr]    Compiling criterion-plot v0.8.2
[INFO] [stderr]    Compiling plotters v0.3.7
[INFO] [stderr]    Compiling getrandom v0.3.4
[INFO] [stderr]    Compiling regex-automata v0.4.14
[INFO] [stderr]    Compiling tempfile v3.23.0
[INFO] [stderr]    Compiling page_size v0.6.0
[INFO] [stderr]    Compiling anes v0.1.6
[INFO] [stderr]    Compiling clap v4.5.60
[INFO] [stderr]    Compiling oorandom v11.1.5
[INFO] [stderr]    Compiling zerocopy-derive v0.8.39
[INFO] [stderr]    Compiling serde_derive v1.0.228
[INFO] [stderr]    Compiling thiserror-impl v2.0.18
[INFO] [stderr]    Compiling bstr v1.12.1
[INFO] [stderr]    Compiling regex v1.12.3
[INFO] [stderr]    Compiling thiserror v2.0.18
[INFO] [stderr]    Compiling noodles-core v0.19.0
[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 tinytemplate v1.2.1
[INFO] [stderr]    Compiling noodles-bam v0.88.0
[INFO] [stderr]    Compiling noodles-cram v0.92.0
[INFO] [stderr]    Compiling half v2.7.1
[INFO] [stderr]    Compiling ahash v0.8.12
[INFO] [stderr]    Compiling ciborium-ll v0.2.2
[INFO] [stderr]    Compiling ciborium v0.2.2
[INFO] [stderr]    Compiling merge_per_sample_vcfs v0.1.0 (/opt/rustwide/workdir)
[INFO] [stderr]    Compiling criterion v0.8.2
[INFO] [stderr]     Finished `test` profile [unoptimized + debuginfo] target(s) in 1m 12s
[INFO] running `Command { std: "docker" "inspect" "0fe88e7d363797c97cbbfaa7fbadd308427faaa0f9b0b99530a5b7b9d86546b4", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "0fe88e7d363797c97cbbfaa7fbadd308427faaa0f9b0b99530a5b7b9d86546b4", kill_on_drop: false }`
[INFO] [stdout] 0fe88e7d363797c97cbbfaa7fbadd308427faaa0f9b0b99530a5b7b9d86546b4
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc1/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "RUSTDOCFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:d429b63d4308055ea97f60fb1d3dfca48854a00942f1bd2ad806beaf015945ec" "/opt/rustwide/cargo-home/bin/cargo" "+f9988fefd3add01f414f52b414308e7872622fee" "test" "--frozen", kill_on_drop: false }`
[INFO] [stdout] c766a9e04968b3af268252e618f0dab7796171f4e0b60917ab8e5b530de2a53c
[INFO] running `Command { std: "docker" "start" "-a" "c766a9e04968b3af268252e618f0dab7796171f4e0b60917ab8e5b530de2a53c", kill_on_drop: false }`
[INFO] [stderr]     Finished `test` profile [unoptimized + debuginfo] target(s) in 0.23s
[INFO] [stderr]      Running unittests src/lib.rs (/opt/rustwide/target/debug/deps/merge_per_sample_vcfs-9babee8607ed3748)
[INFO] [stdout] 
[INFO] [stdout] running 90 tests
[INFO] [stdout] test buffered_peekable::tests::all_ok_in_order ... ok
[INFO] [stdout] test buffered_peekable::tests::peek_consumes_error_only_once ... ok
[INFO] [stdout] test buffered_peekable::tests::peek_does_not_consume_record ... ok
[INFO] [stdout] test buffered_peekable::tests::buffer_size_larger_than_stream ... ok
[INFO] [stdout] test buffered_peekable::tests::single_error_preserves_order ... ok
[INFO] [stdout] test buffered_peekable::tests::peek_then_next_returns_same_record ... ok
[INFO] [stdout] test buffered_peekable::tests::error_first_then_recovers ... ok
[INFO] [stdout] test buffered_peekable::tests::next_after_exhaustion_keeps_returning_none ... ok
[INFO] [stdout] test buffered_peekable::tests::empty_iterator_yields_none_forever ... ok
[INFO] [stdout] test buffered_peekable::tests::multiple_errors_each_surface_in_turn ... ok
[INFO] [stdout] test buffered_peekable::tests::next_surfaces_error_when_called_directly ... ok
[INFO] [stdout] test decompression_pool::tests::test_pool_drop_with_active_readers ... ok
[INFO] [stdout] test decompression_pool::tests::test_error_propagation ... ok
[INFO] [stdout] test buffered_peekable::tests::buffer_size_one_works ... ok
[INFO] [stdout] test decompression_pool::tests::test_multiple_readers_concurrent ... ok
[INFO] [stdout] test decompression_pool::tests::test_gzip_decompression ... ok
[INFO] [stdout] test decompression_pool::tests::test_empty_reader ... ok
[INFO] [stdout] test genotype_posteriors::tests::test_clear_het_gets_high_qual ... ok
[INFO] [stdout] test genotype_posteriors::tests::test_enumerate_genotypes_diploid_biallelic ... ok
[INFO] [stdout] test genotype_posteriors::tests::test_all_hom_ref_gets_low_qual ... ok
[INFO] [stdout] test genotype_posteriors::tests::test_enumerate_genotypes_diploid_triallelic ... ok
[INFO] [stdout] test decompression_pool::tests::test_single_reader_small_data ... ok
[INFO] [stdout] test genotype_posteriors::tests::test_high_f_favors_homozygotes ... ok
[INFO] [stdout] test genotype_posteriors::tests::test_multinomial_coefficients ... ok
[INFO] [stdout] test genotype_posteriors::tests::test_one_het_one_ref_moderate_qual ... ok
[INFO] [stdout] test genotype_posteriors::tests::test_posteriors_sum_to_one ... ok
[INFO] [stdout] test genotype_posteriors::tests::test_f_zero_equals_hardy_weinberg ... ok
[INFO] [stdout] test genotype_posteriors::tests::test_enumerate_genotypes_tetraploid_biallelic ... ok
[INFO] [stdout] test genotype_posteriors::tests::test_prior_pseudocounts ... ok
[INFO] [stdout] test genotype_posteriors::tests::test_synthetic_pls_diploid_het ... ok
[INFO] [stdout] test genotype_posteriors::tests::test_synthetic_pls_diploid_hom_ref ... ok
[INFO] [stdout] test genotype_posteriors::tests::test_synthetic_pls_feed_into_em ... ok
[INFO] [stdout] test genotype_posteriors::tests::test_synthetic_pls_tetraploid ... ok
[INFO] [stdout] test genotype_posteriors::tests::test_f_one_gives_zero_het_prior ... ok
[INFO] [stdout] test genotype_posteriors::tests::test_tetraploid_clear_variant ... ok
[INFO] [stdout] test genotype_posteriors::tests::test_synthetic_pls_missing_genotype ... ok
[INFO] [stdout] test per_sample_caller::cram_input::tests::a12_filter_precedence_is_hit_rate_ordered ... ok
[INFO] [stdout] test per_sample_caller::cram_input::tests::a13_empty_stream ... ok
[INFO] [stdout] test decompression_pool::tests::test_reader_drop_cancels_job ... ok
[INFO] [stdout] test per_sample_caller::cram_input::tests::a10_all_optional_flag_drops_disabled_keeps_everything_except_unmapped ... ok
[INFO] [stdout] test per_sample_caller::cram_input::tests::a11_min_read_length_drops_short_and_empty ... ok
[INFO] [stdout] test genotype_posteriors::tests::test_tetraploid_posteriors_sum_to_one ... ok
[INFO] [stdout] test per_sample_caller::cram_input::tests::a14b_truly_unmapped_record_is_filtered_not_errored ... ok
[INFO] [stdout] test per_sample_caller::cram_input::tests::a15_position_above_u32_max_round_trips_through_mapped_read ... ok
[INFO] [stdout] test per_sample_caller::cram_input::tests::a3_tiebreaker_on_equal_coordinates ... ok
[INFO] [stdout] test per_sample_caller::cram_input::tests::a2_multi_stream_merge_order ... ok
[INFO] [stdout] test decompression_pool::tests::test_many_readers_few_threads ... ok
[INFO] [stdout] test per_sample_caller::cram_input::tests::a1_single_stream_pass_through ... ok
[INFO] [stdout] test per_sample_caller::cram_input::tests::a5_duplicate_read_across_streams ... ok
[INFO] [stdout] test per_sample_caller::cram_input::tests::a4_out_of_order_within_a_single_stream ... ok
[INFO] [stdout] test per_sample_caller::cram_input::tests::a6_duplicate_window_clears_on_advance ... ok
[INFO] [stdout] test per_sample_caller::cram_input::tests::a16_empty_inputs_returns_no_inputs ... ok
[INFO] [stdout] test per_sample_caller::cram_input::tests::a4b_iterator_returns_none_after_first_error ... ok
[INFO] [stdout] test per_sample_caller::cram_input::tests::a7_min_mapq_filter ... ok
[INFO] [stdout] test per_sample_caller::cram_input::tests::a14_mixed_empty_and_non_empty ... ok
[INFO] [stdout] test per_sample_caller::cram_input::tests::a8_min_mapq_none_disables ... ok
[INFO] [stdout] test per_sample_caller::cram_input::tests::a7b_missing_mapq_is_treated_as_zero_and_filtered_by_default ... ok
[INFO] [stdout] test per_sample_caller::cram_input::tests::a9_each_flag_drop_one_at_a_time ... ok
[INFO] [stdout] test per_sample_caller::cram_input::tests::b2_cram_4x_rejected_at_header_time ... ok
[INFO] [stdout] test decompression_pool::tests::test_single_reader_large_data ... ok
[INFO] [stdout] test per_sample_caller::cram_input::tests::b3_non_coordinate_sort_rejected ... ok
[INFO] [stdout] test per_sample_caller::cram_input::tests::p1_contig_list_md5_wildcard_equality ... ok
[INFO] [stdout] test per_sample_caller::cram_input::tests::p2_malformed_record_message_omits_empty_qname ... ok
[INFO] [stdout] test vcf_writer::tests::test_broken_pipe_immediately_on_flush ... ok
[INFO] [stdout] test vcf_writer::tests::test_broken_pipe_mid_variant_stops_silently ... ok
[INFO] [stdout] test vcf_writer::tests::test_broken_pipe_on_write_variant_does_not_error ... ok
[INFO] [stdout] test vcf_writer::tests::test_broken_pipe_on_write_variants_stops_silently ... ok
[INFO] [stdout] test vcf_writer::tests::test_header_format ... ok
[INFO] [stdout] test per_sample_caller::cram_input::tests::b7_end_to_end_smoke ... ok
[INFO] [stdout] test vcf_writer::tests::test_hom_alt ... ok
[INFO] [stdout] test vcf_writer::tests::test_missing_genotype ... ok
[INFO] [stdout] test vcf_writer::tests::test_multi_sample ... ok
[INFO] [stdout] test vcf_writer::tests::test_hom_ref ... ok
[INFO] [stdout] test vcf_writer::tests::test_multiple_variants ... ok
[INFO] [stdout] test vcf_writer::tests::test_partial_missing_genotype ... ok
[INFO] [stdout] test vcf_writer::tests::test_single_sample_het ... ok
[INFO] [stdout] test vcf_writer::tests::test_single_sample_phased_het ... ok
[INFO] [stdout] test vcf_writer::tests::test_write_single_variant ... ok
[INFO] [stdout] test vcf_writer::tests::test_write_to_buffer ... ok
[INFO] [stdout] test vcf_writer::tests::test_no_alt_allele ... ok
[INFO] [stdout] test vcf_writer::tests::test_write_to_gzipped_file ... ok
[INFO] [stdout] test vcf_writer::tests::test_write_variants_error_propagation ... ok
[INFO] [stdout] test vcf_writer::tests::test_write_to_plain_file ... ok
[INFO] [stdout] test vcf_writer::tests::test_write_variants_from_iterator ... ok
[INFO] [stdout] test per_sample_caller::cram_input::tests::b5_contig_list_mismatch_across_crams ... ok
[INFO] [stdout] test per_sample_caller::cram_input::tests::b1_header_parsing_on_known_good_cram ... ok
[INFO] [stdout] test per_sample_caller::cram_input::tests::b6_fasta_agreement ... ok
[INFO] [stdout] test per_sample_caller::cram_input::tests::b4b_malformed_md5_rejected ... ok
[INFO] [stdout] test per_sample_caller::cram_input::tests::b4_sample_tag_handling ... ok
[INFO] [stdout] test buffered_peekable::tests::with_buffer_size_zero_panics - should panic ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 90 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.21s
[INFO] [stdout] 
[INFO] [stderr]      Running unittests src/main.rs (/opt/rustwide/target/debug/deps/merge_per_sample_vcfs-4fa92bc445295061)
[INFO] [stdout] 
[INFO] [stdout] running 0 tests
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 0 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s
[INFO] [stdout] 
[INFO] [stderr]      Running tests/genotype_merging_test.rs (/opt/rustwide/target/debug/deps/genotype_merging_test-e11532d4a0405d56)
[INFO] [stdout] 
[INFO] [stdout] running 25 tests
[INFO] [stdout] test test_deletion_len_2 ... ok
[INFO] [stdout] test test_het_deletion ... ok
[INFO] [stdout] test test_missing_allele_in_merged_haplotype ... ok
[INFO] [stdout] test test_grouper_preserves_genomic_order ... ok
[INFO] [stdout] test test_overlapping_deletions ... ok
[INFO] [stdout] test test_phase_conserved_in_het ... ok
[INFO] [stdout] test test_phase_false_on_first_position_still_solvable ... ok
[INFO] [stdout] test test_phase_first_het_not_at_first_position ... ok
[INFO] [stdout] test test_non_variant_vars_are_removed ... ok
[INFO] [stdout] test test_phase_broken_in_one_sample ... ok
[INFO] [stdout] test test_analyze_single_group_from_merged_bin ... ok
[INFO] [stdout] test test_phase_kept_between_hets ... ok
[INFO] [stdout] test test_allele_merge_with_non_ref_filtered ... ok
[INFO] [stdout] test test_phase_lost_in_het ... ok
[INFO] [stdout] test test_phase_lost_in_het2 ... ok
[INFO] [stdout] test test_phase_lost_in_het_and_not_recovered ... ok
[INFO] [stdout] test test_simple_insertion ... ok
[INFO] [stdout] test test_phase_maintained_despited_not_phased_in_hom_position ... ok
[INFO] [stdout] test test_simple_merge ... ok
[INFO] [stdout] test test_simple_deletion ... ok
[INFO] [stdout] test test_phase_single_het_no_phase_needed ... ok
[INFO] [stdout] test test_two_overlapping_deletions_in_same_sample ... ok
[INFO] [stdout] test test_phase_broken_between_hets_missing_genotype ... ok
[INFO] [stdout] test test_group_merging_creates_correct_number_of_vars ... ok
[INFO] [stdout] test test_two_deletions_in_same_sample ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 25 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.02s
[INFO] [stdout] 
[INFO] [stderr]      Running tests/gvcf_parser_test.rs (/opt/rustwide/target/debug/deps/gvcf_parser_test-e92159b83aec89d2)
[INFO] [stdout] 
[INFO] [stdout] running 26 tests
[INFO] [stdout] test test_genotype_parsing_basic ... ok
[INFO] [stdout] test test_genotype_parsing_missing ... ok
[INFO] [stdout] test test_genotype_performance_with_sample_gvcf ... ok
[INFO] [stdout] test test_dot_alt_not_included_in_alleles ... ok
[INFO] [stdout] test test_g_vcf_record ... ok
[INFO] [stdout] test test_genotype_parsing_multiallelic ... ok
[INFO] [stdout] test test_genotype_with_format_fields ... ok
[INFO] [stdout] test test_gvcf_parsing ... ok
[INFO] [stdout] test test_non_ref_not_included_in_alleles ... ok
[INFO] [stdout] test test_parse_rejects_consecutive_separators ... ok
[INFO] [stdout] test test_haploid_parsing ... ok
[INFO] [stdout] test test_parse_rejects_allele_index_out_of_range ... ok
[INFO] [stdout] test test_parse_rejects_trailing_junk ... ok
[INFO] [stdout] test test_parse_rejects_leading_separator ... ok
[INFO] [stdout] test test_peek_variant_exhausted ... ok
[INFO] [stdout] test test_peek_variant ... ok
[INFO] [stdout] test test_sample_parsing ... ok
[INFO] [stdout] test test_gzip_reader ... ok
[INFO] [stdout] test test_gzip_path ... ok
[INFO] [stdout] test test_get_span_returns_error_on_position_overflow ... ok
[INFO] [stdout] test test_ref_allele_len ... ok
[INFO] [stdout] test test_parse_rejects_invalid_characters ... ok
[INFO] [stdout] test test_ploidy_mismatch_rejected ... ok
[INFO] [stdout] test test_sample_parsing_single_sample ... ok
[INFO] [stdout] test test_tetraploid_parsing ... ok
[INFO] [stderr]      Running tests/integration_test.rs (/opt/rustwide/target/debug/deps/integration_test-d749f800d7f77c93)
[INFO] [stdout] test test_sample_parsing_with_buffer ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 26 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.01s
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] running 17 tests
[INFO] [stdout] test test_all_ref_samples_produce_no_variants ... ok
[INFO] [stdout] test test_del1 ... ok
[INFO] [stdout] test test_del2 ... ok
[INFO] [stdout] test test_del4 ... ok
[INFO] [stdout] test test_del_ins ... ok
[INFO] [stdout] test test_deletion_overlapping_with_snps ... ok
[INFO] [stdout] test test_del_ins_missing_phase ... ok
[INFO] [stdout] test test_missing_phase1 ... ok
[INFO] [stdout] test test_full_pipeline_two_samples ... ok
[INFO] [stdout] test test_missing_genotype_propagation ... ok
[INFO] [stdout] test test_missing_phase3 ... ok
[INFO] [stdout] test test_missing_phase2 ... ok
[INFO] [stdout] test test_multi_chromosome_pipeline ... ok
[INFO] [stdout] test test_template_two_samples_snps ... ok
[INFO] [stdout] test test_snps_some_phases ... ok
[INFO] [stdout] test test_del3 ... ok
[INFO] [stdout] test test_template_two_samples_non_ref_snps ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 17 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.03s
[INFO] [stdout] 
[INFO] [stderr]      Running tests/utils_magic_test.rs (/opt/rustwide/target/debug/deps/utils_magic_test-eaa3987edca54f17)
[INFO] [stdout] 
[INFO] [stdout] running 8 tests
[INFO] [stdout] test are_gzipped_magic_bytes_detects_non_gzip_header ... ok
[INFO] [stdout] test file_is_gzipped_propagates_io_error_for_missing_file ... ok
[INFO] [stdout] test file_is_gzipped_returns_false_for_plain_file ... ok
[INFO] [stdout] test are_gzipped_magic_bytes_detects_gzip_header ... ok
[INFO] [stdout] test are_gzipped_magic_bytes_returns_error_for_insufficient_bytes ... ok
[INFO] [stdout] test file_is_gzipped_works_with_paths_from_fs_module ... ok
[INFO] [stdout] test file_is_gzipped_returns_error_for_short_file ... ok
[INFO] [stdout] test file_is_gzipped_returns_true_for_file_with_gzip_magic_bytes ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 8 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s
[INFO] [stdout] 
[INFO] [stderr]      Running tests/variant_group_test.rs (/opt/rustwide/target/debug/deps/variant_group_test-19cc1aa3c29553e2)
[INFO] [stdout] 
[INFO] [stdout] running 12 tests
[INFO] [stdout] test test_duplicate_samples ... ok
[INFO] [stdout] test test_empty_input ... ok
[INFO] [stdout] test test_single_variant_group ... ok
[INFO] [stdout] test test_bin_contains_expected_variants ... ok
[INFO] [stdout] test test_source_iter_samples ... ok
[INFO] [stdout] test test_no_matching_chromosomes ... ok
[INFO] [stdout] test test_wrong_chrom_order ... ok
[INFO] [stdout] test test_wrong_order ... ok
[INFO] [stdout] test test_non_variable_groups_are_skipped ... ok
[INFO] [stdout] test test_skip_path_produces_fewer_groups ... ok
[INFO] [stdout] test test_simple_binning ... ok
[INFO] [stdout] test test_binning_with_deletion_spanning_several_snps ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 12 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s
[INFO] [stdout] 
[INFO] [stderr]    Doc-tests merge_per_sample_vcfs
[INFO] [stdout] 
[INFO] [stdout] running 1 test
[INFO] [stdout] test src/gvcf_parser.rs - gvcf_parser (line 6) - compile ... FAILED
[INFO] [stdout] 
[INFO] [stdout] failures:
[INFO] [stdout] 
[INFO] [stdout] ---- src/gvcf_parser.rs - gvcf_parser (line 6) stdout ----
[INFO] [stdout] error[E0061]: this function takes 2 arguments but 1 argument was supplied
[INFO] [stdout]    --> src/gvcf_parser.rs:12:14
[INFO] [stdout]     |
[INFO] [stdout]  12 | let parser = VarIterator::from_gzip_path("sample.g.vcf.gz")?;
[INFO] [stdout]     |              ^^^^^^^^^^^^^^^^^^^^^^^^^^^------------------- argument #2 of type `u8` is missing
[INFO] [stdout]     |
[INFO] [stdout] note: associated function defined here
[INFO] [stdout]    --> src/gvcf_parser.rs:741:12
[INFO] [stdout]     |
[INFO] [stdout] 741 |     pub fn from_gzip_path<P: AsRef<Path>>(path: P, ploidy: u8) -> VcfResult<Self> {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^
[INFO] [stdout] help: provide the argument
[INFO] [stdout]     |
[INFO] [stdout]  12 | let parser = VarIterator::from_gzip_path("sample.g.vcf.gz", /* u8 */)?;
[INFO] [stdout]     |                                                           ++++++++++
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 1 previous error
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0061`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] 
[INFO] [stdout] failures:
[INFO] [stdout]     src/gvcf_parser.rs - gvcf_parser (line 6)
[INFO] [stdout] 
[INFO] [stdout] test result: FAILED. 0 passed; 1 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.15s
[INFO] [stdout] 
[INFO] [stdout] all doctests ran in 0.25s; merged doctests compilation took 0.09s
[INFO] [stderr] error: doctest failed, to rerun pass `--doc`
[INFO] running `Command { std: "docker" "inspect" "c766a9e04968b3af268252e618f0dab7796171f4e0b60917ab8e5b530de2a53c", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "c766a9e04968b3af268252e618f0dab7796171f4e0b60917ab8e5b530de2a53c", kill_on_drop: false }`
[INFO] [stdout] c766a9e04968b3af268252e618f0dab7796171f4e0b60917ab8e5b530de2a53c
