[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] 88416e910ebe416a73bd4e9ff82db3ecd875f0b1 [INFO] testing kgori/alignomatic against master#562dee4820c458d823175268e41601d4c060588a for pr-154210-1 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fkgori%2Falignomatic" "/workspace/builds/worker-7-tc1/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-7-tc1/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-7-tc1/source/Cargo.toml [INFO] validating manifest of git repo https://github.com/kgori/alignomatic on toolchain 562dee4820c458d823175268e41601d4c060588a [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+562dee4820c458d823175268e41601d4c060588a" "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" "+562dee4820c458d823175268e41601d4c060588a" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [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] Downloading crates ... [INFO] [stderr] Downloaded rustc_version v0.1.7 [INFO] [stderr] Downloaded ieee754 v0.2.6 [INFO] [stderr] Downloaded semver v0.1.20 [INFO] [stderr] Downloaded linear-map v1.2.0 [INFO] [stderr] Downloaded newtype_derive v0.1.6 [INFO] [stderr] Downloaded serde_bytes v0.11.19 [INFO] [stderr] Downloaded editdistancek v1.0.2 [INFO] [stderr] Downloaded enum-map-derive v0.17.0 [INFO] [stderr] Downloaded bgzf v0.2.0 [INFO] [stderr] Downloaded fs-utils v1.1.4 [INFO] [stderr] Downloaded bio-types v1.0.4 [INFO] [stderr] Downloaded libdeflater v0.7.5 [INFO] [stderr] Downloaded triple_accel v0.4.0 [INFO] [stderr] Downloaded simba v0.9.1 [INFO] [stderr] Downloaded portable-atomic-util v0.2.5 [INFO] [stderr] Downloaded zerocopy-derive v0.8.38 [INFO] [stderr] Downloaded jiff-static v0.2.18 [INFO] [stderr] Downloaded rust-htslib v1.0.0 [INFO] [stderr] Downloaded libdeflate-sys v0.7.5 [INFO] [stderr] Downloaded statrs v0.18.0 [INFO] [stderr] Downloaded liblzma v0.3.6 [INFO] [stderr] Downloaded niffler v2.7.0 [INFO] [stderr] Downloaded blake3 v1.8.3 [INFO] [stderr] Downloaded constant_time_eq v0.4.2 [INFO] [stderr] Downloaded bio v3.0.0 [INFO] [stderr] Downloaded zerocopy v0.8.38 [INFO] [stderr] Downloaded enum-map v2.7.3 [INFO] [stderr] Downloaded ndarray v0.16.1 [INFO] [stderr] Downloaded bgzip v0.3.1 [INFO] [stderr] Downloaded derefable v0.1.0 [INFO] [stderr] Downloaded nalgebra v0.33.2 [INFO] [stderr] Downloaded getset v0.1.6 [INFO] [stderr] Downloaded itertools-num v0.1.3 [INFO] [stderr] Downloaded multimap v0.10.1 [INFO] [stderr] Downloaded derive-new v0.7.0 [INFO] [stderr] Downloaded bzip2-sys v0.1.13+1.0.8 [INFO] [stderr] Downloaded jiff v0.2.18 [INFO] [stderr] Downloaded petgraph v0.8.3 [INFO] [stderr] Downloaded libz-sys v1.1.23 [INFO] [stderr] Downloaded zstd-sys v2.0.16+zstd.1.5.7 [INFO] [stderr] Downloaded csv v1.4.0 [INFO] [stderr] Downloaded liblzma-sys v0.3.13 [INFO] [stderr] Downloaded hts-sys v2.2.0 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-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" "+562dee4820c458d823175268e41601d4c060588a" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 595ed2a8fc7aedd23966d96a2d89f24e2e34767b36ed19b7d4e9c51819b8e780 [INFO] running `Command { std: "docker" "start" "-a" "595ed2a8fc7aedd23966d96a2d89f24e2e34767b36ed19b7d4e9c51819b8e780", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "595ed2a8fc7aedd23966d96a2d89f24e2e34767b36ed19b7d4e9c51819b8e780", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "595ed2a8fc7aedd23966d96a2d89f24e2e34767b36ed19b7d4e9c51819b8e780", kill_on_drop: false }` [INFO] [stdout] 595ed2a8fc7aedd23966d96a2d89f24e2e34767b36ed19b7d4e9c51819b8e780 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-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" "+562dee4820c458d823175268e41601d4c060588a" "build" "--frozen" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 0f00442a0858cc8a27ef4f0bbedd61f72cb5055ddc36960737b92c24b7e46071 [INFO] running `Command { std: "docker" "start" "-a" "0f00442a0858cc8a27ef4f0bbedd61f72cb5055ddc36960737b92c24b7e46071", kill_on_drop: false }` [INFO] [stderr] Compiling unicode-ident v1.0.22 [INFO] [stderr] Compiling libc v0.2.180 [INFO] [stderr] Compiling memchr v2.7.6 [INFO] [stderr] Compiling libm v0.2.16 [INFO] [stderr] Compiling serde_core v1.0.228 [INFO] [stderr] Compiling glob v0.3.3 [INFO] [stderr] Compiling zerocopy v0.8.38 [INFO] [stderr] Compiling num-traits v0.2.19 [INFO] [stderr] Compiling regex-syntax v0.8.9 [INFO] [stderr] Compiling minimal-lexical v0.2.1 [INFO] [stderr] Compiling libloading v0.8.9 [INFO] [stderr] Compiling matrixmultiply v0.3.10 [INFO] [stderr] Compiling proc-macro2 v0.4.30 [INFO] [stderr] Compiling paste v1.0.15 [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Compiling proc-macro2 v1.0.106 [INFO] [stderr] Compiling bytemuck v1.25.0 [INFO] [stderr] Compiling either v1.15.0 [INFO] [stderr] Compiling bindgen v0.69.5 [INFO] [stderr] Compiling rustc_version v0.1.7 [INFO] [stderr] Compiling lazycell v1.3.0 [INFO] [stderr] Compiling clang-sys v1.8.1 [INFO] [stderr] Compiling safe_arch v0.7.4 [INFO] [stderr] Compiling quick-error v1.2.3 [INFO] [stderr] Compiling itertools v0.12.1 [INFO] [stderr] Compiling rawpointer v0.2.1 [INFO] [stderr] Compiling rustc-hash v1.1.0 [INFO] [stderr] Compiling smallvec v1.15.1 [INFO] [stderr] Compiling aho-corasick v1.1.4 [INFO] [stderr] Compiling nom v7.1.3 [INFO] [stderr] Compiling bitflags v2.10.0 [INFO] [stderr] Compiling typenum v1.19.0 [INFO] [stderr] Compiling wide v0.7.33 [INFO] [stderr] Compiling fs-utils v1.1.4 [INFO] [stderr] Compiling quote v1.0.44 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Compiling syn v2.0.114 [INFO] [stderr] Compiling syn v0.15.44 [INFO] [stderr] Compiling jobserver v0.1.34 [INFO] [stderr] Compiling getrandom v0.2.17 [INFO] [stderr] Compiling regex-automata v0.4.14 [INFO] [stderr] Compiling rand_core v0.6.4 [INFO] [stderr] Compiling cc v1.2.55 [INFO] [stderr] Compiling feature-probe v0.1.1 [INFO] [stderr] Compiling bv v0.11.1 [INFO] [stderr] Compiling quote v0.6.13 [INFO] [stderr] Compiling proc-macro-error-attr2 v2.0.0 [INFO] [stderr] Compiling cexpr v0.6.0 [INFO] [stderr] Compiling percent-encoding v2.3.2 [INFO] [stderr] Compiling hashbrown v0.16.1 [INFO] [stderr] Compiling anyhow v1.0.100 [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 zstd-safe v7.2.4 [INFO] [stderr] Compiling foldhash v0.1.5 [INFO] [stderr] Compiling hashbrown v0.15.5 [INFO] [stderr] Compiling cmake v0.1.57 [INFO] [stderr] Compiling num-rational v0.4.2 [INFO] [stderr] Compiling simba v0.9.1 [INFO] [stderr] Compiling indexmap v2.13.0 [INFO] [stderr] Compiling form_urlencoded v1.2.2 [INFO] [stderr] Compiling csv-core v0.1.13 [INFO] [stderr] Compiling bit-vec v0.8.0 [INFO] [stderr] Compiling ryu v1.0.22 [INFO] [stderr] Compiling getrandom v0.3.4 [INFO] [stderr] Compiling fixedbitset v0.5.7 [INFO] [stderr] Compiling zstd-sys v2.0.16+zstd.1.5.7 [INFO] [stderr] Compiling libz-sys v1.1.23 [INFO] [stderr] Compiling regex v1.12.3 [INFO] [stderr] Compiling libdeflate-sys v0.7.5 [INFO] [stderr] Compiling liblzma-sys v0.3.13 [INFO] [stderr] Compiling bzip2-sys v0.1.13+1.0.8 [INFO] [stderr] Compiling bwa-sys v0.1.0 (https://github.com/kgori/rust-bwa.git?tag=v0.1.5#de5e6235) [INFO] [stderr] Compiling custom_derive v0.1.7 [INFO] [stderr] Compiling rustix v1.1.3 [INFO] [stderr] Compiling zmij v1.0.19 [INFO] [stderr] Compiling serde_bytes v0.11.19 [INFO] [stderr] Compiling csv v1.4.0 [INFO] [stderr] Compiling petgraph v0.8.3 [INFO] [stderr] Compiling bit-set v0.8.0 [INFO] [stderr] Compiling blake3 v1.8.3 [INFO] [stderr] Compiling ppv-lite86 v0.2.21 [INFO] [stderr] Compiling itertools v0.14.0 [INFO] [stderr] Compiling synstructure v0.13.2 [INFO] [stderr] Compiling rand_chacha v0.3.1 [INFO] [stderr] Compiling proc-macro-error2 v2.0.1 [INFO] [stderr] Compiling rand v0.8.5 [INFO] [stderr] Compiling derefable v0.1.0 [INFO] [stderr] Compiling ndarray v0.16.1 [INFO] [stderr] Compiling ordered-float v5.1.0 [INFO] [stderr] Compiling itertools-num v0.1.3 [INFO] [stderr] Compiling fxhash v0.2.1 [INFO] [stderr] Compiling rand_distr v0.4.3 [INFO] [stderr] Compiling bytecount v0.6.9 [INFO] [stderr] Compiling editdistancek v1.0.2 [INFO] [stderr] Compiling triple_accel v0.4.0 [INFO] [stderr] Compiling linear-map v1.2.0 [INFO] [stderr] Compiling ieee754 v0.2.6 [INFO] [stderr] Compiling strum v0.26.3 [INFO] [stderr] Compiling env_filter v0.1.4 [INFO] [stderr] Compiling libdeflater v0.7.5 [INFO] [stderr] Compiling bzip2 v0.4.4 [INFO] [stderr] Compiling jiff v0.2.18 [INFO] [stderr] Compiling arrayvec v0.7.6 [INFO] [stderr] Compiling constant_time_eq v0.4.2 [INFO] [stderr] Compiling cpufeatures v0.2.17 [INFO] [stderr] Compiling once_cell v1.21.3 [INFO] [stderr] Compiling serde_json v1.0.149 [INFO] [stderr] Compiling num_cpus v1.17.0 [INFO] [stderr] Compiling zerofrom-derive v0.1.6 [INFO] [stderr] Compiling yoke-derive v0.8.1 [INFO] [stderr] Compiling zerovec-derive v0.11.2 [INFO] [stderr] Compiling displaydoc v0.2.5 [INFO] [stderr] Compiling serde_derive v1.0.228 [INFO] [stderr] Compiling thiserror-impl v1.0.69 [INFO] [stderr] Compiling thiserror-impl v2.0.18 [INFO] [stderr] Compiling derive-new v0.6.0 [INFO] [stderr] Compiling strum_macros v0.26.4 [INFO] [stderr] Compiling nalgebra v0.33.2 [INFO] [stderr] Compiling enum-map-derive v0.17.0 [INFO] [stderr] Compiling derive-new v0.7.0 [INFO] [stderr] Compiling enum-map v2.7.3 [INFO] [stderr] Compiling getset v0.1.6 [INFO] [stderr] Compiling clap_derive v4.5.55 [INFO] [stderr] Compiling tempfile v3.24.0 [INFO] [stderr] Compiling zerofrom v0.1.6 [INFO] [stderr] Compiling yoke v0.8.1 [INFO] [stderr] Compiling thiserror v1.0.69 [INFO] [stderr] Compiling zerovec v0.11.5 [INFO] [stderr] Compiling zerotrie v0.2.3 [INFO] [stderr] Compiling bgzip v0.3.1 [INFO] [stderr] Compiling bgzf v0.2.0 [INFO] [stderr] Compiling thiserror v2.0.18 [INFO] [stderr] Compiling tinystr v0.8.2 [INFO] [stderr] Compiling potential_utf v0.1.4 [INFO] [stderr] Compiling icu_collections v2.1.1 [INFO] [stderr] Compiling icu_locale_core v2.1.1 [INFO] [stderr] Compiling liblzma v0.3.6 [INFO] [stderr] Compiling env_logger v0.11.8 [INFO] [stderr] Compiling hts-sys v2.2.0 [INFO] [stderr] Compiling icu_provider v2.1.1 [INFO] [stderr] Compiling clap v4.5.57 [INFO] [stderr] Compiling icu_properties v2.1.2 [INFO] [stderr] Compiling icu_normalizer v2.1.1 [INFO] [stderr] Compiling serde v1.0.228 [INFO] [stderr] Compiling zstd v0.13.3 [INFO] [stderr] Compiling niffler v2.7.0 [INFO] [stderr] Compiling bio-types v1.0.4 [INFO] [stderr] Compiling multimap v0.10.1 [INFO] [stderr] Compiling vec_map v0.8.2 [INFO] [stderr] Compiling idna_adapter v1.2.1 [INFO] [stderr] Compiling idna v1.1.0 [INFO] [stderr] Compiling url v2.5.8 [INFO] [stderr] Compiling statrs v0.18.0 [INFO] [stderr] Compiling bio v3.0.0 [INFO] [stderr] Compiling rust-htslib v1.0.0 [INFO] [stderr] Compiling bwa v0.1.5 (https://github.com/kgori/rust-bwa.git?tag=v0.1.5#de5e6235) [INFO] [stderr] Compiling alignomatic v0.6.0 (/opt/rustwide/workdir) [INFO] [stderr] Finished `dev` profile [unoptimized + debuginfo] target(s) in 1m 11s [INFO] running `Command { std: "docker" "inspect" "0f00442a0858cc8a27ef4f0bbedd61f72cb5055ddc36960737b92c24b7e46071", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "0f00442a0858cc8a27ef4f0bbedd61f72cb5055ddc36960737b92c24b7e46071", kill_on_drop: false }` [INFO] [stdout] 0f00442a0858cc8a27ef4f0bbedd61f72cb5055ddc36960737b92c24b7e46071 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-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" "+562dee4820c458d823175268e41601d4c060588a" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] d41e9f1f485ec10e3003ba30fdda08ae5ff9b6d898177dcd2adbb3cb4e37d197 [INFO] running `Command { std: "docker" "start" "-a" "d41e9f1f485ec10e3003ba30fdda08ae5ff9b6d898177dcd2adbb3cb4e37d197", kill_on_drop: false }` [INFO] [stderr] Compiling alignomatic v0.6.0 (/opt/rustwide/workdir) [INFO] [stderr] Finished `test` profile [unoptimized + debuginfo] target(s) in 1.90s [INFO] running `Command { std: "docker" "inspect" "d41e9f1f485ec10e3003ba30fdda08ae5ff9b6d898177dcd2adbb3cb4e37d197", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "d41e9f1f485ec10e3003ba30fdda08ae5ff9b6d898177dcd2adbb3cb4e37d197", kill_on_drop: false }` [INFO] [stdout] d41e9f1f485ec10e3003ba30fdda08ae5ff9b6d898177dcd2adbb3cb4e37d197 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-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" "+562dee4820c458d823175268e41601d4c060588a" "test" "--frozen", kill_on_drop: false }` [INFO] [stdout] f0f877acb7702ef318c89bda69cd05a9c3e6316d8e7c095c41980d47d674958a [INFO] running `Command { std: "docker" "start" "-a" "f0f877acb7702ef318c89bda69cd05a9c3e6316d8e7c095c41980d47d674958a", kill_on_drop: false }` [INFO] [stderr] Finished `test` profile [unoptimized + debuginfo] target(s) in 0.24s [INFO] [stderr] Running unittests src/main.rs (/opt/rustwide/target/debug/deps/alignomatic-ab6b956165b767bf) [INFO] [stdout] [INFO] [stdout] running 2 tests [INFO] [stdout] test utils::test::test_bam_to_fastq ... ok [INFO] [stdout] test bam_io::tests::test_collated_bam_reader_merge_logic ... ok [INFO] [stdout] [INFO] [stdout] test result: ok. 2 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 6.57s [INFO] [stdout] [INFO] [stderr] Running tests/integration.rs (/opt/rustwide/target/debug/deps/integration-244da7108d009666) [INFO] [stdout] [INFO] [stdout] running 1 test [INFO] [stderr] Finished `dev` profile [unoptimized + debuginfo] target(s) in 0.21s [INFO] [stderr] Running `/opt/rustwide/target/debug/alignomatic --bam-input data/test.sorted.bam --output-folder test_integration_output` [INFO] [stderr] [2026-04-10T06:03:10Z INFO PARAMS] No index files provided. Skipping alignment step. [INFO] [stderr] [2026-04-10T06:03:10Z INFO PARAMS] First fastq file: None [INFO] [stderr] [2026-04-10T06:03:10Z INFO PARAMS] Second fastq file: None [INFO] [stderr] [2026-04-10T06:03:10Z INFO PARAMS] BAM file: Some("/opt/rustwide/workdir/data/test.sorted.bam") [INFO] [stderr] [2026-04-10T06:03:10Z INFO PARAMS] Index files: [INFO] [stderr] [2026-04-10T06:03:10Z INFO PARAMS] Batch size: 10000000 [INFO] [stderr] [2026-04-10T06:03:10Z INFO PARAMS] Threads: 1 [INFO] [stderr] [2026-04-10T06:03:10Z INFO PARAMS] Minimum block size: 30 [INFO] [stderr] [2026-04-10T06:03:10Z INFO PARAMS] Minimum block quality: 10 [INFO] [stderr] [2026-04-10T06:03:10Z INFO PARAMS] Output folder: "/opt/rustwide/workdir/test_integration_output" [INFO] [stderr] [2026-04-10T06:03:10Z INFO IO] Creating output folder /opt/rustwide/workdir/test_integration_output [INFO] [stderr] Error: Read-only file system (os error 30) [INFO] [stderr] [INFO] [stderr] Stack backtrace: [INFO] [stderr] 0: >::from [INFO] [stderr] at /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/anyhow-1.0.100/src/backtrace.rs:27:14 [INFO] [stderr] 1: as core::ops::try_trait::FromResidual>>::from_residual [INFO] [stderr] at /rustc/562dee4820c458d823175268e41601d4c060588a/library/core/src/result.rs:2189:27 [INFO] [stderr] 2: alignomatic::cli::create_output_folder [INFO] [stderr] at ./src/cli.rs:249:9 [INFO] [stderr] 3: alignomatic::cli::get_program_options [INFO] [stderr] at ./src/cli.rs:268:5 [INFO] [stderr] 4: alignomatic::main [INFO] [stderr] at ./src/main.rs:57:37 [INFO] [stderr] 5: core::result::Result<(), anyhow::Error> as core::ops::function::FnOnce<()>>::call_once [INFO] [stderr] at /rustc/562dee4820c458d823175268e41601d4c060588a/library/core/src/ops/function.rs:250:5 [INFO] [stderr] 6: std::sys::backtrace::__rust_begin_short_backtrace:: core::result::Result<(), anyhow::Error>, core::result::Result<(), anyhow::Error>> [INFO] [stderr] at /rustc/562dee4820c458d823175268e41601d4c060588a/library/std/src/sys/backtrace.rs:166:18 [INFO] [stderr] 7: std::rt::lang_start::>::{closure#0} [INFO] [stderr] at /rustc/562dee4820c458d823175268e41601d4c060588a/library/std/src/rt.rs:206:18 [INFO] [stderr] 8: <&dyn core::ops::function::Fn<(), Output = i32> + core::marker::Sync + core::panic::unwind_safe::RefUnwindSafe as core::ops::function::FnOnce<()>>::call_once [INFO] [stderr] at /rustc/562dee4820c458d823175268e41601d4c060588a/library/core/src/ops/function.rs:287:21 [INFO] [stderr] 9: std::panicking::catch_unwind::do_call::<&dyn core::ops::function::Fn<(), Output = i32> + core::marker::Sync + core::panic::unwind_safe::RefUnwindSafe, i32> [INFO] [stderr] at /rustc/562dee4820c458d823175268e41601d4c060588a/library/std/src/panicking.rs:581:40 [INFO] [stderr] 10: std::panicking::catch_unwind:: + core::marker::Sync + core::panic::unwind_safe::RefUnwindSafe> [INFO] [stderr] at /rustc/562dee4820c458d823175268e41601d4c060588a/library/std/src/panicking.rs:544:19 [INFO] [stderr] 11: std::panic::catch_unwind::<&dyn core::ops::function::Fn<(), Output = i32> + core::marker::Sync + core::panic::unwind_safe::RefUnwindSafe, i32> [INFO] [stderr] at /rustc/562dee4820c458d823175268e41601d4c060588a/library/std/src/panic.rs:359:14 [INFO] [stderr] 12: std::rt::lang_start_internal::{closure#0} [INFO] [stderr] at /rustc/562dee4820c458d823175268e41601d4c060588a/library/std/src/rt.rs:175:24 [INFO] [stderr] 13: std::panicking::catch_unwind::do_call:: [INFO] [stderr] at /rustc/562dee4820c458d823175268e41601d4c060588a/library/std/src/panicking.rs:581:40 [INFO] [stderr] 14: std::panicking::catch_unwind:: [INFO] [stderr] at /rustc/562dee4820c458d823175268e41601d4c060588a/library/std/src/panicking.rs:544:19 [INFO] [stderr] 15: std::panic::catch_unwind:: [INFO] [stderr] at /rustc/562dee4820c458d823175268e41601d4c060588a/library/std/src/panic.rs:359:14 [INFO] [stderr] 16: std::rt::lang_start_internal [INFO] [stderr] at /rustc/562dee4820c458d823175268e41601d4c060588a/library/std/src/rt.rs:171:5 [INFO] [stderr] 17: std::rt::lang_start::> [INFO] [stderr] at /rustc/562dee4820c458d823175268e41601d4c060588a/library/std/src/rt.rs:205:5 [INFO] [stderr] 18: main [INFO] [stderr] 19: [INFO] [stderr] 20: __libc_start_main [INFO] [stderr] 21: _start [INFO] [stdout] test test_bam_input_no_index ... FAILED [INFO] [stdout] [INFO] [stdout] failures: [INFO] [stdout] [INFO] [stdout] ---- test_bam_input_no_index stdout ---- [INFO] [stdout] [INFO] [stdout] thread 'test_bam_input_no_index' (21) panicked at tests/integration.rs:30:5: [INFO] [stdout] Program failed to execute successfully [INFO] [stdout] stack backtrace: [INFO] [stdout] 0: 0x5df688f47d2a - std[31e582c13f4e914f]::backtrace_rs::backtrace::libunwind::trace [INFO] [stdout] at /rustc/562dee4820c458d823175268e41601d4c060588a/library/std/src/../../backtrace/src/backtrace/libunwind.rs:117:9 [INFO] [stdout] 1: 0x5df688f47d2a - std[31e582c13f4e914f]::backtrace_rs::backtrace::trace_unsynchronized:: [INFO] [stdout] at /rustc/562dee4820c458d823175268e41601d4c060588a/library/std/src/../../backtrace/src/backtrace/mod.rs:66:14 [INFO] [stdout] 2: 0x5df688f47d2a - std[31e582c13f4e914f]::sys::backtrace::_print_fmt [INFO] [stdout] at /rustc/562dee4820c458d823175268e41601d4c060588a/library/std/src/sys/backtrace.rs:74:9 [INFO] [stdout] 3: 0x5df688f47d2a - <::print::DisplayBacktrace as core[fa0eadad68403074]::fmt::Display>::fmt [INFO] [stdout] at /rustc/562dee4820c458d823175268e41601d4c060588a/library/std/src/sys/backtrace.rs:44:26 [INFO] [stdout] 4: 0x5df688f5ba5a - ::fmt [INFO] [stdout] at /rustc/562dee4820c458d823175268e41601d4c060588a/library/core/src/fmt/rt.rs:152:76 [INFO] [stdout] 5: 0x5df688f5ba5a - core[fa0eadad68403074]::fmt::write [INFO] [stdout] 6: 0x5df688f4c662 - std[31e582c13f4e914f]::io::default_write_fmt::> [INFO] [stdout] at /rustc/562dee4820c458d823175268e41601d4c060588a/library/std/src/io/mod.rs:639:11 [INFO] [stdout] 7: 0x5df688f4c662 - as std[31e582c13f4e914f]::io::Write>::write_fmt [INFO] [stdout] at /rustc/562dee4820c458d823175268e41601d4c060588a/library/std/src/io/mod.rs:1994:13 [INFO] [stdout] 8: 0x5df688f2654f - ::print [INFO] [stdout] at /rustc/562dee4820c458d823175268e41601d4c060588a/library/std/src/sys/backtrace.rs:47:9 [INFO] [stdout] 9: 0x5df688f2654f - std[31e582c13f4e914f]::panicking::default_hook::{closure#0} [INFO] [stdout] at /rustc/562dee4820c458d823175268e41601d4c060588a/library/std/src/panicking.rs:292:27 [INFO] [stdout] 10: 0x5df688f3fca9 - std[31e582c13f4e914f]::panicking::default_hook [INFO] [stdout] at /rustc/562dee4820c458d823175268e41601d4c060588a/library/std/src/panicking.rs:316:9 [INFO] [stdout] 11: 0x5df688edc8cc - core[fa0eadad68403074]::ops::function::Fn<(&'a std[31e582c13f4e914f]::panic::PanicHookInfo<'b>,), Output = ()> + core[fa0eadad68403074]::marker::Sync + core[fa0eadad68403074]::marker::Send> as core[fa0eadad68403074]::ops::function::Fn<(&std[31e582c13f4e914f]::panic::PanicHookInfo,)>>::call [INFO] [stdout] at /rustc/562dee4820c458d823175268e41601d4c060588a/library/alloc/src/boxed.rs:2254:9 [INFO] [stdout] 12: 0x5df688edc8cc - test[7530e63dc052480e]::test_main_with_exit_callback::::{closure#0} [INFO] [stdout] at /rustc/562dee4820c458d823175268e41601d4c060588a/library/test/src/lib.rs:145:21 [INFO] [stdout] 13: 0x5df688f3fe62 - core[fa0eadad68403074]::ops::function::Fn<(&'a std[31e582c13f4e914f]::panic::PanicHookInfo<'b>,), Output = ()> + core[fa0eadad68403074]::marker::Sync + core[fa0eadad68403074]::marker::Send> as core[fa0eadad68403074]::ops::function::Fn<(&std[31e582c13f4e914f]::panic::PanicHookInfo,)>>::call [INFO] [stdout] at /rustc/562dee4820c458d823175268e41601d4c060588a/library/alloc/src/boxed.rs:2254:9 [INFO] [stdout] 14: 0x5df688f3fe62 - std[31e582c13f4e914f]::panicking::panic_with_hook [INFO] [stdout] at /rustc/562dee4820c458d823175268e41601d4c060588a/library/std/src/panicking.rs:833:13 [INFO] [stdout] 15: 0x5df688f2663a - std[31e582c13f4e914f]::panicking::panic_handler::{closure#0} [INFO] [stdout] at /rustc/562dee4820c458d823175268e41601d4c060588a/library/std/src/panicking.rs:691:13 [INFO] [stdout] 16: 0x5df688f1b769 - std[31e582c13f4e914f]::sys::backtrace::__rust_end_short_backtrace:: [INFO] [stdout] at /rustc/562dee4820c458d823175268e41601d4c060588a/library/std/src/sys/backtrace.rs:182:18 [INFO] [stdout] 17: 0x5df688f2731d - __rustc[fc8e3a9f23f26cb]::rust_begin_unwind [INFO] [stdout] at /rustc/562dee4820c458d823175268e41601d4c060588a/library/std/src/panicking.rs:689:5 [INFO] [stdout] 18: 0x5df688f5c14c - core[fa0eadad68403074]::panicking::panic_fmt [INFO] [stdout] at /rustc/562dee4820c458d823175268e41601d4c060588a/library/core/src/panicking.rs:80:14 [INFO] [stdout] 19: 0x5df688ecd452 - integration[fd783cc9c9f01087]::test_bam_input_no_index [INFO] [stdout] at /opt/rustwide/workdir/tests/integration.rs:30:5 [INFO] [stdout] 20: 0x5df688ecd0f7 - integration[fd783cc9c9f01087]::test_bam_input_no_index::{closure#0} [INFO] [stdout] at /opt/rustwide/workdir/tests/integration.rs:6:29 [INFO] [stdout] 21: 0x5df688ed05d6 - >::call_once [INFO] [stdout] at /rustc/562dee4820c458d823175268e41601d4c060588a/library/core/src/ops/function.rs:250:5 [INFO] [stdout] 22: 0x5df688ed09ab - core[fa0eadad68403074]::result::Result<(), alloc[49b8922c36ca62de]::string::String> as core[fa0eadad68403074]::ops::function::FnOnce<()>>::call_once [INFO] [stdout] at /rustc/562dee4820c458d823175268e41601d4c060588a/library/core/src/ops/function.rs:250:5 [INFO] [stdout] 23: 0x5df688ed09ab - test[7530e63dc052480e]::__rust_begin_short_backtrace::, fn() -> core[fa0eadad68403074]::result::Result<(), alloc[49b8922c36ca62de]::string::String>> [INFO] [stdout] at /rustc/562dee4820c458d823175268e41601d4c060588a/library/test/src/lib.rs:663:18 [INFO] [stdout] 24: 0x5df688edd39b - test[7530e63dc052480e]::run_test_in_process::{closure#0} [INFO] [stdout] at /rustc/562dee4820c458d823175268e41601d4c060588a/library/test/src/lib.rs:686:74 [INFO] [stdout] 25: 0x5df688edd39b - as core[fa0eadad68403074]::ops::function::FnOnce<()>>::call_once [INFO] [stdout] at /rustc/562dee4820c458d823175268e41601d4c060588a/library/core/src/panic/unwind_safe.rs:275:9 [INFO] [stdout] 26: 0x5df688edd39b - std[31e582c13f4e914f]::panicking::catch_unwind::do_call::, core[fa0eadad68403074]::result::Result<(), alloc[49b8922c36ca62de]::string::String>> [INFO] [stdout] at /rustc/562dee4820c458d823175268e41601d4c060588a/library/std/src/panicking.rs:581:40 [INFO] [stdout] 27: 0x5df688edd39b - std[31e582c13f4e914f]::panicking::catch_unwind::, core[fa0eadad68403074]::panic::unwind_safe::AssertUnwindSafe> [INFO] [stdout] at /rustc/562dee4820c458d823175268e41601d4c060588a/library/std/src/panicking.rs:544:19 [INFO] [stdout] 28: 0x5df688edd39b - std[31e582c13f4e914f]::panic::catch_unwind::, core[fa0eadad68403074]::result::Result<(), alloc[49b8922c36ca62de]::string::String>> [INFO] [stdout] at /rustc/562dee4820c458d823175268e41601d4c060588a/library/std/src/panic.rs:359:14 [INFO] [stdout] 29: 0x5df688edd39b - test[7530e63dc052480e]::run_test_in_process [INFO] [stdout] at /rustc/562dee4820c458d823175268e41601d4c060588a/library/test/src/lib.rs:686:27 [INFO] [stdout] 30: 0x5df688edd39b - test[7530e63dc052480e]::run_test::{closure#0} [INFO] [stdout] at /rustc/562dee4820c458d823175268e41601d4c060588a/library/test/src/lib.rs:607:43 [INFO] [stdout] 31: 0x5df688ed77f4 - test[7530e63dc052480e]::run_test::{closure#1} [INFO] [stdout] at /rustc/562dee4820c458d823175268e41601d4c060588a/library/test/src/lib.rs:637:41 [INFO] [stdout] 32: 0x5df688ed77f4 - std[31e582c13f4e914f]::sys::backtrace::__rust_begin_short_backtrace:: [INFO] [stdout] at /rustc/562dee4820c458d823175268e41601d4c060588a/library/std/src/sys/backtrace.rs:166:18 [INFO] [stdout] 33: 0x5df688edffa2 - std[31e582c13f4e914f]::thread::lifecycle::spawn_unchecked::::{closure#1}::{closure#0} [INFO] [stdout] at /rustc/562dee4820c458d823175268e41601d4c060588a/library/std/src/thread/lifecycle.rs:91:13 [INFO] [stdout] 34: 0x5df688edffa2 - ::{closure#1}::{closure#0}> as core[fa0eadad68403074]::ops::function::FnOnce<()>>::call_once [INFO] [stdout] at /rustc/562dee4820c458d823175268e41601d4c060588a/library/core/src/panic/unwind_safe.rs:275:9 [INFO] [stdout] 35: 0x5df688edffa2 - std[31e582c13f4e914f]::panicking::catch_unwind::do_call::::{closure#1}::{closure#0}>, ()> [INFO] [stdout] at /rustc/562dee4820c458d823175268e41601d4c060588a/library/std/src/panicking.rs:581:40 [INFO] [stdout] 36: 0x5df688edffa2 - std[31e582c13f4e914f]::panicking::catch_unwind::<(), core[fa0eadad68403074]::panic::unwind_safe::AssertUnwindSafe::{closure#1}::{closure#0}>> [INFO] [stdout] at /rustc/562dee4820c458d823175268e41601d4c060588a/library/std/src/panicking.rs:544:19 [INFO] [stdout] 37: 0x5df688edffa2 - std[31e582c13f4e914f]::panic::catch_unwind::::{closure#1}::{closure#0}>, ()> [INFO] [stdout] at /rustc/562dee4820c458d823175268e41601d4c060588a/library/std/src/panic.rs:359:14 [INFO] [stdout] 38: 0x5df688edffa2 - std[31e582c13f4e914f]::thread::lifecycle::spawn_unchecked::::{closure#1} [INFO] [stdout] at /rustc/562dee4820c458d823175268e41601d4c060588a/library/std/src/thread/lifecycle.rs:89:26 [INFO] [stdout] 39: 0x5df688edffa2 - ::{closure#1} as core[fa0eadad68403074]::ops::function::FnOnce<()>>::call_once::{shim:vtable#0} [INFO] [stdout] at /rustc/562dee4820c458d823175268e41601d4c060588a/library/core/src/ops/function.rs:250:5 [INFO] [stdout] 40: 0x5df688f4763f - + core[fa0eadad68403074]::marker::Send> as core[fa0eadad68403074]::ops::function::FnOnce<()>>::call_once [INFO] [stdout] at /rustc/562dee4820c458d823175268e41601d4c060588a/library/alloc/src/boxed.rs:2240:9 [INFO] [stdout] 41: 0x5df688f4763f - ::new::thread_start [INFO] [stdout] at /rustc/562dee4820c458d823175268e41601d4c060588a/library/std/src/sys/thread/unix.rs:118:17 [INFO] [stdout] 42: 0x7a3b5e98faa4 - [INFO] [stdout] 43: 0x7a3b5ea1ca64 - clone [INFO] [stdout] 44: 0x0 - [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] failures: [INFO] [stdout] test_bam_input_no_index [INFO] [stdout] [INFO] [stdout] test result: FAILED. 0 passed; 1 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.34s [INFO] [stdout] [INFO] [stderr] error: test failed, to rerun pass `--test integration` [INFO] running `Command { std: "docker" "inspect" "f0f877acb7702ef318c89bda69cd05a9c3e6316d8e7c095c41980d47d674958a", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "f0f877acb7702ef318c89bda69cd05a9c3e6316d8e7c095c41980d47d674958a", kill_on_drop: false }` [INFO] [stdout] f0f877acb7702ef318c89bda69cd05a9c3e6316d8e7c095c41980d47d674958a