[INFO] cloning repository https://github.com/informationsea/sequencetoolkit
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/informationsea/sequencetoolkit" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Finformationsea%2Fsequencetoolkit", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Finformationsea%2Fsequencetoolkit'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] 1b99116de888026854a0e07b5d5b55c602827592
[INFO] checking informationsea/sequencetoolkit against try#15e8bc6907ab2b3623cb52acc726f4787458df64 for pr-141352
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Finformationsea%2Fsequencetoolkit" "/workspace/builds/worker-3-tc2/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-3-tc2/source'...
[INFO] [stderr] done.
[INFO] validating manifest of git repo https://github.com/informationsea/sequencetoolkit on toolchain 15e8bc6907ab2b3623cb52acc726f4787458df64
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+15e8bc6907ab2b3623cb52acc726f4787458df64" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] started tweaking git repo https://github.com/informationsea/sequencetoolkit
[INFO] finished tweaking git repo https://github.com/informationsea/sequencetoolkit
[INFO] tweaked toml for git repo https://github.com/informationsea/sequencetoolkit written to /workspace/builds/worker-3-tc2/source/Cargo.toml
[INFO] crate git repo https://github.com/informationsea/sequencetoolkit 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" "+15e8bc6907ab2b3623cb52acc726f4787458df64" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Blocking waiting for file lock on package cache
[ERROR] error running command: no output for 300 seconds
[INFO] checking informationsea/sequencetoolkit against try#15e8bc6907ab2b3623cb52acc726f4787458df64 for pr-141352
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Finformationsea%2Fsequencetoolkit" "/workspace/builds/worker-3-tc2/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-3-tc2/source'...
[INFO] [stderr] done.
[INFO] validating manifest of git repo https://github.com/informationsea/sequencetoolkit on toolchain 15e8bc6907ab2b3623cb52acc726f4787458df64
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+15e8bc6907ab2b3623cb52acc726f4787458df64" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] started tweaking git repo https://github.com/informationsea/sequencetoolkit
[INFO] finished tweaking git repo https://github.com/informationsea/sequencetoolkit
[INFO] tweaked toml for git repo https://github.com/informationsea/sequencetoolkit written to /workspace/builds/worker-3-tc2/source/Cargo.toml
[INFO] crate git repo https://github.com/informationsea/sequencetoolkit 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" "+15e8bc6907ab2b3623cb52acc726f4787458df64" "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] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-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:eea15d5475069c3ef791f10c2c6b5af2ee421ef2da1e680ecce1cba46243983b" "/opt/rustwide/cargo-home/bin/cargo" "+15e8bc6907ab2b3623cb52acc726f4787458df64" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] 286eb46c60473cd84ec6eafcd4440722c333797d88948ec2c61da7f5afa46a56
[INFO] running `Command { std: "docker" "start" "-a" "286eb46c60473cd84ec6eafcd4440722c333797d88948ec2c61da7f5afa46a56", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "286eb46c60473cd84ec6eafcd4440722c333797d88948ec2c61da7f5afa46a56", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "286eb46c60473cd84ec6eafcd4440722c333797d88948ec2c61da7f5afa46a56", kill_on_drop: false }`
[INFO] [stdout] 286eb46c60473cd84ec6eafcd4440722c333797d88948ec2c61da7f5afa46a56
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-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:eea15d5475069c3ef791f10c2c6b5af2ee421ef2da1e680ecce1cba46243983b" "/opt/rustwide/cargo-home/bin/cargo" "+15e8bc6907ab2b3623cb52acc726f4787458df64" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 9efe57e9d80153fd8ad2c899a78a1cc006befa76f99450617e7f6209d076d80d
[INFO] running `Command { std: "docker" "start" "-a" "9efe57e9d80153fd8ad2c899a78a1cc006befa76f99450617e7f6209d076d80d", kill_on_drop: false }`
[INFO] [stderr]    Compiling libc v0.2.155
[INFO] [stderr]    Compiling proc-macro2 v1.0.86
[INFO] [stderr]    Compiling pkg-config v0.3.30
[INFO] [stderr]    Compiling libm v0.2.8
[INFO] [stderr]     Checking memchr v2.7.4
[INFO] [stderr]    Compiling thiserror v1.0.63
[INFO] [stderr]    Compiling crossbeam-utils v0.8.20
[INFO] [stderr]    Compiling syn v1.0.109
[INFO] [stderr]    Compiling num-traits v0.2.19
[INFO] [stderr]    Compiling serde v1.0.204
[INFO] [stderr]     Checking miniz_oxide v0.7.4
[INFO] [stderr]     Checking either v1.13.0
[INFO] [stderr]    Compiling glob v0.3.1
[INFO] [stderr]     Checking utf8parse v0.2.2
[INFO] [stderr]    Compiling rayon-core v1.12.1
[INFO] [stderr]     Checking anstyle-query v1.1.1
[INFO] [stderr]     Checking anstyle v1.0.8
[INFO] [stderr]     Checking anstyle-parse v0.2.5
[INFO] [stderr]    Compiling rustversion v1.0.17
[INFO] [stderr]     Checking regex-syntax v0.8.4
[INFO] [stderr]     Checking is_terminal_polyfill v1.70.1
[INFO] [stderr]     Checking colorchoice v1.0.2
[INFO] [stderr]     Checking bytes v1.7.1
[INFO] [stderr]     Checking clap_lex v0.7.2
[INFO] [stderr]    Compiling semver v0.1.20
[INFO] [stderr]    Compiling matrixmultiply v0.3.9
[INFO] [stderr]     Checking bytemuck v1.16.3
[INFO] [stderr]     Checking anstream v0.6.15
[INFO] [stderr]     Checking rawpointer v0.2.1
[INFO] [stderr]     Checking custom_derive v0.1.7
[INFO] [stderr]    Compiling rustc_version v0.1.7
[INFO] [stderr]     Checking safe_arch v0.7.2
[INFO] [stderr]     Checking flate2 v1.0.31
[INFO] [stderr]     Checking aho-corasick v1.1.3
[INFO] [stderr]    Compiling feature-probe v0.1.1
[INFO] [stderr]     Checking indexmap v2.3.0
[INFO] [stderr]     Checking clap_builder v4.5.13
[INFO] [stderr]    Compiling newtype_derive v0.1.6
[INFO] [stderr]     Checking crossbeam-epoch v0.9.18
[INFO] [stderr]     Checking tokio v1.39.2
[INFO] [stderr]    Compiling bv v0.11.1
[INFO] [stderr]    Compiling quote v1.0.36
[INFO] [stderr]     Checking wide v0.7.26
[INFO] [stderr]     Checking crossbeam-deque v0.8.5
[INFO] [stderr]     Checking csv-core v0.1.11
[INFO] [stderr]    Compiling clang-sys v1.8.1
[INFO] [stderr]    Compiling rustix v0.38.34
[INFO] [stderr]    Compiling syn v2.0.72
[INFO] [stderr]    Compiling jobserver v0.1.32
[INFO] [stderr]    Compiling prettyplease v0.2.20
[INFO] [stderr]     Checking getrandom v0.2.15
[INFO] [stderr]     Checking bit-vec v0.6.3
[INFO] [stderr]     Checking fixedbitset v0.4.2
[INFO] [stderr]    Compiling heck v0.4.1
[INFO] [stderr]     Checking rand_core v0.6.4
[INFO] [stderr]     Checking bit-set v0.5.3
[INFO] [stderr]    Compiling cc v1.1.7
[INFO] [stderr]     Checking itertools v0.11.0
[INFO] [stderr]     Checking petgraph v0.6.5
[INFO] [stderr]     Checking fxhash v0.2.1
[INFO] [stderr]     Checking strum v0.25.0
[INFO] [stderr]     Checking bytecount v0.6.8
[INFO] [stderr]     Checking rayon v1.10.0
[INFO] [stderr]    Compiling linux-raw-sys v0.4.14
[INFO] [stderr]     Checking triple_accel v0.4.0
[INFO] [stderr]    Compiling quick-error v1.2.3
[INFO] [stderr]     Checking editdistancek v1.0.2
[INFO] [stderr]    Compiling bitflags v2.6.0
[INFO] [stderr]    Compiling fs-utils v1.1.4
[INFO] [stderr]     Checking num-integer v0.1.46
[INFO] [stderr]     Checking num-complex v0.4.6
[INFO] [stderr]     Checking approx v0.5.1
[INFO] [stderr]     Checking itertools-num v0.1.3
[INFO] [stderr]     Checking num-rational v0.4.2
[INFO] [stderr]     Checking ordered-float v3.9.2
[INFO] [stderr]     Checking ndarray v0.15.6
[INFO] [stderr]     Checking regex-automata v0.4.7
[INFO] [stderr]    Compiling cmake v0.1.50
[INFO] [stderr]    Compiling openssl-src v300.3.1+3.3.1
[INFO] [stderr]     Checking simba v0.6.0
[INFO] [stderr]    Compiling nom v7.1.3
[INFO] [stderr]     Checking tinyvec v1.8.0
[INFO] [stderr]    Compiling libloading v0.8.5
[INFO] [stderr]    Compiling home v0.5.9
[INFO] [stderr]    Compiling bindgen v0.69.4
[INFO] [stderr]    Compiling itertools v0.12.1
[INFO] [stderr]    Compiling lazy_static v1.5.0
[INFO] [stderr]    Compiling getrandom v0.1.16
[INFO] [stderr]    Compiling rustc-hash v1.1.0
[INFO] [stderr]    Compiling bzip2-sys v0.1.11+1.0.8
[INFO] [stderr]    Compiling lzma-sys v0.1.20
[INFO] [stderr]    Compiling zstd-sys v2.0.13+zstd.1.5.6
[INFO] [stderr]    Compiling libz-sys v1.1.18
[INFO] [stderr]    Compiling openssl-sys v0.9.103
[INFO] [stderr]    Compiling curl-sys v0.4.74+curl-8.9.0
[INFO] [stderr]    Compiling which v4.4.2
[INFO] [stderr]     Checking regex v1.10.6
[INFO] [stderr]     Checking unicode-normalization v0.1.23
[INFO] [stderr]    Compiling hts-sys v2.1.4
[INFO] [stderr]    Compiling lazycell v1.3.0
[INFO] [stderr]    Compiling cexpr v0.6.0
[INFO] [stderr]    Compiling lexical-core v0.7.6
[INFO] [stderr]     Checking unicode-bidi v0.3.15
[INFO] [stderr]    Compiling nom v5.1.3
[INFO] [stderr]     Checking static_assertions v1.1.0
[INFO] [stderr]     Checking arrayvec v0.5.2
[INFO] [stderr]     Checking idna v0.5.0
[INFO] [stderr]    Compiling backtrace v0.3.73
[INFO] [stderr]     Checking bzip2 v0.4.4
[INFO] [stderr]     Checking url v2.5.2
[INFO] [stderr]     Checking gimli v0.29.0
[INFO] [stderr]     Checking ieee754 v0.2.6
[INFO] [stderr]    Compiling unicode-xid v0.2.4
[INFO] [stderr]     Checking linear-map v1.2.0
[INFO] [stderr]    Compiling failure_derive v0.1.8
[INFO] [stderr]    Compiling synstructure v0.12.6
[INFO] [stderr]     Checking rand_core v0.5.1
[INFO] [stderr]     Checking md-5 v0.10.6
[INFO] [stderr]     Checking object v0.36.2
[INFO] [stderr]     Checking iana-time-zone v0.1.60
[INFO] [stderr]     Checking rustc-demangle v0.1.24
[INFO] [stderr]     Checking cpufeatures v0.2.12
[INFO] [stderr]    Compiling serde_json v1.0.122
[INFO] [stderr]     Checking chrono v0.4.38
[INFO] [stderr]     Checking rmp v0.8.14
[INFO] [stderr]     Checking humantime v1.3.0
[INFO] [stderr]     Checking sha1 v0.10.6
[INFO] [stderr]     Checking sha2 v0.10.8
[INFO] [stderr]     Checking atty v0.2.14
[INFO] [stderr]     Checking crossbeam-channel v0.5.13
[INFO] [stderr]     Checking itertools v0.9.0
[INFO] [stderr]    Compiling nalgebra-macros v0.1.0
[INFO] [stderr]    Compiling derive-new v0.5.9
[INFO] [stderr]    Compiling thiserror-impl v1.0.63
[INFO] [stderr]    Compiling zerocopy-derive v0.7.35
[INFO] [stderr]    Compiling serde_derive v1.0.204
[INFO] [stderr]    Compiling clap_derive v4.5.13
[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 strum_macros v0.25.3
[INFO] [stderr]     Checking addr2line v0.22.0
[INFO] [stderr]     Checking temp-file v0.1.8
[INFO] [stderr]     Checking zerocopy v0.7.35
[INFO] [stderr]     Checking enum-map v2.7.3
[INFO] [stderr]     Checking termcolor v1.4.1
[INFO] [stderr]    Compiling sequencetoolkit v0.4.4 (/opt/rustwide/workdir/sequencetoolkit)
[INFO] [stderr]     Checking env_logger v0.7.1
[INFO] [stderr]     Checking bgzip v0.3.1
[INFO] [stderr]     Checking vcf v0.6.1
[INFO] [stderr]     Checking pretty_env_logger v0.4.0
[INFO] [stderr]     Checking ppv-lite86 v0.2.20
[INFO] [stderr]     Checking rand_chacha v0.3.1
[INFO] [stderr]     Checking rand_chacha v0.2.2
[INFO] [stderr]     Checking bio-types v1.0.3
[INFO] [stderr]     Checking rand v0.8.5
[INFO] [stderr]     Checking rand v0.7.3
[INFO] [stderr]     Checking clap v4.5.13
[INFO] [stderr]     Checking rand_distr v0.4.3
[INFO] [stderr]     Checking failure v0.1.8
[INFO] [stderr]     Checking nalgebra v0.29.0
[INFO] [stderr]     Checking xz2 v0.1.7
[INFO] [stderr]    Compiling libxlsxwriter-sys v1.1.7
[INFO] [stderr]    Compiling zstd-safe v7.2.1
[INFO] [stderr]     Checking zstd v0.13.2
[INFO] [stderr]     Checking autocompress v0.6.0
[INFO] [stderr]     Checking vec_map v0.8.2
[INFO] [stderr]     Checking multimap v0.9.1
[INFO] [stderr]     Checking csv v1.3.0
[INFO] [stderr]     Checking rmp-serde v1.3.0
[INFO] [stderr]     Checking bincode v1.3.3
[INFO] [stderr]     Checking fastqutils v0.1.0 (/opt/rustwide/workdir/fastqutils)
[INFO] [stderr]     Checking fsutils v0.1.0 (/opt/rustwide/workdir/fsutils)
[INFO] [stderr]     Checking xlsxwriter v0.6.1
[INFO] [stderr]     Checking statrs v0.16.1
[INFO] [stderr]     Checking bio v1.6.0
[INFO] [stderr]     Checking vcfutils v0.1.0 (/opt/rustwide/workdir/vcfutils)
[INFO] [stderr]     Checking bedutils v0.1.0 (/opt/rustwide/workdir/bedutils)
[INFO] [stderr]     Checking geneannot v0.1.0 (/opt/rustwide/workdir/geneannot)
[INFO] [stderr]     Checking rust-htslib v0.44.1
[INFO] [stderr]     Checking bam2fastq v0.1.0 (/opt/rustwide/workdir/bam2fastq)
[INFO] [stderr]     Checking bamutils v0.1.0 (/opt/rustwide/workdir/bamutils)
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 40.42s
[INFO] running `Command { std: "docker" "inspect" "9efe57e9d80153fd8ad2c899a78a1cc006befa76f99450617e7f6209d076d80d", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "9efe57e9d80153fd8ad2c899a78a1cc006befa76f99450617e7f6209d076d80d", kill_on_drop: false }`
[INFO] [stdout] 9efe57e9d80153fd8ad2c899a78a1cc006befa76f99450617e7f6209d076d80d