[INFO] cloning repository https://github.com/kgori/alignomatic
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/kgori/alignomatic" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fkgori%2Falignomatic", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fkgori%2Falignomatic'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] df45c7126ade2e424f0738fc7f4ed59f4e056640
[INFO] testing kgori/alignomatic against try#bd7d74411512a3dd3b35d2f699c51dd2557c7e7e+cargoflags=-Zbuild-dir-new-layout for pr-149852-1
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fkgori%2Falignomatic" "/workspace/builds/worker-4-tc2/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-4-tc2/source'...
[INFO] [stderr] done.
[INFO] started tweaking git repo https://github.com/kgori/alignomatic
[INFO] finished tweaking git repo https://github.com/kgori/alignomatic
[INFO] tweaked toml for git repo https://github.com/kgori/alignomatic written to /workspace/builds/worker-4-tc2/source/Cargo.toml
[INFO] validating manifest of git repo https://github.com/kgori/alignomatic on toolchain bd7d74411512a3dd3b35d2f699c51dd2557c7e7e
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+bd7d74411512a3dd3b35d2f699c51dd2557c7e7e" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate git repo https://github.com/kgori/alignomatic 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" "+bd7d74411512a3dd3b35d2f699c51dd2557c7e7e" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-tc2/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:aa71247004a7fa38d13ec170f48f06cdedf5bc50b2a8645e56ed7e992e6fa513" "/opt/rustwide/cargo-home/bin/cargo" "+bd7d74411512a3dd3b35d2f699c51dd2557c7e7e" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] 4fcea35d9524bac88f7b7b45798db5963554604fe7279420fd2f5ccbd02a0145
[INFO] running `Command { std: "docker" "start" "-a" "4fcea35d9524bac88f7b7b45798db5963554604fe7279420fd2f5ccbd02a0145", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "4fcea35d9524bac88f7b7b45798db5963554604fe7279420fd2f5ccbd02a0145", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "4fcea35d9524bac88f7b7b45798db5963554604fe7279420fd2f5ccbd02a0145", kill_on_drop: false }`
[INFO] [stdout] 4fcea35d9524bac88f7b7b45798db5963554604fe7279420fd2f5ccbd02a0145
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-tc2/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "RUSTDOCFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:aa71247004a7fa38d13ec170f48f06cdedf5bc50b2a8645e56ed7e992e6fa513" "/opt/rustwide/cargo-home/bin/cargo" "+bd7d74411512a3dd3b35d2f699c51dd2557c7e7e" "build" "--frozen" "--message-format=json" "-Zbuild-dir-new-layout", kill_on_drop: false }`
[INFO] [stdout] 5ec7880e22863620eb5ee576e6b4e07631bd4e36ea0167cad005a7f814efd44c
[INFO] running `Command { std: "docker" "start" "-a" "5ec7880e22863620eb5ee576e6b4e07631bd4e36ea0167cad005a7f814efd44c", kill_on_drop: false }`
[INFO] [stderr]    Compiling libm v0.2.11
[INFO] [stderr]    Compiling zerocopy v0.8.24
[INFO] [stderr]    Compiling glob v0.3.2
[INFO] [stderr]    Compiling num-traits v0.2.19
[INFO] [stderr]    Compiling aho-corasick v1.1.3
[INFO] [stderr]    Compiling regex-syntax v0.8.5
[INFO] [stderr]    Compiling jobserver v0.1.33
[INFO] [stderr]    Compiling getrandom v0.2.15
[INFO] [stderr]    Compiling nom v7.1.3
[INFO] [stderr]    Compiling matrixmultiply v0.3.9
[INFO] [stderr]    Compiling libloading v0.8.6
[INFO] [stderr]    Compiling either v1.15.0
[INFO] [stderr]    Compiling syn v2.0.100
[INFO] [stderr]    Compiling getrandom v0.3.2
[INFO] [stderr]    Compiling bytemuck v1.22.0
[INFO] [stderr]    Compiling bindgen v0.69.5
[INFO] [stderr]    Compiling cc v1.2.19
[INFO] [stderr]    Compiling quick-error v1.2.3
[INFO] [stderr]    Compiling bitflags v2.9.0
[INFO] [stderr]    Compiling itertools v0.12.1
[INFO] [stderr]    Compiling safe_arch v0.7.4
[INFO] [stderr]    Compiling fs-utils v1.1.4
[INFO] [stderr]    Compiling newtype_derive v0.1.6
[INFO] [stderr]    Compiling clang-sys v1.8.1
[INFO] [stderr]    Compiling rand_core v0.6.4
[INFO] [stderr]    Compiling zstd-safe v7.2.4
[INFO] [stderr]    Compiling rand_core v0.9.3
[INFO] [stderr]    Compiling hashbrown v0.15.2
[INFO] [stderr]    Compiling anyhow v1.0.98
[INFO] [stderr]    Compiling form_urlencoded v1.2.1
[INFO] [stderr]    Compiling miniz_oxide v0.8.8
[INFO] [stderr]    Compiling csv-core v0.1.12
[INFO] [stderr]    Compiling bit-vec v0.8.0
[INFO] [stderr]    Compiling wide v0.7.32
[INFO] [stderr]    Compiling fixedbitset v0.5.7
[INFO] [stderr]    Compiling custom_derive v0.1.7
[INFO] [stderr]    Compiling bit-set v0.8.0
[INFO] [stderr]    Compiling fxhash v0.2.1
[INFO] [stderr]    Compiling cmake v0.1.54
[INFO] [stderr]    Compiling flate2 v1.1.1
[INFO] [stderr]    Compiling ieee754 v0.2.6
[INFO] [stderr]    Compiling indexmap v2.9.0
[INFO] [stderr]    Compiling strum v0.26.3
[INFO] [stderr]    Compiling editdistancek v1.0.2
[INFO] [stderr]    Compiling linear-map v1.2.0
[INFO] [stderr]    Compiling triple_accel v0.4.0
[INFO] [stderr]    Compiling bytecount v0.6.8
[INFO] [stderr]    Compiling clap_builder v4.5.36
[INFO] [stderr]    Compiling ppv-lite86 v0.2.21
[INFO] [stderr]    Compiling regex-automata v0.4.9
[INFO] [stderr]    Compiling jiff v0.2.8
[INFO] [stderr]    Compiling num_cpus v1.16.0
[INFO] [stderr]    Compiling num-complex v0.4.6
[INFO] [stderr]    Compiling num-integer v0.1.46
[INFO] [stderr]    Compiling approx v0.5.1
[INFO] [stderr]    Compiling petgraph v0.7.1
[INFO] [stderr]    Compiling ordered-float v5.0.0
[INFO] [stderr]    Compiling rand_chacha v0.3.1
[INFO] [stderr]    Compiling rand_chacha v0.9.0
[INFO] [stderr]    Compiling libz-sys v1.1.22
[INFO] [stderr]    Compiling zstd-sys v2.0.15+zstd.1.5.7
[INFO] [stderr]    Compiling cexpr v0.6.0
[INFO] [stderr]    Compiling rand v0.8.5
[INFO] [stderr]    Compiling simba v0.9.0
[INFO] [stderr]    Compiling num-rational v0.4.2
[INFO] [stderr]    Compiling bzip2-sys v0.1.13+1.0.8
[INFO] [stderr]    Compiling liblzma-sys v0.3.13
[INFO] [stderr]    Compiling libdeflate-sys v0.7.5
[INFO] [stderr]    Compiling regex v1.11.1
[INFO] [stderr]    Compiling rand_distr v0.4.3
[INFO] [stderr]    Compiling bwa-sys v0.1.0 (https://github.com/kgori/rust-bwa.git?branch=dev#4a2f4ce0)
[INFO] [stderr]    Compiling rand v0.9.0
[INFO] [stderr]    Compiling ndarray v0.16.1
[INFO] [stderr]    Compiling synstructure v0.13.1
[INFO] [stderr]    Compiling blake3 v1.8.1
[INFO] [stderr]    Compiling itertools-num v0.1.3
[INFO] [stderr]    Compiling libdeflater v0.7.5
[INFO] [stderr]    Compiling env_filter v0.1.3
[INFO] [stderr]    Compiling bzip2 v0.4.4
[INFO] [stderr]    Compiling zerofrom-derive v0.1.6
[INFO] [stderr]    Compiling yoke-derive v0.7.5
[INFO] [stderr]    Compiling zerovec-derive v0.10.3
[INFO] [stderr]    Compiling displaydoc v0.2.5
[INFO] [stderr]    Compiling serde_derive v1.0.219
[INFO] [stderr]    Compiling icu_provider_macros v1.5.0
[INFO] [stderr]    Compiling thiserror-impl v1.0.69
[INFO] [stderr]    Compiling thiserror-impl v2.0.12
[INFO] [stderr]    Compiling strum_macros v0.26.4
[INFO] [stderr]    Compiling derive-new v0.6.0
[INFO] [stderr]    Compiling enum-map-derive v0.17.0
[INFO] [stderr]    Compiling nalgebra v0.33.2
[INFO] [stderr]    Compiling enum-map v2.7.3
[INFO] [stderr]    Compiling derive-new v0.7.0
[INFO] [stderr]    Compiling clap_derive v4.5.32
[INFO] [stderr]    Compiling env_logger v0.11.8
[INFO] [stderr]    Compiling zerofrom v0.1.6
[INFO] [stderr]    Compiling yoke v0.7.5
[INFO] [stderr]    Compiling thiserror v1.0.69
[INFO] [stderr]    Compiling bgzip v0.3.1
[INFO] [stderr]    Compiling thiserror v2.0.12
[INFO] [stderr]    Compiling bgzf v0.2.0
[INFO] [stderr]    Compiling zerovec v0.10.4
[INFO] [stderr]    Compiling clap v4.5.36
[INFO] [stderr]    Compiling serde v1.0.219
[INFO] [stderr]    Compiling tinystr v0.7.6
[INFO] [stderr]    Compiling icu_collections v1.5.0
[INFO] [stderr]    Compiling icu_locid v1.5.0
[INFO] [stderr]    Compiling liblzma v0.3.6
[INFO] [stderr]    Compiling icu_provider v1.5.0
[INFO] [stderr]    Compiling icu_locid_transform v1.5.0
[INFO] [stderr]    Compiling zstd v0.13.3
[INFO] [stderr]    Compiling niffler v2.7.0
[INFO] [stderr]    Compiling hts-sys v2.2.0
[INFO] [stderr]    Compiling icu_properties v1.5.1
[INFO] [stderr]    Compiling bio-types v1.0.4
[INFO] [stderr]    Compiling csv v1.3.1
[INFO] [stderr]    Compiling multimap v0.10.0
[INFO] [stderr]    Compiling bv v0.11.1
[INFO] [stderr]    Compiling vec_map v0.8.2
[INFO] [stderr]    Compiling serde_bytes v0.11.17
[INFO] [stderr]    Compiling serde_json v1.0.140
[INFO] [stderr]    Compiling icu_normalizer v1.5.0
[INFO] [stderr]    Compiling idna_adapter v1.2.0
[INFO] [stderr]    Compiling idna v1.0.3
[INFO] [stderr]    Compiling url v2.5.4
[INFO] [stderr]    Compiling statrs v0.18.0
[INFO] [stderr]    Compiling bio v2.2.0
[INFO] [stderr]    Compiling rust-htslib v0.49.0
[INFO] [stderr]    Compiling bwa v0.1.2 (https://github.com/kgori/rust-bwa.git?branch=dev#4a2f4ce0)
[INFO] [stderr]    Compiling alignomatic v0.3.2 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 1m 04s
[INFO] running `Command { std: "docker" "inspect" "5ec7880e22863620eb5ee576e6b4e07631bd4e36ea0167cad005a7f814efd44c", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "5ec7880e22863620eb5ee576e6b4e07631bd4e36ea0167cad005a7f814efd44c", kill_on_drop: false }`
[INFO] [stdout] 5ec7880e22863620eb5ee576e6b4e07631bd4e36ea0167cad005a7f814efd44c
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-tc2/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "RUSTDOCFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:aa71247004a7fa38d13ec170f48f06cdedf5bc50b2a8645e56ed7e992e6fa513" "/opt/rustwide/cargo-home/bin/cargo" "+bd7d74411512a3dd3b35d2f699c51dd2557c7e7e" "test" "--frozen" "--no-run" "--message-format=json" "-Zbuild-dir-new-layout", kill_on_drop: false }`
[INFO] [stdout] d26e1b0b9ba9c1c685b70a84819d409da67f8b7b8aebaa8ca3c7da8d2924c826
[INFO] running `Command { std: "docker" "start" "-a" "d26e1b0b9ba9c1c685b70a84819d409da67f8b7b8aebaa8ca3c7da8d2924c826", kill_on_drop: false }`
[INFO] [stderr]    Compiling alignomatic v0.3.2 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished `test` profile [unoptimized + debuginfo] target(s) in 1.08s
[INFO] running `Command { std: "docker" "inspect" "d26e1b0b9ba9c1c685b70a84819d409da67f8b7b8aebaa8ca3c7da8d2924c826", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "d26e1b0b9ba9c1c685b70a84819d409da67f8b7b8aebaa8ca3c7da8d2924c826", kill_on_drop: false }`
[INFO] [stdout] d26e1b0b9ba9c1c685b70a84819d409da67f8b7b8aebaa8ca3c7da8d2924c826
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-tc2/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "RUSTDOCFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:aa71247004a7fa38d13ec170f48f06cdedf5bc50b2a8645e56ed7e992e6fa513" "/opt/rustwide/cargo-home/bin/cargo" "+bd7d74411512a3dd3b35d2f699c51dd2557c7e7e" "test" "--frozen" "-Zbuild-dir-new-layout", kill_on_drop: false }`
[INFO] [stdout] c9a2745eb13482435e565ab4738a6811d0884eec8a6efc506f9c12f65fcf5412
[INFO] running `Command { std: "docker" "start" "-a" "c9a2745eb13482435e565ab4738a6811d0884eec8a6efc506f9c12f65fcf5412", kill_on_drop: false }`
[INFO] [stderr]     Finished `test` profile [unoptimized + debuginfo] target(s) in 0.16s
[INFO] [stderr]      Running unittests src/main.rs (/opt/rustwide/target/debug/build/alignomatic/1230ac5423072571/deps/alignomatic-1230ac5423072571)
[INFO] [stdout] 
[INFO] [stdout] running 1 test
[INFO] [stdout] test utils::test::test_bam_to_fastq ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 1 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.34s
[INFO] [stdout] 
[INFO] running `Command { std: "docker" "inspect" "c9a2745eb13482435e565ab4738a6811d0884eec8a6efc506f9c12f65fcf5412", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "c9a2745eb13482435e565ab4738a6811d0884eec8a6efc506f9c12f65fcf5412", kill_on_drop: false }`
[INFO] [stdout] c9a2745eb13482435e565ab4738a6811d0884eec8a6efc506f9c12f65fcf5412