[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] fb763c823b626497a1e60f2067cbce6f1d7ac88b
[INFO] checking kgori/alignomatic against try#5de9e0e6cf775e94e0de2003f35e183f3f77bfe8 for pr-143808
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fkgori%2Falignomatic" "/workspace/builds/worker-0-tc2/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-0-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-0-tc2/source/Cargo.toml
[INFO] validating manifest of git repo https://github.com/kgori/alignomatic on toolchain 5de9e0e6cf775e94e0de2003f35e183f3f77bfe8
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+5de9e0e6cf775e94e0de2003f35e183f3f77bfe8" "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" "+5de9e0e6cf775e94e0de2003f35e183f3f77bfe8" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Blocking waiting for file lock on package cache
[INFO] [stderr]     Updating crates.io index
[INFO] [stderr]     Updating git repository `https://github.com/kgori/rust-bwa.git`
[INFO] [stderr]     Updating git submodule `https://github.com/10XGenomics/bwa.git`
[INFO] [stderr]     Blocking waiting for file lock on package cache
[ERROR] error running command: no output for 300 seconds
[INFO] checking kgori/alignomatic against try#5de9e0e6cf775e94e0de2003f35e183f3f77bfe8 for pr-143808
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fkgori%2Falignomatic" "/workspace/builds/worker-0-tc2/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-0-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-0-tc2/source/Cargo.toml
[INFO] validating manifest of git repo https://github.com/kgori/alignomatic on toolchain 5de9e0e6cf775e94e0de2003f35e183f3f77bfe8
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+5de9e0e6cf775e94e0de2003f35e183f3f77bfe8" "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" "+5de9e0e6cf775e94e0de2003f35e183f3f77bfe8" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Blocking waiting for file lock on package cache
[INFO] [stderr]     Blocking waiting for file lock on package cache
[INFO] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded bio-types v1.0.4
[INFO] [stderr]   Downloaded editdistancek v1.0.2
[INFO] [stderr]   Downloaded fs-utils v1.1.4
[INFO] [stderr]   Downloaded bgzf v0.2.0
[INFO] [stderr]   Downloaded libdeflater v0.7.5
[INFO] [stderr]   Downloaded bgzip v0.3.1
[INFO] [stderr]   Downloaded niffler v2.7.0
[INFO] [stderr]   Downloaded rust-htslib v0.49.0
[INFO] [stderr]   Downloaded bio v2.2.0
[INFO] [stderr]   Downloaded libdeflate-sys v0.7.5
[INFO] [stderr]   Downloaded hts-sys v2.2.0
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-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:cf8efcab8866f2cf4285301c7418e2f4f2a9b088c91ba69c40d5b659f81557f7" "/opt/rustwide/cargo-home/bin/cargo" "+5de9e0e6cf775e94e0de2003f35e183f3f77bfe8" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] c50e6f38a93ec6c2f346b3281074099f3e89511909ba43a0ad9aae20fd079a92
[INFO] running `Command { std: "docker" "start" "-a" "c50e6f38a93ec6c2f346b3281074099f3e89511909ba43a0ad9aae20fd079a92", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "c50e6f38a93ec6c2f346b3281074099f3e89511909ba43a0ad9aae20fd079a92", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "c50e6f38a93ec6c2f346b3281074099f3e89511909ba43a0ad9aae20fd079a92", kill_on_drop: false }`
[INFO] [stdout] c50e6f38a93ec6c2f346b3281074099f3e89511909ba43a0ad9aae20fd079a92
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-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:cf8efcab8866f2cf4285301c7418e2f4f2a9b088c91ba69c40d5b659f81557f7" "/opt/rustwide/cargo-home/bin/cargo" "+5de9e0e6cf775e94e0de2003f35e183f3f77bfe8" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] db540c1aa1ba4d5f8cf8f4e2c97312c7ca888dd0509fbb31dabc3a84b02804c8
[INFO] running `Command { std: "docker" "start" "-a" "db540c1aa1ba4d5f8cf8f4e2c97312c7ca888dd0509fbb31dabc3a84b02804c8", kill_on_drop: false }`
[INFO] [stderr]    Compiling libc v0.2.172
[INFO] [stderr]    Compiling shlex v1.3.0
[INFO] [stderr]    Compiling pkg-config v0.3.32
[INFO] [stderr]     Checking stable_deref_trait v1.2.0
[INFO] [stderr]     Checking writeable v0.5.5
[INFO] [stderr]     Checking litemap v0.7.5
[INFO] [stderr]    Compiling glob v0.3.2
[INFO] [stderr]    Compiling icu_locid_transform_data v1.5.1
[INFO] [stderr]    Compiling num-traits v0.2.19
[INFO] [stderr]    Compiling icu_properties_data v1.5.1
[INFO] [stderr]     Checking aho-corasick v1.1.3
[INFO] [stderr]    Compiling cfg-if v1.0.0
[INFO] [stderr]    Compiling minimal-lexical v0.2.1
[INFO] [stderr]    Compiling regex-syntax v0.8.5
[INFO] [stderr]    Compiling syn v2.0.100
[INFO] [stderr]    Compiling icu_normalizer_data v1.5.1
[INFO] [stderr]    Compiling memchr v2.7.4
[INFO] [stderr]    Compiling libloading v0.8.6
[INFO] [stderr]    Compiling matrixmultiply v0.3.9
[INFO] [stderr]    Compiling either v1.15.0
[INFO] [stderr]    Compiling rustversion v1.0.20
[INFO] [stderr]    Compiling paste v1.0.15
[INFO] [stderr]    Compiling bindgen v0.69.5
[INFO] [stderr]     Checking bytemuck v1.22.0
[INFO] [stderr]    Compiling vcpkg v0.2.15
[INFO] [stderr]    Compiling getrandom v0.3.2
[INFO] [stderr]    Compiling heck v0.5.0
[INFO] [stderr]     Checking safe_arch v0.7.4
[INFO] [stderr]    Compiling itertools v0.12.1
[INFO] [stderr]     Checking utf8_iter v1.0.4
[INFO] [stderr]    Compiling clang-sys v1.8.1
[INFO] [stderr]    Compiling nom v7.1.3
[INFO] [stderr]    Compiling bitflags v2.9.0
[INFO] [stderr]     Checking rawpointer v0.2.1
[INFO] [stderr]     Checking utf16_iter v1.0.5
[INFO] [stderr]     Checking write16 v1.0.0
[INFO] [stderr]    Compiling lazycell v1.3.0
[INFO] [stderr]    Compiling lazy_static v1.5.0
[INFO] [stderr]     Checking smallvec v1.15.0
[INFO] [stderr]    Compiling quick-error v1.2.3
[INFO] [stderr]    Compiling thiserror v2.0.12
[INFO] [stderr]    Compiling rustc-hash v1.1.0
[INFO] [stderr]    Compiling fs-utils v1.1.4
[INFO] [stderr]    Compiling newtype_derive v0.1.6
[INFO] [stderr]     Checking wide v0.7.32
[INFO] [stderr]     Checking utf8parse v0.2.2
[INFO] [stderr]    Compiling feature-probe v0.1.1
[INFO] [stderr]     Checking regex-automata v0.4.9
[INFO] [stderr]     Checking anstyle-parse v0.2.6
[INFO] [stderr]     Checking num-complex v0.4.6
[INFO] [stderr]     Checking num-integer v0.1.46
[INFO] [stderr]     Checking approx v0.5.1
[INFO] [stderr]     Checking percent-encoding v2.3.1
[INFO] [stderr]    Compiling bv v0.11.1
[INFO] [stderr]    Compiling jobserver v0.1.33
[INFO] [stderr]     Checking getrandom v0.2.15
[INFO] [stderr]    Compiling zstd-safe v7.2.4
[INFO] [stderr]     Checking anstyle-query v1.1.2
[INFO] [stderr]     Checking num-rational v0.4.2
[INFO] [stderr]    Compiling anyhow v1.0.98
[INFO] [stderr]     Checking rand_core v0.6.4
[INFO] [stderr]     Checking rand_core v0.9.3
[INFO] [stderr]     Checking itoa v1.0.15
[INFO] [stderr]    Compiling cc v1.2.19
[INFO] [stderr]     Checking ryu v1.0.20
[INFO] [stderr]     Checking is_terminal_polyfill v1.70.1
[INFO] [stderr]     Checking colorchoice v1.0.3
[INFO] [stderr]     Checking rand_chacha v0.3.1
[INFO] [stderr]     Checking hashbrown v0.15.2
[INFO] [stderr]     Checking anstyle v1.0.10
[INFO] [stderr]     Checking miniz_oxide v0.8.8
[INFO] [stderr]     Checking rand_chacha v0.9.0
[INFO] [stderr]     Checking form_urlencoded v1.2.1
[INFO] [stderr]     Checking csv-core v0.1.12
[INFO] [stderr]     Checking anstream v0.6.18
[INFO] [stderr]     Checking rand v0.8.5
[INFO] [stderr]     Checking bit-vec v0.8.0
[INFO] [stderr]     Checking fixedbitset v0.5.7
[INFO] [stderr]     Checking custom_derive v0.1.7
[INFO] [stderr]     Checking rand v0.9.0
[INFO] [stderr]     Checking bit-set v0.8.0
[INFO] [stderr]     Checking ndarray v0.16.1
[INFO] [stderr]     Checking flate2 v1.1.1
[INFO] [stderr]    Compiling cexpr v0.6.0
[INFO] [stderr]     Checking indexmap v2.9.0
[INFO] [stderr]     Checking itertools v0.14.0
[INFO] [stderr]     Checking itertools-num v0.1.3
[INFO] [stderr]     Checking ordered-float v5.0.0
[INFO] [stderr]     Checking fxhash v0.2.1
[INFO] [stderr]    Compiling cmake v0.1.54
[INFO] [stderr]     Checking simba v0.9.0
[INFO] [stderr]     Checking bytecount v0.6.8
[INFO] [stderr]     Checking strsim v0.11.1
[INFO] [stderr]     Checking strum v0.26.3
[INFO] [stderr]     Checking rand_distr v0.4.3
[INFO] [stderr]     Checking triple_accel v0.4.0
[INFO] [stderr]     Checking regex v1.11.1
[INFO] [stderr]     Checking clap_lex v0.7.4
[INFO] [stderr]     Checking linear-map v1.2.0
[INFO] [stderr]     Checking editdistancek v1.0.2
[INFO] [stderr]     Checking ieee754 v0.2.6
[INFO] [stderr]    Compiling serde_json v1.0.140
[INFO] [stderr]     Checking clap_builder v4.5.36
[INFO] [stderr]     Checking arrayvec v0.7.6
[INFO] [stderr]     Checking jiff v0.2.8
[INFO] [stderr]     Checking env_filter v0.1.3
[INFO] [stderr]     Checking arrayref v0.3.9
[INFO] [stderr]     Checking constant_time_eq v0.3.1
[INFO] [stderr]     Checking petgraph v0.7.1
[INFO] [stderr]     Checking num_cpus v1.16.0
[INFO] [stderr]    Compiling zstd-sys v2.0.15+zstd.1.5.7
[INFO] [stderr]    Compiling libz-sys v1.1.22
[INFO] [stderr]    Compiling bzip2-sys v0.1.13+1.0.8
[INFO] [stderr]    Compiling libdeflate-sys v0.7.5
[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 synstructure v0.13.1
[INFO] [stderr]     Checking 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 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]     Checking libdeflater v0.7.5
[INFO] [stderr]    Compiling clap_derive v4.5.32
[INFO] [stderr]     Checking enum-map v2.7.3
[INFO] [stderr]     Checking env_logger v0.11.8
[INFO] [stderr]     Checking zerofrom v0.1.6
[INFO] [stderr]     Checking thiserror v1.0.69
[INFO] [stderr]     Checking yoke v0.7.5
[INFO] [stderr]     Checking bgzip v0.3.1
[INFO] [stderr]     Checking bgzf v0.2.0
[INFO] [stderr]     Checking zerovec v0.10.4
[INFO] [stderr]     Checking tinystr v0.7.6
[INFO] [stderr]     Checking icu_collections v1.5.0
[INFO] [stderr]     Checking clap v4.5.36
[INFO] [stderr]     Checking nalgebra v0.33.2
[INFO] [stderr]     Checking icu_locid v1.5.0
[INFO] [stderr]     Checking liblzma v0.3.6
[INFO] [stderr]     Checking serde v1.0.219
[INFO] [stderr]     Checking icu_provider v1.5.0
[INFO] [stderr]     Checking icu_locid_transform v1.5.0
[INFO] [stderr]    Compiling hts-sys v2.2.0
[INFO] [stderr]     Checking icu_properties v1.5.1
[INFO] [stderr]     Checking bio-types v1.0.4
[INFO] [stderr]     Checking multimap v0.10.0
[INFO] [stderr]     Checking csv v1.3.1
[INFO] [stderr]     Checking serde_bytes v0.11.17
[INFO] [stderr]     Checking vec_map v0.8.2
[INFO] [stderr]     Checking icu_normalizer v1.5.0
[INFO] [stderr]     Checking zstd v0.13.3
[INFO] [stderr]     Checking idna_adapter v1.2.0
[INFO] [stderr]     Checking idna v1.0.3
[INFO] [stderr]     Checking niffler v2.7.0
[INFO] [stderr]     Checking url v2.5.4
[INFO] [stderr]     Checking statrs v0.18.0
[INFO] [stderr]     Checking bio v2.2.0
[INFO] [stderr]     Checking rust-htslib v0.49.0
[INFO] [stderr]     Checking bwa v0.1.2 (https://github.com/kgori/rust-bwa.git?branch=dev#4a2f4ce0)
[INFO] [stderr]     Checking alignomatic v0.3.2 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 21.79s
[INFO] running `Command { std: "docker" "inspect" "db540c1aa1ba4d5f8cf8f4e2c97312c7ca888dd0509fbb31dabc3a84b02804c8", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "db540c1aa1ba4d5f8cf8f4e2c97312c7ca888dd0509fbb31dabc3a84b02804c8", kill_on_drop: false }`
[INFO] [stdout] db540c1aa1ba4d5f8cf8f4e2c97312c7ca888dd0509fbb31dabc3a84b02804c8