[INFO] cloning repository https://github.com/fmarchiano/MIRA
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/fmarchiano/MIRA" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Ffmarchiano%2FMIRA", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Ffmarchiano%2FMIRA'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] 8bb56ef514076c358ed24894be19b5a414c6f0b0
[INFO] testing fmarchiano/MIRA against 1.100.0-beta.1 for beta-1.100-2
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Ffmarchiano%2FMIRA" "/workspace/builds/worker-5-tc2/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-5-tc2/source'...
[INFO] [stderr] done.
[INFO] started tweaking git repo https://github.com/fmarchiano/MIRA
[INFO] finished tweaking git repo https://github.com/fmarchiano/MIRA
[INFO] tweaked toml for git repo https://github.com/fmarchiano/MIRA written to /workspace/builds/worker-5-tc2/source/Cargo.toml
[INFO] validating manifest of git repo https://github.com/fmarchiano/MIRA on toolchain 1.100.0-beta.1
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+1.100.0-beta.1" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate git repo https://github.com/fmarchiano/MIRA 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" "+1.100.0-beta.1" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc2/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc2/target:/opt/rustwide/target:rw,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" "-m" "1610612736" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:3111399a4047eeb3a02b7a90e478d715f38a8c6669b5c4b49d30a17385265909" "sleep" "infinity", kill_on_drop: false }`
[INFO] [stdout] eea66fa0799b63fa52b00b1c9baaa8ce37b9e6ba2c60c40648eba431011b2f61
[INFO] running `Command { std: "docker" "start" "eea66fa0799b63fa52b00b1c9baaa8ce37b9e6ba2c60c40648eba431011b2f61", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "eea66fa0799b63fa52b00b1c9baaa8ce37b9e6ba2c60c40648eba431011b2f61", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "exec" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-w" "/opt/rustwide/workdir" "--user" "0:0" "eea66fa0799b63fa52b00b1c9baaa8ce37b9e6ba2c60c40648eba431011b2f61" "/opt/rustwide/cargo-home/bin/cargo" "+1.100.0-beta.1" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "eea66fa0799b63fa52b00b1c9baaa8ce37b9e6ba2c60c40648eba431011b2f61", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "exec" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=warn" "-e" "RUSTDOCFLAGS=--cap-lints=warn" "-w" "/opt/rustwide/workdir" "--user" "0:0" "eea66fa0799b63fa52b00b1c9baaa8ce37b9e6ba2c60c40648eba431011b2f61" "/opt/rustwide/cargo-home/bin/cargo" "+1.100.0-beta.1" "build" "--frozen" "--message-format=json", kill_on_drop: false }`
[INFO] [stderr]    Compiling proc-macro2 v1.0.106
[INFO] [stderr]    Compiling quote v1.0.45
[INFO] [stderr]    Compiling autocfg v1.5.0
[INFO] [stderr]    Compiling libc v0.2.186
[INFO] [stderr]    Compiling libm v0.2.16
[INFO] [stderr]    Compiling find-msvc-tools v0.1.9
[INFO] [stderr]    Compiling zerocopy v0.8.48
[INFO] [stderr]    Compiling pkg-config v0.3.33
[INFO] [stderr]    Compiling memchr v2.8.0
[INFO] [stderr]    Compiling serde_core v1.0.228
[INFO] [stderr]    Compiling serde v1.0.228
[INFO] [stderr]    Compiling crossbeam-utils v0.8.21
[INFO] [stderr]    Compiling bytemuck v1.25.0
[INFO] [stderr]    Compiling rustversion v1.0.22
[INFO] [stderr]    Compiling heck v0.5.0
[INFO] [stderr]    Compiling rawpointer v0.2.1
[INFO] [stderr]    Compiling semver v0.1.20
[INFO] [stderr]    Compiling cc v1.2.62
[INFO] [stderr]    Compiling safe_arch v0.7.4
[INFO] [stderr]    Compiling crc32fast v1.5.0
[INFO] [stderr]    Compiling utf8parse v0.2.2
[INFO] [stderr]    Compiling rustc_version v0.1.7
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[INFO] [stderr]    Compiling num-traits v0.2.19
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[INFO] [stderr]    Compiling simd-adler32 v0.3.9
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[INFO] [stderr]    Compiling buffer-redux v1.1.0
[INFO] [stderr]    Compiling itertools v0.14.0
[INFO] [stderr]    Compiling strum v0.26.3
[INFO] [stderr]    Compiling triple_accel v0.4.0
[INFO] [stderr]    Compiling once_cell v1.21.4
[INFO] [stderr]    Compiling custom_derive v0.1.7
[INFO] [stderr]    Compiling editdistancek v1.0.2
[INFO] [stderr]    Compiling rayon v1.12.0
[INFO] [stderr]    Compiling md5 v0.8.0
[INFO] [stderr]    Compiling regex-automata v0.4.14
[INFO] [stderr]    Compiling needletail v0.5.1
[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 itertools-num v0.1.3
[INFO] [stderr]    Compiling ordered-float v5.3.0
[INFO] [stderr]    Compiling num-rational v0.4.2
[INFO] [stderr]    Compiling simba v0.9.1
[INFO] [stderr]    Compiling ndarray v0.16.1
[INFO] [stderr]    Compiling csv v1.4.0
[INFO] [stderr]    Compiling serde_derive v1.0.228
[INFO] [stderr]    Compiling thiserror-impl v1.0.69
[INFO] [stderr]    Compiling derive-new v0.6.0
[INFO] [stderr]    Compiling thiserror-impl v2.0.18
[INFO] [stderr]    Compiling strum_macros v0.26.4
[INFO] [stderr]    Compiling enum-map-derive v0.17.0
[INFO] [stderr]    Compiling clap_derive v4.6.1
[INFO] [stderr]    Compiling ppv-lite86 v0.2.21
[INFO] [stderr]    Compiling ahash v0.8.12
[INFO] [stderr]    Compiling enum-map v2.7.3
[INFO] [stderr]    Compiling rand_chacha v0.3.1
[INFO] [stderr]    Compiling regex v1.12.3
[INFO] [stderr]    Compiling rand v0.8.6
[INFO] [stderr]    Compiling thiserror v1.0.69
[INFO] [stderr]    Compiling clap v4.6.1
[INFO] [stderr]    Compiling bio-types v1.0.4
[INFO] [stderr]    Compiling rand_distr v0.4.3
[INFO] [stderr]    Compiling multimap v0.10.1
[INFO] [stderr]    Compiling vec_map v0.8.2
[INFO] [stderr]    Compiling bv v0.11.1
[INFO] [stderr]    Compiling nalgebra v0.33.3
[INFO] [stderr]    Compiling statrs v0.18.0
[INFO] [stderr]    Compiling bio v2.3.0
[INFO] [stderr]    Compiling mira v0.2.0 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 1m 05s
[INFO] running `Command { std: "docker" "inspect" "eea66fa0799b63fa52b00b1c9baaa8ce37b9e6ba2c60c40648eba431011b2f61", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "exec" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=warn" "-e" "RUSTDOCFLAGS=--cap-lints=warn" "-w" "/opt/rustwide/workdir" "--user" "0:0" "eea66fa0799b63fa52b00b1c9baaa8ce37b9e6ba2c60c40648eba431011b2f61" "/opt/rustwide/cargo-home/bin/cargo" "+1.100.0-beta.1" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }`
[INFO] [stderr]    Compiling rustix v1.1.4
[INFO] [stderr]    Compiling once_cell v1.21.4
[INFO] [stderr]    Compiling linux-raw-sys v0.12.1
[INFO] [stderr]    Compiling bitflags v2.11.1
[INFO] [stderr]    Compiling fastrand v2.4.1
[INFO] [stderr]    Compiling ahash v0.8.12
[INFO] [stderr]    Compiling mira v0.2.0 (/opt/rustwide/workdir)
[INFO] [stderr]    Compiling tempfile v3.27.0
[INFO] [stderr]     Finished `test` profile [unoptimized + debuginfo] target(s) in 5.33s
[INFO] running `Command { std: "docker" "inspect" "eea66fa0799b63fa52b00b1c9baaa8ce37b9e6ba2c60c40648eba431011b2f61", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "exec" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=warn" "-e" "RUSTDOCFLAGS=--cap-lints=warn" "-w" "/opt/rustwide/workdir" "--user" "0:0" "eea66fa0799b63fa52b00b1c9baaa8ce37b9e6ba2c60c40648eba431011b2f61" "/opt/rustwide/cargo-home/bin/cargo" "+1.100.0-beta.1" "test" "--frozen", kill_on_drop: false }`
[INFO] [stderr]     Finished `test` profile [unoptimized + debuginfo] target(s) in 0.23s
[INFO] [stderr]      Running unittests src/main.rs (/opt/rustwide/target/debug/build/mira/8327a99a243a6421/out/mira-8327a99a243a6421)
[INFO] [stderr]      Running tests/integration_test.rs (/opt/rustwide/target/debug/build/mira/cf751b3d9e299e74/out/integration_test-cf751b3d9e299e74)
[INFO] [stdout] 
[INFO] [stdout] running 0 tests
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 0 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] running 7 tests
[INFO] [stderr] [mira] Building k-mer index from /tmp/.tmpWZW6Eh/ref.fa
[INFO] [stderr] [mira] 1 targets loaded, k=20
[INFO] [stderr] [mira] Scanning FASTQ...
[INFO] [stderr] [mira] Building k-mer index from /tmp/.tmpiXCXZl/ref.fa
[INFO] [stderr] [mira] 1 targets loaded, k=20
[INFO] [stderr] [mira] Scanning FASTQ...
[INFO] [stderr] [mira] 12 read-target hits extracted
[INFO] [stderr] [mira] Dedup: 12 → 12 hits (0 duplicates removed)
[INFO] [stderr] [mira] Aligning and building pileups...
[INFO] [stderr] [mira] Building k-mer index from /tmp/.tmpTOjB8m/ref.fa
[INFO] [stderr] [mira] 1 targets loaded, k=20
[INFO] [stderr] Error: Reference codon mismatch in target 'bad':
[INFO] [stderr]   FASTA at offset=4: 'ACG'
[INFO] [stderr]   Header _ref=: 'TTT'
[INFO] [stderr]   Check that offset and _ref= in the FASTA header are correct.[mira] Building k-mer index from /tmp/.tmpVnx9ZE/ref.fa
[INFO] [stderr] [mira] 1 targets loaded, k=20
[INFO] [stderr] [mira] Scanning FASTQ...
[INFO] [stderr] [mira] 15 read-target hits extracted
[INFO] [stderr] [mira] Dedup: 15 → 4 hits (11 duplicates removed)
[INFO] [stderr] [mira] Aligning and building pileups...
[INFO] [stderr] [mira] Building k-mer index from /tmp/.tmpa6Yy5t/ref.fa
[INFO] [stderr] [mira] 1 targets loaded, k=20
[INFO] [stderr] [mira] Scanning FASTQ...
[INFO] [stderr] [mira] WARNING: zero k-mer hits. Check reference FASTA and input file.
[INFO] [stderr] [mira] Dedup: 0 → 0 hits (0 duplicates removed)
[INFO] [stderr] [mira] Aligning and building pileups...
[INFO] [stderr] [mira] 1 variant/presence rows called
[INFO] [stderr] [mira] Computing reference checksum for provenance...
[INFO] [stderr] [mira] Results written to /tmp/.tmpa6Yy5t/out.tsv
[INFO] [stderr] [mira] Summary written to /tmp/.tmpa6Yy5t/out.summary.tsv
[INFO] [stderr] [mira] Novel variants written to /tmp/.tmpa6Yy5t/out.novel.tsv
[INFO] [stdout] test test_empty_fastq_no_crash ... ok
[INFO] [stderr] [mira] 40 read-target hits extracted
[INFO] [stderr] [mira] Aligning and building pileups...
[INFO] [stderr] [mira] Building k-mer index from /tmp/.tmp7o2KML/ref.fa
[INFO] [stderr] [mira] 1 targets loaded, k=20
[INFO] [stderr] [mira] Scanning FASTQ...
[INFO] [stderr] [mira] 1 variant/presence rows called
[INFO] [stdout] test test_no_kmer_hits_warns_not_crashes ... ok
[INFO] [stderr] [mira] Computing reference checksum for provenance...
[INFO] [stdout] test test_splice_junction_presence ... ok
[INFO] [stderr] [mira] Results written to /tmp/.tmpiXCXZl/out.tsv
[INFO] [stderr] [mira] Summary written to /tmp/.tmpiXCXZl/out.summary.tsv
[INFO] [stderr] [mira] Novel variants written to /tmp/.tmpiXCXZl/out.novel.tsv
[INFO] [stderr] [mira] 1 variant/presence rows called
[INFO] [stderr] [mira] Computing reference checksum for provenance...
[INFO] [stderr] [mira] Results written to /tmp/.tmpWZW6Eh/out.tsv
[INFO] [stderr] [mira] Summary written to /tmp/.tmpWZW6Eh/out.summary.tsv
[INFO] [stderr] [mira] Novel variants written to /tmp/.tmpWZW6Eh/out.novel.tsv
[INFO] [stderr] [mira] 1 variant/presence rows called
[INFO] [stderr] [mira] Computing reference checksum for provenance...
[INFO] [stderr] [mira] Results written to /tmp/.tmpVnx9ZE/out.tsv
[INFO] [stderr] [mira] Summary written to /tmp/.tmpVnx9ZE/out.summary.tsv
[INFO] [stderr] [mira] Novel variants written to /tmp/.tmpVnx9ZE/out.novel.tsv
[INFO] [stdout] test test_low_coverage_indeterminate ... ok
[INFO] [stdout] test test_wt_reads_no_false_mut ... ok
[INFO] [stderr] 
[INFO] [stdout] test test_codon_validation_fails_on_mismatch ... ok
[INFO] [stderr] 
[INFO] [stderr] Stack backtrace:
[INFO] [stderr]    0: <anyhow::Error>::msg::<alloc::string::String>
[INFO] [stderr]              at /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/anyhow-1.0.102/src/backtrace.rs:10:14
[INFO] [stderr]    1: mira::validate_reference_codons
[INFO] [stderr]              at ./src/main.rs:162:13
[INFO] [stderr]    2: mira::main
[INFO] [stderr]              at ./src/main.rs:29:5
[INFO] [stderr]    3: <fn() -> core::result::Result<(), anyhow::Error> as core::ops::function::FnOnce<()>>::call_once
[INFO] [stderr]              at /rustc/e3feeb59cd1bdd011a2bfcc0747b55125d9b8527/library/core/src/ops/function.rs:250:5
[INFO] [stderr]    4: std::sys::backtrace::__rust_begin_short_backtrace::<fn() -> core::result::Result<(), anyhow::Error>, core::result::Result<(), anyhow::Error>>
[INFO] [stderr]              at /rustc/e3feeb59cd1bdd011a2bfcc0747b55125d9b8527/library/std/src/sys/backtrace.rs:166:18
[INFO] [stderr]    5: std::rt::lang_start::<core::result::Result<(), anyhow::Error>>::{closure#0}
[INFO] [stderr]              at /rustc/e3feeb59cd1bdd011a2bfcc0747b55125d9b8527/library/std/src/rt.rs:206:18
[INFO] [stderr]    6: <&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/e3feeb59cd1bdd011a2bfcc0747b55125d9b8527/library/core/src/ops/function.rs:287:21
[INFO] [stderr]    7: 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/e3feeb59cd1bdd011a2bfcc0747b55125d9b8527/library/std/src/panicking.rs:573:43
[INFO] [stderr]    8: std::panicking::catch_unwind::<i32, &dyn core::ops::function::Fn<(), Output = i32> + core::marker::Sync + core::panic::unwind_safe::RefUnwindSafe>
[INFO] [stderr]              at /rustc/e3feeb59cd1bdd011a2bfcc0747b55125d9b8527/library/std/src/panicking.rs:541:19
[INFO] [stderr]    9: std::panic::catch_unwind::<&dyn core::ops::function::Fn<(), Output = i32> + core::marker::Sync + core::panic::unwind_safe::RefUnwindSafe, i32>
[INFO] [stderr]              at /rustc/e3feeb59cd1bdd011a2bfcc0747b55125d9b8527/library/std/src/panic.rs:359:14
[INFO] [stderr]   10: std::rt::lang_start_internal::{closure#0}
[INFO] [stderr]              at /rustc/e3feeb59cd1bdd011a2bfcc0747b55125d9b8527/library/std/src/rt.rs:175:24
[INFO] [stderr]   11: std::panicking::catch_unwind::do_call::<std::rt::lang_start_internal::{closure#0}, isize>
[INFO] [stderr]              at /rustc/e3feeb59cd1bdd011a2bfcc0747b55125d9b8527/library/std/src/panicking.rs:573:43
[INFO] [stderr]   12: std::panicking::catch_unwind::<isize, std::rt::lang_start_internal::{closure#0}>
[INFO] [stderr]              at /rustc/e3feeb59cd1bdd011a2bfcc0747b55125d9b8527/library/std/src/panicking.rs:541:19
[INFO] [stderr]   13: std::panic::catch_unwind::<std::rt::lang_start_internal::{closure#0}, isize>
[INFO] [stderr]              at /rustc/e3feeb59cd1bdd011a2bfcc0747b55125d9b8527/library/std/src/panic.rs:359:14
[INFO] [stderr]   14: std::rt::lang_start_internal
[INFO] [stderr]              at /rustc/e3feeb59cd1bdd011a2bfcc0747b55125d9b8527/library/std/src/rt.rs:171:5
[INFO] [stderr]   15: std::rt::lang_start::<core::result::Result<(), anyhow::Error>>
[INFO] [stderr]              at /rustc/e3feeb59cd1bdd011a2bfcc0747b55125d9b8527/library/std/src/rt.rs:205:5
[INFO] [stderr]   16: main
[INFO] [stderr]   17: <unknown>
[INFO] [stderr]   18: __libc_start_main
[INFO] [stderr]   19: _start
[INFO] [stderr] [mira] 20 read-target hits extracted
[INFO] [stderr] [mira] Aligning and building pileups...
[INFO] [stderr] [mira] 2 variant/presence rows called
[INFO] [stderr] [mira] Computing reference checksum for provenance...
[INFO] [stderr] [mira] Results written to /tmp/.tmp7o2KML/out.tsv
[INFO] [stderr] [mira] Summary written to /tmp/.tmp7o2KML/out.summary.tsv
[INFO] [stderr] [mira] Novel variants written to /tmp/.tmp7o2KML/out.novel.tsv
[INFO] [stdout] test test_snp_detection ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 7 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.20s
[INFO] [stdout] 
[INFO] running `Command { std: "docker" "inspect" "eea66fa0799b63fa52b00b1c9baaa8ce37b9e6ba2c60c40648eba431011b2f61", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "eea66fa0799b63fa52b00b1c9baaa8ce37b9e6ba2c60c40648eba431011b2f61", kill_on_drop: false }`
[INFO] [stdout] eea66fa0799b63fa52b00b1c9baaa8ce37b9e6ba2c60c40648eba431011b2f61
