[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] 7513aade84315b0bf8baf95a16aa6738f17a1e6b
[INFO] testing kgori/alignomatic against try#c2e32f1c9652b13ed99608599c1e855462f421f3 for pr-146098-7
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fkgori%2Falignomatic" "/workspace/builds/worker-6-tc2/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-6-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-6-tc2/source/Cargo.toml
[INFO] validating manifest of git repo https://github.com/kgori/alignomatic on toolchain c2e32f1c9652b13ed99608599c1e855462f421f3
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+c2e32f1c9652b13ed99608599c1e855462f421f3" "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" "+c2e32f1c9652b13ed99608599c1e855462f421f3" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-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@sha256:4848fb76d95f26979359cc7e45710b1dbc8f3acb7aeedee7c460d7702230f228" "/opt/rustwide/cargo-home/bin/cargo" "+c2e32f1c9652b13ed99608599c1e855462f421f3" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] f66d7243754a9812d093257168416fbcf7ce3c5751372ab932798e1608a4e39c
[INFO] running `Command { std: "docker" "start" "-a" "f66d7243754a9812d093257168416fbcf7ce3c5751372ab932798e1608a4e39c", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "f66d7243754a9812d093257168416fbcf7ce3c5751372ab932798e1608a4e39c", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "f66d7243754a9812d093257168416fbcf7ce3c5751372ab932798e1608a4e39c", kill_on_drop: false }`
[INFO] [stdout] f66d7243754a9812d093257168416fbcf7ce3c5751372ab932798e1608a4e39c
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-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@sha256:4848fb76d95f26979359cc7e45710b1dbc8f3acb7aeedee7c460d7702230f228" "/opt/rustwide/cargo-home/bin/cargo" "+c2e32f1c9652b13ed99608599c1e855462f421f3" "build" "--frozen" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 8dea93ffa447c51041cd600982f51e801c867ddf5ee4d97c367ad339a51770ad
[INFO] running `Command { std: "docker" "start" "-a" "8dea93ffa447c51041cd600982f51e801c867ddf5ee4d97c367ad339a51770ad", kill_on_drop: false }`
[INFO] [stderr]    Compiling libc v0.2.172
[INFO] [stderr]    Compiling libm v0.2.11
[INFO] [stderr]    Compiling serde v1.0.219
[INFO] [stderr]    Compiling glob v0.3.2
[INFO] [stderr]    Compiling num-traits v0.2.19
[INFO] [stderr]    Compiling regex-syntax v0.8.5
[INFO] [stderr]    Compiling minimal-lexical v0.2.1
[INFO] [stderr]    Compiling libloading v0.8.6
[INFO] [stderr]    Compiling matrixmultiply v0.3.9
[INFO] [stderr]    Compiling bytemuck v1.22.0
[INFO] [stderr]    Compiling getrandom v0.3.2
[INFO] [stderr]    Compiling syn v2.0.100
[INFO] [stderr]    Compiling bindgen v0.69.5
[INFO] [stderr]    Compiling semver v0.1.20
[INFO] [stderr]    Compiling itertools v0.12.1
[INFO] [stderr]    Compiling quick-error v1.2.3
[INFO] [stderr]    Compiling nom v7.1.3
[INFO] [stderr]    Compiling rustc_version v0.1.7
[INFO] [stderr]    Compiling rawpointer v0.2.1
[INFO] [stderr]    Compiling lazycell v1.3.0
[INFO] [stderr]    Compiling bitflags v2.9.0
[INFO] [stderr]    Compiling smallvec v1.15.0
[INFO] [stderr]    Compiling rustc-hash v1.1.0
[INFO] [stderr]    Compiling fs-utils v1.1.4
[INFO] [stderr]    Compiling feature-probe v0.1.1
[INFO] [stderr]    Compiling newtype_derive v0.1.6
[INFO] [stderr]    Compiling safe_arch v0.7.4
[INFO] [stderr]    Compiling percent-encoding v2.3.1
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[INFO] [stderr]    Compiling clang-sys v1.8.1
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[INFO] [stderr]    Compiling bv v0.11.1
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[INFO] [stderr]    Compiling fxhash v0.2.1
[INFO] [stderr]    Compiling strum v0.26.3
[INFO] [stderr]    Compiling triple_accel v0.4.0
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[INFO] [stderr]    Compiling petgraph v0.7.1
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[INFO] [stderr]    Compiling cc v1.2.19
[INFO] [stderr]    Compiling rand_core v0.9.3
[INFO] [stderr]    Compiling ndarray v0.16.1
[INFO] [stderr]    Compiling rand_chacha v0.3.1
[INFO] [stderr]    Compiling rand_chacha v0.9.0
[INFO] [stderr]    Compiling ordered-float v5.0.0
[INFO] [stderr]    Compiling rand v0.9.0
[INFO] [stderr]    Compiling itertools-num v0.1.3
[INFO] [stderr]    Compiling rand v0.8.5
[INFO] [stderr]    Compiling ieee754 v0.2.6
[INFO] [stderr]    Compiling regex-automata v0.4.9
[INFO] [stderr]    Compiling bytecount v0.6.8
[INFO] [stderr]    Compiling editdistancek v1.0.2
[INFO] [stderr]    Compiling log v0.4.27
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[INFO] [stderr]    Compiling env_filter v0.1.3
[INFO] [stderr]    Compiling clap_builder v4.5.36
[INFO] [stderr]    Compiling jiff v0.2.8
[INFO] [stderr]    Compiling cexpr v0.6.0
[INFO] [stderr]    Compiling simba v0.9.0
[INFO] [stderr]    Compiling num_cpus v1.16.0
[INFO] [stderr]    Compiling cmake v0.1.54
[INFO] [stderr]    Compiling rand_distr v0.4.3
[INFO] [stderr]    Compiling libz-sys v1.1.22
[INFO] [stderr]    Compiling zstd-sys v2.0.15+zstd.1.5.7
[INFO] [stderr]    Compiling libdeflate-sys v0.7.5
[INFO] [stderr]    Compiling bzip2-sys v0.1.13+1.0.8
[INFO] [stderr]    Compiling liblzma-sys v0.3.13
[INFO] [stderr]    Compiling bwa-sys v0.1.0 (https://github.com/kgori/rust-bwa.git?branch=dev#4a2f4ce0)
[INFO] [stderr]    Compiling blake3 v1.8.1
[INFO] [stderr]    Compiling regex v1.11.1
[INFO] [stderr]    Compiling libdeflater v0.7.5
[INFO] [stderr]    Compiling bzip2 v0.4.4
[INFO] [stderr]    Compiling synstructure v0.13.1
[INFO] [stderr]    Compiling liblzma v0.3.6
[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 derive-new v0.6.0
[INFO] [stderr]    Compiling strum_macros v0.26.4
[INFO] [stderr]    Compiling enum-map-derive v0.17.0
[INFO] [stderr]    Compiling derive-new v0.7.0
[INFO] [stderr]    Compiling clap_derive v4.5.32
[INFO] [stderr]    Compiling enum-map v2.7.3
[INFO] [stderr]    Compiling env_logger v0.11.8
[INFO] [stderr]    Compiling nalgebra v0.33.2
[INFO] [stderr]    Compiling thiserror v2.0.12
[INFO] [stderr]    Compiling zerofrom v0.1.6
[INFO] [stderr]    Compiling yoke v0.7.5
[INFO] [stderr]    Compiling thiserror v1.0.69
[INFO] [stderr]    Compiling zerovec v0.10.4
[INFO] [stderr]    Compiling bgzip v0.3.1
[INFO] [stderr]    Compiling bgzf v0.2.0
[INFO] [stderr]    Compiling zstd v0.13.3
[INFO] [stderr]    Compiling niffler v2.7.0
[INFO] [stderr]    Compiling tinystr v0.7.6
[INFO] [stderr]    Compiling icu_collections v1.5.0
[INFO] [stderr]    Compiling clap v4.5.36
[INFO] [stderr]    Compiling icu_locid v1.5.0
[INFO] [stderr]    Compiling icu_provider v1.5.0
[INFO] [stderr]    Compiling icu_locid_transform v1.5.0
[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 vec_map v0.8.2
[INFO] [stderr]    Compiling serde_bytes v0.11.17
[INFO] [stderr]    Compiling multimap v0.10.0
[INFO] [stderr]    Compiling serde_json v1.0.140
[INFO] [stderr]    Compiling hts-sys v2.2.0
[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 21s
[INFO] running `Command { std: "docker" "inspect" "8dea93ffa447c51041cd600982f51e801c867ddf5ee4d97c367ad339a51770ad", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "8dea93ffa447c51041cd600982f51e801c867ddf5ee4d97c367ad339a51770ad", kill_on_drop: false }`
[INFO] [stdout] 8dea93ffa447c51041cd600982f51e801c867ddf5ee4d97c367ad339a51770ad
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-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@sha256:4848fb76d95f26979359cc7e45710b1dbc8f3acb7aeedee7c460d7702230f228" "/opt/rustwide/cargo-home/bin/cargo" "+c2e32f1c9652b13ed99608599c1e855462f421f3" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] eda3df1654d07c64a54d614de4d8c7b8ef8d07f6fe4c7ca1d36d88a6451c4bf8
[INFO] running `Command { std: "docker" "start" "-a" "eda3df1654d07c64a54d614de4d8c7b8ef8d07f6fe4c7ca1d36d88a6451c4bf8", kill_on_drop: false }`
[INFO] [stderr]    Compiling alignomatic v0.3.2 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished `test` profile [unoptimized + debuginfo] target(s) in 2.06s
[INFO] running `Command { std: "docker" "inspect" "eda3df1654d07c64a54d614de4d8c7b8ef8d07f6fe4c7ca1d36d88a6451c4bf8", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "eda3df1654d07c64a54d614de4d8c7b8ef8d07f6fe4c7ca1d36d88a6451c4bf8", kill_on_drop: false }`
[INFO] [stdout] eda3df1654d07c64a54d614de4d8c7b8ef8d07f6fe4c7ca1d36d88a6451c4bf8
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-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@sha256:4848fb76d95f26979359cc7e45710b1dbc8f3acb7aeedee7c460d7702230f228" "/opt/rustwide/cargo-home/bin/cargo" "+c2e32f1c9652b13ed99608599c1e855462f421f3" "test" "--frozen", kill_on_drop: false }`
[INFO] [stdout] cea611fae9e67d87f3687817b76630d67695649015588831aa282947f90674dc
[INFO] running `Command { std: "docker" "start" "-a" "cea611fae9e67d87f3687817b76630d67695649015588831aa282947f90674dc", kill_on_drop: false }`
[INFO] [stderr]     Finished `test` profile [unoptimized + debuginfo] target(s) in 0.32s
[INFO] [stderr]      Running unittests src/main.rs (/opt/rustwide/target/debug/deps/alignomatic-30425756cbe12b45)
[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 0.65s
[INFO] [stdout] 
[INFO] running `Command { std: "docker" "inspect" "cea611fae9e67d87f3687817b76630d67695649015588831aa282947f90674dc", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "cea611fae9e67d87f3687817b76630d67695649015588831aa282947f90674dc", kill_on_drop: false }`
[INFO] [stdout] cea611fae9e67d87f3687817b76630d67695649015588831aa282947f90674dc
