[INFO] fetching crate scrubby 0.4.0...
[INFO] testing scrubby-0.4.0 against 1.95.0 for beta-1.96-2
[INFO] extracting crate scrubby 0.4.0 into /workspace/builds/worker-5-tc1/source
[INFO] started tweaking crates.io crate scrubby 0.4.0
[INFO] finished tweaking crates.io crate scrubby 0.4.0
[INFO] tweaked toml for crates.io crate scrubby 0.4.0 written to /workspace/builds/worker-5-tc1/source/Cargo.toml
[INFO] validating manifest of crates.io crate scrubby 0.4.0 on toolchain 1.95.0
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+1.95.0" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate crates.io crate scrubby 0.4.0 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" "+1.95.0" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Updating crates.io index
[INFO] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded zerocopy v0.6.6
[INFO] [stderr]   Downloaded buffer-redux v1.0.2
[INFO] [stderr]   Downloaded clap v4.5.13
[INFO] [stderr]   Downloaded minimap2 v0.1.20+minimap2.2.28
[INFO] [stderr]   Downloaded addr2line v0.24.1
[INFO] [stderr]   Downloaded reqwest v0.12.7
[INFO] [stderr]   Downloaded cc v1.1.6
[INFO] [stderr]   Downloaded rust-htslib v0.47.0
[INFO] [stderr]   Downloaded torch-sys v0.16.0
[INFO] [stderr]   Downloaded clap_builder v4.5.13
[INFO] [stderr]   Downloaded matrixmultiply v0.3.9
[INFO] [stderr]   Downloaded gimli v0.31.0
[INFO] [stderr]   Downloaded hyper v1.4.1
[INFO] [stderr]   Downloaded zerocopy-derive v0.6.6
[INFO] [stderr]   Downloaded rustls v0.23.13
[INFO] [stderr]   Downloaded object v0.36.4
[INFO] [stderr]   Downloaded minimap2-sys v0.1.19+minimap2.2.28
[INFO] [stderr]   Downloaded serde_json v1.0.121
[INFO] [stderr]   Downloaded bgzip v0.2.2
[INFO] [stderr]   Downloaded schannel v0.1.24
[INFO] [stderr]   Downloaded bio-types v1.0.3
[INFO] [stderr]   Downloaded redox_syscall v0.5.6
[INFO] [stderr]   Downloaded needletail v0.5.1
[INFO] [stderr]   Downloaded niffler v2.5.0
[INFO] [stderr]   Downloaded ipnet v2.10.0
[INFO] [stderr]   Downloaded ieee754 v0.2.6
[INFO] [stderr]   Downloaded rustc_version v0.1.7
[INFO] [stderr]   Downloaded tar v0.4.42
[INFO] [stderr]   Downloaded zstd-sys v2.0.12+zstd.1.5.6
[INFO] [stderr]   Downloaded newtype_derive v0.1.6
[INFO] [stderr]   Downloaded safetensors v0.3.3
[INFO] [stderr]   Downloaded rustls-pemfile v2.1.3
[INFO] [stderr]   Downloaded derive-new v0.6.0
[INFO] [stderr]   Downloaded fs-utils v1.1.4
[INFO] [stderr]   Downloaded semver v0.1.20
[INFO] [stderr]   Downloaded libz-sys v1.1.18
[INFO] [stderr]   Downloaded curl-sys v0.4.73+curl-8.8.0
[INFO] [stderr]   Downloaded tch v0.16.0
[INFO] [stderr]   Downloaded ppv-lite86 v0.2.18
[INFO] [stderr]   Downloaded hts-sys v2.1.4
[INFO] [stderr]   Downloaded rustls-pki-types v1.9.0
[INFO] [stderr]   Downloaded openssl-src v300.3.1+3.3.1
[INFO] [stderr]   Downloaded openssl v0.10.66
[INFO] [stderr]   Downloaded httparse v1.9.4
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-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" "+1.95.0" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] 60ab6435d66e4e78b53f25630dc8882159b96ec7d5df2cb194db03c71108c6e7
[INFO] running `Command { std: "docker" "start" "-a" "60ab6435d66e4e78b53f25630dc8882159b96ec7d5df2cb194db03c71108c6e7", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "60ab6435d66e4e78b53f25630dc8882159b96ec7d5df2cb194db03c71108c6e7", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "60ab6435d66e4e78b53f25630dc8882159b96ec7d5df2cb194db03c71108c6e7", kill_on_drop: false }`
[INFO] [stdout] 60ab6435d66e4e78b53f25630dc8882159b96ec7d5df2cb194db03c71108c6e7
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-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=warn" "-e" "RUSTDOCFLAGS=--cap-lints=warn" "-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" "+1.95.0" "build" "--frozen" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 8c70ed916301c655c4817a987577c12b1125a5f9800810454dd5bcd444310f4e
[INFO] running `Command { std: "docker" "start" "-a" "8c70ed916301c655c4817a987577c12b1125a5f9800810454dd5bcd444310f4e", kill_on_drop: false }`
[INFO] [stderr]    Compiling libc v0.2.159
[INFO] [stderr]    Compiling pkg-config v0.3.30
[INFO] [stderr]    Compiling proc-macro2 v1.0.86
[INFO] [stderr]    Compiling autocfg v1.3.0
[INFO] [stderr]    Compiling itoa v1.0.11
[INFO] [stderr]    Compiling pin-project-lite v0.2.14
[INFO] [stderr]    Compiling bytes v1.7.2
[INFO] [stderr]    Compiling futures-core v0.3.30
[INFO] [stderr]    Compiling bitflags v2.6.0
[INFO] [stderr]    Compiling futures-sink v0.3.30
[INFO] [stderr]    Compiling tracing-core v0.1.32
[INFO] [stderr]    Compiling log v0.4.22
[INFO] [stderr]    Compiling serde v1.0.204
[INFO] [stderr]    Compiling httparse v1.9.4
[INFO] [stderr]    Compiling hashbrown v0.14.5
[INFO] [stderr]    Compiling futures-task v0.3.30
[INFO] [stderr]    Compiling futures-io v0.3.30
[INFO] [stderr]    Compiling openssl v0.10.66
[INFO] [stderr]    Compiling rustix v0.38.37
[INFO] [stderr]    Compiling native-tls v0.2.12
[INFO] [stderr]    Compiling anstyle-parse v0.2.5
[INFO] [stderr]    Compiling tinyvec v1.8.0
[INFO] [stderr]    Compiling miniz_oxide v0.7.4
[INFO] [stderr]    Compiling slab v0.4.9
[INFO] [stderr]    Compiling tracing v0.1.40
[INFO] [stderr]    Compiling futures-channel v0.3.30
[INFO] [stderr]    Compiling crc32fast v1.4.2
[INFO] [stderr]    Compiling anstyle-query v1.1.1
[INFO] [stderr]    Compiling is_terminal_polyfill v1.70.1
[INFO] [stderr]    Compiling linux-raw-sys v0.4.14
[INFO] [stderr]    Compiling http v1.1.0
[INFO] [stderr]    Compiling anstyle v1.0.7
[INFO] [stderr]    Compiling ryu v1.0.18
[INFO] [stderr]    Compiling regex-syntax v0.8.4
[INFO] [stderr]    Compiling indexmap v2.5.0
[INFO] [stderr]    Compiling thiserror v1.0.63
[INFO] [stderr]    Compiling colorchoice v1.0.2
[INFO] [stderr]    Compiling flate2 v1.0.30
[INFO] [stderr]    Compiling crossbeam-epoch v0.9.18
[INFO] [stderr]    Compiling num-traits v0.2.19
[INFO] [stderr]    Compiling jobserver v0.1.32
[INFO] [stderr]    Compiling mio v1.0.2
[INFO] [stderr]    Compiling socket2 v0.5.7
[INFO] [stderr]    Compiling futures-util v0.3.30
[INFO] [stderr]    Compiling cc v1.1.6
[INFO] [stderr]    Compiling anstream v0.6.15
[INFO] [stderr]    Compiling rayon-core v1.12.1
[INFO] [stderr]    Compiling unicode-bidi v0.3.15
[INFO] [stderr]    Compiling http-body v1.0.1
[INFO] [stderr]    Compiling quote v1.0.36
[INFO] [stderr]    Compiling crossbeam-deque v0.8.5
[INFO] [stderr]    Compiling rustls-pki-types v1.9.0
[INFO] [stderr]    Compiling anyhow v1.0.86
[INFO] [stderr]    Compiling serde_json v1.0.121
[INFO] [stderr]    Compiling unicode-normalization v0.1.23
[INFO] [stderr]    Compiling syn v2.0.72
[INFO] [stderr]    Compiling openssl-src v300.3.1+3.3.1
[INFO] [stderr]    Compiling clap_lex v0.7.2
[INFO] [stderr]    Compiling rustls-pemfile v2.1.3
[INFO] [stderr]    Compiling tokio v1.40.0
[INFO] [stderr]    Compiling clap_builder v4.5.13
[INFO] [stderr]    Compiling filetime v0.2.25
[INFO] [stderr]    Compiling sync_wrapper v1.0.1
[INFO] [stderr]    Compiling buffer-redux v1.0.2
[INFO] [stderr]    Compiling idna v0.5.0
[INFO] [stderr]    Compiling regex-automata v0.4.7
[INFO] [stderr]    Compiling csv-core v0.1.11
[INFO] [stderr]    Compiling encoding_rs v0.8.34
[INFO] [stderr]    Compiling fastrand v2.1.1
[INFO] [stderr]    Compiling ipnet v2.10.0
[INFO] [stderr]    Compiling either v1.13.0
[INFO] [stderr]    Compiling iana-time-zone v0.1.60
[INFO] [stderr]    Compiling url v2.5.2
[INFO] [stderr]    Compiling bytecount v0.6.8
[INFO] [stderr]    Compiling chrono v0.4.38
[INFO] [stderr]    Compiling rayon v1.10.0
[INFO] [stderr]    Compiling openssl-sys v0.9.103
[INFO] [stderr]    Compiling zstd-sys v2.0.12+zstd.1.5.6
[INFO] [stderr]    Compiling bzip2-sys v0.1.11+1.0.8
[INFO] [stderr]    Compiling lzma-sys v0.1.20
[INFO] [stderr]    Compiling xattr v1.3.1
[INFO] [stderr]    Compiling tempfile v3.13.0
[INFO] [stderr]    Compiling xz2 v0.1.7
[INFO] [stderr]    Compiling tar v0.4.42
[INFO] [stderr]    Compiling http-body-util v0.1.2
[INFO] [stderr]    Compiling regex v1.10.5
[INFO] [stderr]    Compiling bzip2 v0.4.4
[INFO] [stderr]    Compiling env_filter v0.1.2
[INFO] [stderr]    Compiling needletail v0.5.1
[INFO] [stderr]    Compiling env_logger v0.11.5
[INFO] [stderr]    Compiling tokio-util v0.7.12
[INFO] [stderr]    Compiling openssl-macros v0.1.1
[INFO] [stderr]    Compiling serde_derive v1.0.204
[INFO] [stderr]    Compiling thiserror-impl v1.0.63
[INFO] [stderr]    Compiling clap_derive v4.5.13
[INFO] [stderr]    Compiling h2 v0.4.6
[INFO] [stderr]    Compiling bgzip v0.2.2
[INFO] [stderr]    Compiling clap v4.5.13
[INFO] [stderr]    Compiling zstd-safe v6.0.6
[INFO] [stderr]    Compiling zstd v0.12.4
[INFO] [stderr]    Compiling niffler v2.5.0
[INFO] [stderr]    Compiling hyper v1.4.1
[INFO] [stderr]    Compiling hyper-util v0.1.9
[INFO] [stderr]    Compiling serde_urlencoded v0.7.1
[INFO] [stderr]    Compiling csv v1.3.0
[INFO] [stderr]    Compiling tokio-native-tls v0.3.1
[INFO] [stderr]    Compiling hyper-tls v0.6.0
[INFO] [stderr]    Compiling reqwest v0.12.7
[INFO] [stderr]    Compiling scrubby v0.4.0 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 1m 16s
[INFO] running `Command { std: "docker" "inspect" "8c70ed916301c655c4817a987577c12b1125a5f9800810454dd5bcd444310f4e", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "8c70ed916301c655c4817a987577c12b1125a5f9800810454dd5bcd444310f4e", kill_on_drop: false }`
[INFO] [stdout] 8c70ed916301c655c4817a987577c12b1125a5f9800810454dd5bcd444310f4e
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-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=warn" "-e" "RUSTDOCFLAGS=--cap-lints=warn" "-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" "+1.95.0" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 0539d593a17e8533ebc0b80256ce32c24d67bca2e6f2d5da691b1b0d3e79f03f
[INFO] running `Command { std: "docker" "start" "-a" "0539d593a17e8533ebc0b80256ce32c24d67bca2e6f2d5da691b1b0d3e79f03f", kill_on_drop: false }`
[INFO] [stderr]    Compiling scrubby v0.4.0 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished `test` profile [unoptimized + debuginfo] target(s) in 0.90s
[INFO] running `Command { std: "docker" "inspect" "0539d593a17e8533ebc0b80256ce32c24d67bca2e6f2d5da691b1b0d3e79f03f", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "0539d593a17e8533ebc0b80256ce32c24d67bca2e6f2d5da691b1b0d3e79f03f", kill_on_drop: false }`
[INFO] [stdout] 0539d593a17e8533ebc0b80256ce32c24d67bca2e6f2d5da691b1b0d3e79f03f
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-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=warn" "-e" "RUSTDOCFLAGS=--cap-lints=warn" "-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" "+1.95.0" "test" "--frozen", kill_on_drop: false }`
[INFO] [stdout] 7a4020379f8d6b051095055db7e993ee6ff3d94df86c82bd026edccccaebe5a1
[INFO] running `Command { std: "docker" "start" "-a" "7a4020379f8d6b051095055db7e993ee6ff3d94df86c82bd026edccccaebe5a1", kill_on_drop: false }`
[INFO] [stderr]     Finished `test` profile [unoptimized + debuginfo] target(s) in 0.12s
[INFO] [stderr]      Running unittests src/lib.rs (/opt/rustwide/target/debug/deps/scrubby-8e76e3ca5f1ef146)
[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] [stderr]      Running unittests src/main.rs (/opt/rustwide/target/debug/deps/scrubby-2b11153709b8d786)
[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] [stderr]    Doc-tests scrubby
[INFO] [stdout] 
[INFO] [stdout] running 80 tests
[INFO] [stdout] test src/cleaner.rs - cleaner::Cleaner::clean_reads (line 230) ... FAILED
[INFO] [stdout] test src/cleaner.rs - cleaner::Cleaner::run_classifier_output (line 172) ... FAILED
[INFO] [stdout] test src/classifier.rs - classifier::TaxonCounts::update (line 88) ... FAILED
[INFO] [stdout] test src/classifier.rs - classifier::KrakenReadRecord::from_str (line 398) ... FAILED
[INFO] [stdout] test src/cleaner.rs - cleaner::Cleaner::from_scrubby (line 102) ... FAILED
[INFO] [stdout] test src/cleaner.rs - cleaner::Cleaner::run_aligner (line 129) ... FAILED
[INFO] [stdout] test src/classifier.rs - classifier::TaxonCounts::new (line 68) ... FAILED
[INFO] [stdout] test src/cleaner.rs - cleaner::Cleaner::run_aligner_output (line 201) ... FAILED
[INFO] [stdout] test src/classifier.rs - classifier::get_tax_level (line 342) ... FAILED
[INFO] [stdout] test src/classifier.rs - classifier::get_taxid_reads_kraken (line 267) ... FAILED
[INFO] [stdout] test src/classifier.rs - classifier::get_taxids_from_report (line 121) ... FAILED
[INFO] [stdout] test src/classifier.rs - classifier::MetabuliReadRecord::from_str (line 494) ... FAILED
[INFO] [stdout] test src/classifier.rs - classifier::KrakenReportRecord::from_str (line 446) ... FAILED
[INFO] [stdout] test src/cleaner.rs - cleaner::FastqCleaner::clean_reads (line 727) ... FAILED
[INFO] [stdout] test src/classifier.rs - classifier::get_taxid_reads_metabuli (line 305) ... FAILED
[INFO] [stdout] test src/cleaner.rs - cleaner::Cleaner::run_classifier (line 153) ... FAILED
[INFO] [stdout] test src/cleaner.rs - cleaner::SamtoolsConfig::get_pipeline (line 75) ... FAILED
[INFO] [stdout] test src/cleaner.rs - cleaner::SamtoolsConfig::from_scrubby (line 43) ... FAILED
[INFO] [stdout] test src/download.rs - download::ScrubbyDownloader::list (line 130) ... FAILED
[INFO] [stdout] test src/cleaner.rs - cleaner::FastqCleaner::from (line 706) ... FAILED
[INFO] [stdout] test src/download.rs - download::ScrubbyDownloaderBuilder::build (line 397) ... FAILED
[INFO] [stdout] test src/download.rs - download::ScrubbyDownloader::download_index (line 160) ... FAILED
[INFO] [stdout] test src/download.rs - download::ScrubbyDownloader::unpack (line 206) ... FAILED
[INFO] [stdout] test src/download.rs - download::ScrubbyDownloader::download (line 237) ... FAILED
[INFO] [stdout] test src/download.rs - download::ScrubbyDownloader::new (line 101) ... FAILED
[INFO] [stdout] test src/download.rs - download::ScrubbyDownloaderBuilder::aligner (line 307) ... FAILED
[INFO] [stdout] test src/download.rs - download::ScrubbyDownloaderBuilder::new (line 282) ... FAILED
[INFO] [stdout] test src/download.rs - download::ScrubbyDownloaderBuilder::timeout (line 337) ... FAILED
[INFO] [stdout] test src/download.rs - download::ScrubbyDownloaderBuilder::classifier (line 322) ... FAILED
[INFO] [stdout] test src/download.rs - download::ScrubbyDownloaderBuilder::password (line 382) ... FAILED
[INFO] [stdout] test src/download.rs - download::ScrubbyDownloaderBuilder::base_url (line 352) ... FAILED
[INFO] [stdout] test src/download.rs - download::ScrubbyDownloader::builder (line 118) ... FAILED
[INFO] [stdout] test src/scrubby.rs - scrubby::Scrubby::new (line 193) ... FAILED
[INFO] [stdout] test src/scrubby.rs - scrubby::Scrubby::clean (line 249) ... FAILED
[INFO] [stdout] test src/scrubby.rs - scrubby::Scrubby::builder (line 228) ... FAILED
[INFO] [stdout] test src/download.rs - download::ScrubbyIndex::fmt (line 63) ... FAILED
[INFO] [stdout] test src/download.rs - download::ScrubbyDownloaderBuilder::username (line 367) ... FAILED
[INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::aligner_args (line 705) ... FAILED
[INFO] [stdout] test src/download.rs - download::ScrubbyIndex::aligner_name (line 28) ... FAILED
[INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::alignment (line 513) ... FAILED
[INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::aligner_index (line 638) ... FAILED
[INFO] [stdout] test src/download.rs - download::ScrubbyIndex::classifier_name (line 44) ... FAILED
[INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::aligner (line 500) ... FAILED
[INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::build_alignment (line 1008) ... FAILED
[INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::build (line 802) ... FAILED
[INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::alignment_format (line 527) ... FAILED
[INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::classifier (line 583) ... FAILED
[INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::build_classifier (line 967) ... FAILED
[INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::classifier_args (line 692) ... FAILED
[INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::classifier_index (line 652) ... FAILED
[INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::command (line 420) ... FAILED
[INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::new (line 337) ... FAILED
[INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::keep (line 461) ... FAILED
[INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::index (line 624) ... FAILED
[INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::extract (line 448) ... FAILED
[INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::json (line 406) ... FAILED
[INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::min_query_coverage (line 555) ... FAILED
[INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::min_mapq (line 569) ... FAILED
[INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::preset (line 744) ... FAILED
[INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::min_query_length (line 541) ... FAILED
[INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::needletail_parallel (line 731) ... FAILED
[INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::read_ids (line 392) ... FAILED
[INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::reads (line 596) ... FAILED
[INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::report (line 610) ... FAILED
[INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::samtools_threads (line 718) ... FAILED
[INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::taxa (line 666) ... FAILED
[INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::workdir (line 434) ... FAILED
[INFO] [stdout] test src/terminal.rs - terminal::AlignmentArgs::validate_and_build (line 406) ... FAILED
[INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::threads (line 487) ... FAILED
[INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::taxa_direct (line 679) ... FAILED
[INFO] [stdout] test src/utils.rs - utils::get_fastx_writer (line 53) ... FAILED
[INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::unpaired (line 474) ... FAILED
[INFO] [stdout] test src/terminal.rs - terminal::DownloadArgs::validate_and_build (line 475) ... FAILED
[INFO] [stdout] test src/terminal.rs - terminal::ClassifierArgs::validate_and_build (line 294) ... FAILED
[INFO] [stdout] test src/terminal.rs - terminal::DiffArgs::validate_and_build (line 540) ... FAILED
[INFO] [stdout] test src/utils.rs - utils::ReadDifferenceBuilder::read_ids (line 309) ... FAILED
[INFO] [stdout] test src/terminal.rs - terminal::ReadsArgs::validate_and_build (line 172) ... FAILED
[INFO] [stdout] test src/utils.rs - utils::ReadDifferenceBuilder::json (line 323) ... FAILED
[INFO] [stdout] test src/utils.rs - utils::get_id (line 88) ... FAILED
[INFO] [stdout] test src/utils.rs - utils::niffler::compression::Format::from_path (line 24) ... FAILED
[INFO] [stdout] 
[INFO] [stdout] failures:
[INFO] [stdout] 
[INFO] [stdout] ---- src/cleaner.rs - cleaner::Cleaner::clean_reads (line 230) stdout ----
[INFO] [stdout] error[E0433]: cannot find type `HashSet` in this scope
[INFO] [stdout]    --> src/cleaner.rs:231:16
[INFO] [stdout]     |
[INFO] [stdout] 231 | let read_ids = HashSet::new();
[INFO] [stdout]     |                ^^^^^^^ use of undeclared type `HashSet`
[INFO] [stdout]     |
[INFO] [stdout] help: consider importing this struct
[INFO] [stdout]     |
[INFO] [stdout] 230 + use std::collections::HashSet;
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `cleaner` in this scope
[INFO] [stdout]    --> src/cleaner.rs:232:1
[INFO] [stdout]     |
[INFO] [stdout] 232 | cleaner.clean_reads(&read_ids).unwrap();
[INFO] [stdout]     | ^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 2 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0425, E0433.
[INFO] [stdout] For more information about an error, try `rustc --explain E0425`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/cleaner.rs - cleaner::Cleaner::run_classifier_output (line 172) stdout ----
[INFO] [stdout] error[E0425]: cannot find value `cleaner` in this scope
[INFO] [stdout]    --> src/cleaner.rs:173:1
[INFO] [stdout]     |
[INFO] [stdout] 173 | cleaner.run_classifier_output().unwrap();
[INFO] [stdout]     | ^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 1 previous error
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0425`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/classifier.rs - classifier::TaxonCounts::update (line 88) stdout ----
[INFO] [stdout] error[E0425]: cannot find value `taxon_counts` in this scope
[INFO] [stdout]   --> src/classifier.rs:89:1
[INFO] [stdout]    |
[INFO] [stdout] 89 | taxon_counts.update("GenusA".to_string(), "FamilyA".to_string(), 10);
[INFO] [stdout]    | ^^^^^^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 1 previous error
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0425`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/classifier.rs - classifier::KrakenReadRecord::from_str (line 398) stdout ----
[INFO] [stdout] error[E0433]: cannot find type `KrakenReadRecord` in this scope
[INFO] [stdout]    --> src/classifier.rs:399:14
[INFO] [stdout]     |
[INFO] [stdout] 399 | let record = KrakenReadRecord::from_str("C\tread1\t12345\t100\tannotation".to_string()).unwrap();
[INFO] [stdout]     |              ^^^^^^^^^^^^^^^^ use of undeclared type `KrakenReadRecord`
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 1 previous error
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0433`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/cleaner.rs - cleaner::Cleaner::from_scrubby (line 102) stdout ----
[INFO] [stdout] error[E0432]: unresolved import `scrubby::Cleaner`
[INFO] [stdout]    --> src/cleaner.rs:104:5
[INFO] [stdout]     |
[INFO] [stdout] 104 | use scrubby::Cleaner;
[INFO] [stdout]     |     ^^^^^^^^^^^^^^^^ no `Cleaner` in the root
[INFO] [stdout]     |
[INFO] [stdout] help: a similar name exists in the module (notice the capitalization)
[INFO] [stdout]     |
[INFO] [stdout] 104 - use scrubby::Cleaner;
[INFO] [stdout] 104 + use scrubby::cleaner;
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `scrubby_instance` in this scope
[INFO] [stdout]    --> src/cleaner.rs:105:38
[INFO] [stdout]     |
[INFO] [stdout] 105 | let cleaner = Cleaner::from_scrubby(&scrubby_instance).unwrap();
[INFO] [stdout]     |                                      ^^^^^^^^^^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 2 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0425, E0432.
[INFO] [stdout] For more information about an error, try `rustc --explain E0425`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/cleaner.rs - cleaner::Cleaner::run_aligner (line 129) stdout ----
[INFO] [stdout] error[E0425]: cannot find value `cleaner` in this scope
[INFO] [stdout]    --> src/cleaner.rs:130:1
[INFO] [stdout]     |
[INFO] [stdout] 130 | cleaner.run_aligner().unwrap();
[INFO] [stdout]     | ^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 1 previous error
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0425`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/classifier.rs - classifier::TaxonCounts::new (line 68) stdout ----
[INFO] [stdout] error[E0432]: unresolved import `scrubby::TaxonCounts`
[INFO] [stdout]   --> src/classifier.rs:70:5
[INFO] [stdout]    |
[INFO] [stdout] 70 | use scrubby::TaxonCounts;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^ no `TaxonCounts` in the root
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 1 previous error
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0432`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/cleaner.rs - cleaner::Cleaner::run_aligner_output (line 201) stdout ----
[INFO] [stdout] error[E0425]: cannot find value `cleaner` in this scope
[INFO] [stdout]    --> src/cleaner.rs:202:1
[INFO] [stdout]     |
[INFO] [stdout] 202 | cleaner.run_aligner_output().unwrap();
[INFO] [stdout]     | ^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 1 previous error
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0425`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/classifier.rs - classifier::get_tax_level (line 342) stdout ----
[INFO] [stdout] error[E0425]: cannot find value `record` in this scope
[INFO] [stdout]    --> src/classifier.rs:343:32
[INFO] [stdout]     |
[INFO] [stdout] 343 | let tax_level = get_tax_level(&record);
[INFO] [stdout]     |                                ^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find function `get_tax_level` in this scope
[INFO] [stdout]    --> src/classifier.rs:343:17
[INFO] [stdout]     |
[INFO] [stdout] 343 | let tax_level = get_tax_level(&record);
[INFO] [stdout]     |                 ^^^^^^^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 2 previous errors
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0425`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/classifier.rs - classifier::get_taxid_reads_kraken (line 267) stdout ----
[INFO] [stdout] error[E0425]: cannot find value `taxids` in this scope
[INFO] [stdout]    --> src/classifier.rs:268:39
[INFO] [stdout]     |
[INFO] [stdout] 268 | let read_ids = get_taxid_reads_kraken(taxids, &reads_path).unwrap();
[INFO] [stdout]     |                                       ^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `reads_path` in this scope
[INFO] [stdout]    --> src/classifier.rs:268:48
[INFO] [stdout]     |
[INFO] [stdout] 268 | let read_ids = get_taxid_reads_kraken(taxids, &reads_path).unwrap();
[INFO] [stdout]     |                                                ^^^^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find function `get_taxid_reads_kraken` in this scope
[INFO] [stdout]    --> src/classifier.rs:268:16
[INFO] [stdout]     |
[INFO] [stdout] 268 | let read_ids = get_taxid_reads_kraken(taxids, &reads_path).unwrap();
[INFO] [stdout]     |                ^^^^^^^^^^^^^^^^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 3 previous errors
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0425`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/classifier.rs - classifier::get_taxids_from_report (line 121) stdout ----
[INFO] [stdout] error[E0425]: cannot find value `report_path` in this scope
[INFO] [stdout]    --> src/classifier.rs:122:38
[INFO] [stdout]     |
[INFO] [stdout] 122 | let taxids = get_taxids_from_report(&report_path, &vec!["Eukaryota".to_string()], &vec![]).unwrap();
[INFO] [stdout]     |                                      ^^^^^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find function `get_taxids_from_report` in this scope
[INFO] [stdout]    --> src/classifier.rs:122:14
[INFO] [stdout]     |
[INFO] [stdout] 122 | let taxids = get_taxids_from_report(&report_path, &vec!["Eukaryota".to_string()], &vec![]).unwrap();
[INFO] [stdout]     |              ^^^^^^^^^^^^^^^^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 2 previous errors
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0425`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/classifier.rs - classifier::MetabuliReadRecord::from_str (line 494) stdout ----
[INFO] [stdout] error[E0433]: cannot find type `MetabuliReadRecord` in this scope
[INFO] [stdout]    --> src/classifier.rs:495:14
[INFO] [stdout]     |
[INFO] [stdout] 495 | let record = MetabuliReadRecord::from_str("1\tread1\t12345\t100\t80.5\tgenus\tannotation".to_string()).unwrap();
[INFO] [stdout]     |              ^^^^^^^^^^^^^^^^^^ use of undeclared type `MetabuliReadRecord`
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 1 previous error
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0433`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/classifier.rs - classifier::KrakenReportRecord::from_str (line 446) stdout ----
[INFO] [stdout] error[E0433]: cannot find type `KrakenReportRecord` in this scope
[INFO] [stdout]    --> src/classifier.rs:447:14
[INFO] [stdout]     |
[INFO] [stdout] 447 | let record = KrakenReportRecord::from_str("0.05\t100\t50\tS\t12345\ttaxon_name".to_string()).unwrap();
[INFO] [stdout]     |              ^^^^^^^^^^^^^^^^^^ use of undeclared type `KrakenReportRecord`
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 1 previous error
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0433`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/cleaner.rs - cleaner::FastqCleaner::clean_reads (line 727) stdout ----
[INFO] [stdout] error[E0433]: cannot find type `HashSet` in this scope
[INFO] [stdout]    --> src/cleaner.rs:728:16
[INFO] [stdout]     |
[INFO] [stdout] 728 | let read_ids = HashSet::new();
[INFO] [stdout]     |                ^^^^^^^ use of undeclared type `HashSet`
[INFO] [stdout]     |
[INFO] [stdout] help: consider importing this struct
[INFO] [stdout]     |
[INFO] [stdout] 727 + use std::collections::HashSet;
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `cleaner` in this scope
[INFO] [stdout]    --> src/cleaner.rs:729:1
[INFO] [stdout]     |
[INFO] [stdout] 729 | cleaner.clean_reads(&read_ids, false).unwrap();
[INFO] [stdout]     | ^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 2 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0425, E0433.
[INFO] [stdout] For more information about an error, try `rustc --explain E0425`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/classifier.rs - classifier::get_taxid_reads_metabuli (line 305) stdout ----
[INFO] [stdout] error[E0425]: cannot find value `taxids` in this scope
[INFO] [stdout]    --> src/classifier.rs:306:41
[INFO] [stdout]     |
[INFO] [stdout] 306 | let read_ids = get_taxid_reads_metabuli(taxids, &reads_path).unwrap();
[INFO] [stdout]     |                                         ^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `reads_path` in this scope
[INFO] [stdout]    --> src/classifier.rs:306:50
[INFO] [stdout]     |
[INFO] [stdout] 306 | let read_ids = get_taxid_reads_metabuli(taxids, &reads_path).unwrap();
[INFO] [stdout]     |                                                  ^^^^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find function `get_taxid_reads_metabuli` in this scope
[INFO] [stdout]    --> src/classifier.rs:306:16
[INFO] [stdout]     |
[INFO] [stdout] 306 | let read_ids = get_taxid_reads_metabuli(taxids, &reads_path).unwrap();
[INFO] [stdout]     |                ^^^^^^^^^^^^^^^^^^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 3 previous errors
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0425`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/cleaner.rs - cleaner::Cleaner::run_classifier (line 153) stdout ----
[INFO] [stdout] error[E0425]: cannot find value `cleaner` in this scope
[INFO] [stdout]    --> src/cleaner.rs:154:1
[INFO] [stdout]     |
[INFO] [stdout] 154 | cleaner.run_classifier().unwrap();
[INFO] [stdout]     | ^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 1 previous error
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0425`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/cleaner.rs - cleaner::SamtoolsConfig::get_pipeline (line 75) stdout ----
[INFO] [stdout] error[E0425]: cannot find value `samtools_config` in this scope
[INFO] [stdout]   --> src/cleaner.rs:76:16
[INFO] [stdout]    |
[INFO] [stdout] 76 | let pipeline = samtools_config.get_pipeline();
[INFO] [stdout]    |                ^^^^^^^^^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 1 previous error
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0425`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/cleaner.rs - cleaner::SamtoolsConfig::from_scrubby (line 43) stdout ----
[INFO] [stdout] error[E0432]: unresolved import `scrubby::SamtoolsConfig`
[INFO] [stdout]   --> src/cleaner.rs:45:5
[INFO] [stdout]    |
[INFO] [stdout] 45 | use scrubby::SamtoolsConfig;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^ no `SamtoolsConfig` in the root
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `scrubby_instance` in this scope
[INFO] [stdout]   --> src/cleaner.rs:46:53
[INFO] [stdout]    |
[INFO] [stdout] 46 | let samtools_config = SamtoolsConfig::from_scrubby(&scrubby_instance);
[INFO] [stdout]    |                                                     ^^^^^^^^^^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 2 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0425, E0432.
[INFO] [stdout] For more information about an error, try `rustc --explain E0425`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/download.rs - download::ScrubbyDownloader::list (line 130) stdout ----
[INFO] [stdout] error[E0425]: cannot find value `outdir` in this scope
[INFO] [stdout]    --> src/download.rs:131:41
[INFO] [stdout]     |
[INFO] [stdout] 131 | let downloader = ScrubbyDownloader::new(outdir, indices);
[INFO] [stdout]     |                                         ^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `indices` in this scope
[INFO] [stdout]    --> src/download.rs:131:49
[INFO] [stdout]     |
[INFO] [stdout] 131 | let downloader = ScrubbyDownloader::new(outdir, indices);
[INFO] [stdout]     |                                                 ^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `ScrubbyDownloader` in this scope
[INFO] [stdout]    --> src/download.rs:131:18
[INFO] [stdout]     |
[INFO] [stdout] 131 | let downloader = ScrubbyDownloader::new(outdir, indices);
[INFO] [stdout]     |                  ^^^^^^^^^^^^^^^^^ use of undeclared type `ScrubbyDownloader`
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 3 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0425, E0433.
[INFO] [stdout] For more information about an error, try `rustc --explain E0425`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/cleaner.rs - cleaner::FastqCleaner::from (line 706) stdout ----
[INFO] [stdout] error[E0432]: unresolved import `scrubby::FastqCleaner`
[INFO] [stdout]    --> src/cleaner.rs:708:5
[INFO] [stdout]     |
[INFO] [stdout] 708 | use scrubby::FastqCleaner;
[INFO] [stdout]     |     ^^^^^^^^^^^^^^^^^^^^^ no `FastqCleaner` in the root
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `input_path` in this scope
[INFO] [stdout]    --> src/cleaner.rs:709:35
[INFO] [stdout]     |
[INFO] [stdout] 709 | let cleaner = FastqCleaner::from(&input_path, &output_path);
[INFO] [stdout]     |                                   ^^^^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `output_path` in this scope
[INFO] [stdout]    --> src/cleaner.rs:709:48
[INFO] [stdout]     |
[INFO] [stdout] 709 | let cleaner = FastqCleaner::from(&input_path, &output_path);
[INFO] [stdout]     |                                                ^^^^^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 3 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0425, E0432.
[INFO] [stdout] For more information about an error, try `rustc --explain E0425`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/download.rs - download::ScrubbyDownloaderBuilder::build (line 397) stdout ----
[INFO] [stdout] error[E0425]: cannot find value `outdir` in this scope
[INFO] [stdout]    --> src/download.rs:398:45
[INFO] [stdout]     |
[INFO] [stdout] 398 | let builder = ScrubbyDownloaderBuilder::new(outdir, indices);
[INFO] [stdout]     |                                             ^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `indices` in this scope
[INFO] [stdout]    --> src/download.rs:398:53
[INFO] [stdout]     |
[INFO] [stdout] 398 | let builder = ScrubbyDownloaderBuilder::new(outdir, indices);
[INFO] [stdout]     |                                                     ^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `ScrubbyDownloaderBuilder` in this scope
[INFO] [stdout]    --> src/download.rs:398:15
[INFO] [stdout]     |
[INFO] [stdout] 398 | let builder = ScrubbyDownloaderBuilder::new(outdir, indices);
[INFO] [stdout]     |               ^^^^^^^^^^^^^^^^^^^^^^^^ use of undeclared type `ScrubbyDownloaderBuilder`
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 3 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0425, E0433.
[INFO] [stdout] For more information about an error, try `rustc --explain E0425`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/download.rs - download::ScrubbyDownloader::download_index (line 160) stdout ----
[INFO] [stdout] error[E0425]: cannot find value `outdir` in this scope
[INFO] [stdout]    --> src/download.rs:161:41
[INFO] [stdout]     |
[INFO] [stdout] 161 | let downloader = ScrubbyDownloader::new(outdir, indices);
[INFO] [stdout]     |                                         ^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `indices` in this scope
[INFO] [stdout]    --> src/download.rs:161:49
[INFO] [stdout]     |
[INFO] [stdout] 161 | let downloader = ScrubbyDownloader::new(outdir, indices);
[INFO] [stdout]     |                                                 ^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `ScrubbyDownloader` in this scope
[INFO] [stdout]    --> src/download.rs:161:18
[INFO] [stdout]     |
[INFO] [stdout] 161 | let downloader = ScrubbyDownloader::new(outdir, indices);
[INFO] [stdout]     |                  ^^^^^^^^^^^^^^^^^ use of undeclared type `ScrubbyDownloader`
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 3 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0425, E0433.
[INFO] [stdout] For more information about an error, try `rustc --explain E0425`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/download.rs - download::ScrubbyDownloader::unpack (line 206) stdout ----
[INFO] [stdout] error[E0425]: cannot find value `outdir` in this scope
[INFO] [stdout]    --> src/download.rs:207:41
[INFO] [stdout]     |
[INFO] [stdout] 207 | let downloader = ScrubbyDownloader::new(outdir, indices);
[INFO] [stdout]     |                                         ^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `indices` in this scope
[INFO] [stdout]    --> src/download.rs:207:49
[INFO] [stdout]     |
[INFO] [stdout] 207 | let downloader = ScrubbyDownloader::new(outdir, indices);
[INFO] [stdout]     |                                                 ^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `download_path` in this scope
[INFO] [stdout]    --> src/download.rs:208:20
[INFO] [stdout]     |
[INFO] [stdout] 208 | downloader.unpack(&download_path, &outdir);
[INFO] [stdout]     |                    ^^^^^^^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `outdir` in this scope
[INFO] [stdout]    --> src/download.rs:208:36
[INFO] [stdout]     |
[INFO] [stdout] 208 | downloader.unpack(&download_path, &outdir);
[INFO] [stdout]     |                                    ^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `ScrubbyDownloader` in this scope
[INFO] [stdout]    --> src/download.rs:207:18
[INFO] [stdout]     |
[INFO] [stdout] 207 | let downloader = ScrubbyDownloader::new(outdir, indices);
[INFO] [stdout]     |                  ^^^^^^^^^^^^^^^^^ use of undeclared type `ScrubbyDownloader`
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 5 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0425, E0433.
[INFO] [stdout] For more information about an error, try `rustc --explain E0425`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/download.rs - download::ScrubbyDownloader::download (line 237) stdout ----
[INFO] [stdout] error[E0425]: cannot find value `outdir` in this scope
[INFO] [stdout]    --> src/download.rs:238:41
[INFO] [stdout]     |
[INFO] [stdout] 238 | let downloader = ScrubbyDownloader::new(outdir, indices);
[INFO] [stdout]     |                                         ^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `indices` in this scope
[INFO] [stdout]    --> src/download.rs:238:49
[INFO] [stdout]     |
[INFO] [stdout] 238 | let downloader = ScrubbyDownloader::new(outdir, indices);
[INFO] [stdout]     |                                                 ^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0423]: expected value, found built-in attribute `path`
[INFO] [stdout]    --> src/download.rs:239:42
[INFO] [stdout]     |
[INFO] [stdout] 239 | downloader.download("file_name.tar.xz", &path);
[INFO] [stdout]     |                                          ^^^^ not a value
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `ScrubbyDownloader` in this scope
[INFO] [stdout]    --> src/download.rs:238:18
[INFO] [stdout]     |
[INFO] [stdout] 238 | let downloader = ScrubbyDownloader::new(outdir, indices);
[INFO] [stdout]     |                  ^^^^^^^^^^^^^^^^^ use of undeclared type `ScrubbyDownloader`
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 4 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0423, E0425, E0433.
[INFO] [stdout] For more information about an error, try `rustc --explain E0423`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/download.rs - download::ScrubbyDownloader::new (line 101) stdout ----
[INFO] [stdout] error[E0433]: cannot find type `PathBuf` in this scope
[INFO] [stdout]    --> src/download.rs:102:14
[INFO] [stdout]     |
[INFO] [stdout] 102 | let outdir = PathBuf::from("/path/to/output");
[INFO] [stdout]     |              ^^^^^^^ use of undeclared type `PathBuf`
[INFO] [stdout]     |
[INFO] [stdout] help: consider importing this struct
[INFO] [stdout]     |
[INFO] [stdout] 101 + use std::path::PathBuf;
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `ScrubbyIndex` in this scope
[INFO] [stdout]    --> src/download.rs:103:20
[INFO] [stdout]     |
[INFO] [stdout] 103 | let indices = vec![ScrubbyIndex::Chm13v2];
[INFO] [stdout]     |                    ^^^^^^^^^^^^ use of undeclared type `ScrubbyIndex`
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `ScrubbyDownloader` in this scope
[INFO] [stdout]    --> src/download.rs:104:18
[INFO] [stdout]     |
[INFO] [stdout] 104 | let downloader = ScrubbyDownloader::new(outdir, indices);
[INFO] [stdout]     |                  ^^^^^^^^^^^^^^^^^ use of undeclared type `ScrubbyDownloader`
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 3 previous errors
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0433`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/download.rs - download::ScrubbyDownloaderBuilder::aligner (line 307) stdout ----
[INFO] [stdout] error[E0425]: cannot find value `outdir` in this scope
[INFO] [stdout]    --> src/download.rs:308:45
[INFO] [stdout]     |
[INFO] [stdout] 308 | let builder = ScrubbyDownloaderBuilder::new(outdir, indices).aligner(vec![Aligner::Bowtie2]);
[INFO] [stdout]     |                                             ^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `indices` in this scope
[INFO] [stdout]    --> src/download.rs:308:53
[INFO] [stdout]     |
[INFO] [stdout] 308 | let builder = ScrubbyDownloaderBuilder::new(outdir, indices).aligner(vec![Aligner::Bowtie2]);
[INFO] [stdout]     |                                                     ^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `ScrubbyDownloaderBuilder` in this scope
[INFO] [stdout]    --> src/download.rs:308:15
[INFO] [stdout]     |
[INFO] [stdout] 308 | let builder = ScrubbyDownloaderBuilder::new(outdir, indices).aligner(vec![Aligner::Bowtie2]);
[INFO] [stdout]     |               ^^^^^^^^^^^^^^^^^^^^^^^^ use of undeclared type `ScrubbyDownloaderBuilder`
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `Aligner` in this scope
[INFO] [stdout]    --> src/download.rs:308:75
[INFO] [stdout]     |
[INFO] [stdout] 308 | let builder = ScrubbyDownloaderBuilder::new(outdir, indices).aligner(vec![Aligner::Bowtie2]);
[INFO] [stdout]     |                                                                           ^^^^^^^ use of undeclared type `Aligner`
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 4 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0425, E0433.
[INFO] [stdout] For more information about an error, try `rustc --explain E0425`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/download.rs - download::ScrubbyDownloaderBuilder::new (line 282) stdout ----
[INFO] [stdout] error[E0433]: cannot find type `PathBuf` in this scope
[INFO] [stdout]    --> src/download.rs:283:14
[INFO] [stdout]     |
[INFO] [stdout] 283 | let outdir = PathBuf::from("/path/to/output");
[INFO] [stdout]     |              ^^^^^^^ use of undeclared type `PathBuf`
[INFO] [stdout]     |
[INFO] [stdout] help: consider importing this struct
[INFO] [stdout]     |
[INFO] [stdout] 282 + use std::path::PathBuf;
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `ScrubbyIndex` in this scope
[INFO] [stdout]    --> src/download.rs:284:20
[INFO] [stdout]     |
[INFO] [stdout] 284 | let indices = vec![ScrubbyIndex::Chm13v2];
[INFO] [stdout]     |                    ^^^^^^^^^^^^ use of undeclared type `ScrubbyIndex`
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `ScrubbyDownloaderBuilder` in this scope
[INFO] [stdout]    --> src/download.rs:285:15
[INFO] [stdout]     |
[INFO] [stdout] 285 | let builder = ScrubbyDownloaderBuilder::new(outdir, indices);
[INFO] [stdout]     |               ^^^^^^^^^^^^^^^^^^^^^^^^ use of undeclared type `ScrubbyDownloaderBuilder`
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 3 previous errors
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0433`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/download.rs - download::ScrubbyDownloaderBuilder::timeout (line 337) stdout ----
[INFO] [stdout] error[E0425]: cannot find value `outdir` in this scope
[INFO] [stdout]    --> src/download.rs:338:45
[INFO] [stdout]     |
[INFO] [stdout] 338 | let builder = ScrubbyDownloaderBuilder::new(outdir, indices).timeout(60);
[INFO] [stdout]     |                                             ^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `indices` in this scope
[INFO] [stdout]    --> src/download.rs:338:53
[INFO] [stdout]     |
[INFO] [stdout] 338 | let builder = ScrubbyDownloaderBuilder::new(outdir, indices).timeout(60);
[INFO] [stdout]     |                                                     ^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `ScrubbyDownloaderBuilder` in this scope
[INFO] [stdout]    --> src/download.rs:338:15
[INFO] [stdout]     |
[INFO] [stdout] 338 | let builder = ScrubbyDownloaderBuilder::new(outdir, indices).timeout(60);
[INFO] [stdout]     |               ^^^^^^^^^^^^^^^^^^^^^^^^ use of undeclared type `ScrubbyDownloaderBuilder`
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 3 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0425, E0433.
[INFO] [stdout] For more information about an error, try `rustc --explain E0425`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/download.rs - download::ScrubbyDownloaderBuilder::classifier (line 322) stdout ----
[INFO] [stdout] error[E0425]: cannot find value `outdir` in this scope
[INFO] [stdout]    --> src/download.rs:323:45
[INFO] [stdout]     |
[INFO] [stdout] 323 | let builder = ScrubbyDownloaderBuilder::new(outdir, indices).classifier(vec![Classifier::new()]);
[INFO] [stdout]     |                                             ^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `indices` in this scope
[INFO] [stdout]    --> src/download.rs:323:53
[INFO] [stdout]     |
[INFO] [stdout] 323 | let builder = ScrubbyDownloaderBuilder::new(outdir, indices).classifier(vec![Classifier::new()]);
[INFO] [stdout]     |                                                     ^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `ScrubbyDownloaderBuilder` in this scope
[INFO] [stdout]    --> src/download.rs:323:15
[INFO] [stdout]     |
[INFO] [stdout] 323 | let builder = ScrubbyDownloaderBuilder::new(outdir, indices).classifier(vec![Classifier::new()]);
[INFO] [stdout]     |               ^^^^^^^^^^^^^^^^^^^^^^^^ use of undeclared type `ScrubbyDownloaderBuilder`
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `Classifier` in this scope
[INFO] [stdout]    --> src/download.rs:323:78
[INFO] [stdout]     |
[INFO] [stdout] 323 | let builder = ScrubbyDownloaderBuilder::new(outdir, indices).classifier(vec![Classifier::new()]);
[INFO] [stdout]     |                                                                              ^^^^^^^^^^ use of undeclared type `Classifier`
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 4 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0425, E0433.
[INFO] [stdout] For more information about an error, try `rustc --explain E0425`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/download.rs - download::ScrubbyDownloaderBuilder::password (line 382) stdout ----
[INFO] [stdout] error[E0425]: cannot find value `outdir` in this scope
[INFO] [stdout]    --> src/download.rs:383:45
[INFO] [stdout]     |
[INFO] [stdout] 383 | let builder = ScrubbyDownloaderBuilder::new(outdir, indices).password("pass");
[INFO] [stdout]     |                                             ^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `indices` in this scope
[INFO] [stdout]    --> src/download.rs:383:53
[INFO] [stdout]     |
[INFO] [stdout] 383 | let builder = ScrubbyDownloaderBuilder::new(outdir, indices).password("pass");
[INFO] [stdout]     |                                                     ^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `ScrubbyDownloaderBuilder` in this scope
[INFO] [stdout]    --> src/download.rs:383:15
[INFO] [stdout]     |
[INFO] [stdout] 383 | let builder = ScrubbyDownloaderBuilder::new(outdir, indices).password("pass");
[INFO] [stdout]     |               ^^^^^^^^^^^^^^^^^^^^^^^^ use of undeclared type `ScrubbyDownloaderBuilder`
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 3 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0425, E0433.
[INFO] [stdout] For more information about an error, try `rustc --explain E0425`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/download.rs - download::ScrubbyDownloaderBuilder::base_url (line 352) stdout ----
[INFO] [stdout] error[E0425]: cannot find value `outdir` in this scope
[INFO] [stdout]    --> src/download.rs:353:45
[INFO] [stdout]     |
[INFO] [stdout] 353 | let builder = ScrubbyDownloaderBuilder::new(outdir, indices).base_url("https://example.com");
[INFO] [stdout]     |                                             ^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `indices` in this scope
[INFO] [stdout]    --> src/download.rs:353:53
[INFO] [stdout]     |
[INFO] [stdout] 353 | let builder = ScrubbyDownloaderBuilder::new(outdir, indices).base_url("https://example.com");
[INFO] [stdout]     |                                                     ^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `ScrubbyDownloaderBuilder` in this scope
[INFO] [stdout]    --> src/download.rs:353:15
[INFO] [stdout]     |
[INFO] [stdout] 353 | let builder = ScrubbyDownloaderBuilder::new(outdir, indices).base_url("https://example.com");
[INFO] [stdout]     |               ^^^^^^^^^^^^^^^^^^^^^^^^ use of undeclared type `ScrubbyDownloaderBuilder`
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 3 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0425, E0433.
[INFO] [stdout] For more information about an error, try `rustc --explain E0425`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/download.rs - download::ScrubbyDownloader::builder (line 118) stdout ----
[INFO] [stdout] error[E0433]: cannot find type `PathBuf` in this scope
[INFO] [stdout]    --> src/download.rs:119:14
[INFO] [stdout]     |
[INFO] [stdout] 119 | let outdir = PathBuf::from("/path/to/output");
[INFO] [stdout]     |              ^^^^^^^ use of undeclared type `PathBuf`
[INFO] [stdout]     |
[INFO] [stdout] help: consider importing this struct
[INFO] [stdout]     |
[INFO] [stdout] 118 + use std::path::PathBuf;
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `ScrubbyIndex` in this scope
[INFO] [stdout]    --> src/download.rs:120:20
[INFO] [stdout]     |
[INFO] [stdout] 120 | let indices = vec![ScrubbyIndex::Chm13v2];
[INFO] [stdout]     |                    ^^^^^^^^^^^^ use of undeclared type `ScrubbyIndex`
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `ScrubbyDownloader` in this scope
[INFO] [stdout]    --> src/download.rs:121:15
[INFO] [stdout]     |
[INFO] [stdout] 121 | let builder = ScrubbyDownloader::builder(outdir, indices);
[INFO] [stdout]     |               ^^^^^^^^^^^^^^^^^ use of undeclared type `ScrubbyDownloader`
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 3 previous errors
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0433`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/scrubby.rs - scrubby::Scrubby::new (line 193) stdout ----
[INFO] [stdout] error: unexpected closing delimiter: `)`
[INFO] [stdout]    --> src/scrubby.rs:203:2
[INFO] [stdout]     |
[INFO] [stdout] 194 | use scrubby::{Scrubby, Aligner, Classifier};
[INFO] [stdout]     |              - this opening brace...      - ...matches this closing brace
[INFO] [stdout] ...
[INFO] [stdout] 203 | )).unwrap();
[INFO] [stdout]     |  ^ unexpected closing delimiter
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 1 previous error
[INFO] [stdout] 
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/scrubby.rs - scrubby::Scrubby::clean (line 249) stdout ----
[INFO] [stdout] error: unexpected token: `...`
[INFO] [stdout]    --> src/scrubby.rs:253:28
[INFO] [stdout]     |
[INFO] [stdout] 253 | let scrubby = Scrubby::new(...).unwrap();
[INFO] [stdout]     |                            ^^^
[INFO] [stdout]     |
[INFO] [stdout] help: use `..` for an exclusive range
[INFO] [stdout]     |
[INFO] [stdout] 253 - let scrubby = Scrubby::new(...).unwrap();
[INFO] [stdout] 253 + let scrubby = Scrubby::new(..).unwrap();
[INFO] [stdout]     |
[INFO] [stdout] help: or `..=` for an inclusive range
[INFO] [stdout]     |
[INFO] [stdout] 253 - let scrubby = Scrubby::new(...).unwrap();
[INFO] [stdout] 253 + let scrubby = Scrubby::new(..=).unwrap();
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0586]: inclusive range with no end
[INFO] [stdout]    --> src/scrubby.rs:253:28
[INFO] [stdout]     |
[INFO] [stdout] 253 | let scrubby = Scrubby::new(...).unwrap();
[INFO] [stdout]     |                            ^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`)
[INFO] [stdout] help: use `..` instead
[INFO] [stdout]     |
[INFO] [stdout] 253 - let scrubby = Scrubby::new(...).unwrap();
[INFO] [stdout] 253 + let scrubby = Scrubby::new(..).unwrap();
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0432]: unresolved import `scrubby::Scrubby`
[INFO] [stdout]    --> src/scrubby.rs:251:5
[INFO] [stdout]     |
[INFO] [stdout] 251 | use scrubby::Scrubby;
[INFO] [stdout]     |     ^^^^^^^^^^^^^^^^ no `Scrubby` in the root
[INFO] [stdout]     |
[INFO] [stdout] help: a similar name exists in the module (notice the capitalization)
[INFO] [stdout]     |
[INFO] [stdout] 251 - use scrubby::Scrubby;
[INFO] [stdout] 251 + use scrubby::scrubby;
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 3 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0432, E0586.
[INFO] [stdout] For more information about an error, try `rustc --explain E0432`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/scrubby.rs - scrubby::Scrubby::builder (line 228) stdout ----
[INFO] [stdout] error[E0432]: unresolved import `scrubby::Scrubby`
[INFO] [stdout]    --> src/scrubby.rs:230:5
[INFO] [stdout]     |
[INFO] [stdout] 230 | use scrubby::Scrubby;
[INFO] [stdout]     |     ^^^^^^^^^^^^^^^^ no `Scrubby` in the root
[INFO] [stdout]     |
[INFO] [stdout] help: a similar name exists in the module (notice the capitalization)
[INFO] [stdout]     |
[INFO] [stdout] 230 - use scrubby::Scrubby;
[INFO] [stdout] 230 + use scrubby::scrubby;
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 1 previous error
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0432`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/download.rs - download::ScrubbyIndex::fmt (line 63) stdout ----
[INFO] [stdout] error[E0433]: cannot find type `ScrubbyIndex` in this scope
[INFO] [stdout]   --> src/download.rs:64:13
[INFO] [stdout]    |
[INFO] [stdout] 64 | let index = ScrubbyIndex::Chm13v2;
[INFO] [stdout]    |             ^^^^^^^^^^^^ use of undeclared type `ScrubbyIndex`
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 1 previous error
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0433`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/download.rs - download::ScrubbyDownloaderBuilder::username (line 367) stdout ----
[INFO] [stdout] error[E0425]: cannot find value `outdir` in this scope
[INFO] [stdout]    --> src/download.rs:368:45
[INFO] [stdout]     |
[INFO] [stdout] 368 | let builder = ScrubbyDownloaderBuilder::new(outdir, indices).username("user");
[INFO] [stdout]     |                                             ^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `indices` in this scope
[INFO] [stdout]    --> src/download.rs:368:53
[INFO] [stdout]     |
[INFO] [stdout] 368 | let builder = ScrubbyDownloaderBuilder::new(outdir, indices).username("user");
[INFO] [stdout]     |                                                     ^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `ScrubbyDownloaderBuilder` in this scope
[INFO] [stdout]    --> src/download.rs:368:15
[INFO] [stdout]     |
[INFO] [stdout] 368 | let builder = ScrubbyDownloaderBuilder::new(outdir, indices).username("user");
[INFO] [stdout]     |               ^^^^^^^^^^^^^^^^^^^^^^^^ use of undeclared type `ScrubbyDownloaderBuilder`
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 3 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0425, E0433.
[INFO] [stdout] For more information about an error, try `rustc --explain E0425`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::aligner_args (line 705) stdout ----
[INFO] [stdout] error: unexpected token: `...`
[INFO] [stdout]    --> src/scrubby.rs:709:35
[INFO] [stdout]     |
[INFO] [stdout] 709 | let builder = ScrubbyBuilder::new(...).aligner_args("aligner_args".to_string());
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout] help: use `..` for an exclusive range
[INFO] [stdout]     |
[INFO] [stdout] 709 - let builder = ScrubbyBuilder::new(...).aligner_args("aligner_args".to_string());
[INFO] [stdout] 709 + let builder = ScrubbyBuilder::new(..).aligner_args("aligner_args".to_string());
[INFO] [stdout]     |
[INFO] [stdout] help: or `..=` for an inclusive range
[INFO] [stdout]     |
[INFO] [stdout] 709 - let builder = ScrubbyBuilder::new(...).aligner_args("aligner_args".to_string());
[INFO] [stdout] 709 + let builder = ScrubbyBuilder::new(..=).aligner_args("aligner_args".to_string());
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0586]: inclusive range with no end
[INFO] [stdout]    --> src/scrubby.rs:709:35
[INFO] [stdout]     |
[INFO] [stdout] 709 | let builder = ScrubbyBuilder::new(...).aligner_args("aligner_args".to_string());
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`)
[INFO] [stdout] help: use `..` instead
[INFO] [stdout]     |
[INFO] [stdout] 709 - let builder = ScrubbyBuilder::new(...).aligner_args("aligner_args".to_string());
[INFO] [stdout] 709 + let builder = ScrubbyBuilder::new(..).aligner_args("aligner_args".to_string());
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder`
[INFO] [stdout]    --> src/scrubby.rs:707:5
[INFO] [stdout]     |
[INFO] [stdout] 707 | use scrubby::ScrubbyBuilder;
[INFO] [stdout]     |     ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 3 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0432, E0586.
[INFO] [stdout] For more information about an error, try `rustc --explain E0432`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/download.rs - download::ScrubbyIndex::aligner_name (line 28) stdout ----
[INFO] [stdout] error[E0433]: cannot find type `ScrubbyIndex` in this scope
[INFO] [stdout]   --> src/download.rs:29:13
[INFO] [stdout]    |
[INFO] [stdout] 29 | let index = ScrubbyIndex::Chm13v2;
[INFO] [stdout]    |             ^^^^^^^^^^^^ use of undeclared type `ScrubbyIndex`
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `Aligner` in this scope
[INFO] [stdout]   --> src/download.rs:30:15
[INFO] [stdout]    |
[INFO] [stdout] 30 | let aligner = Aligner::new();
[INFO] [stdout]    |               ^^^^^^^ use of undeclared type `Aligner`
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 2 previous errors
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0433`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::alignment (line 513) stdout ----
[INFO] [stdout] error: unexpected token: `...`
[INFO] [stdout]    --> src/scrubby.rs:518:35
[INFO] [stdout]     |
[INFO] [stdout] 518 | let builder = ScrubbyBuilder::new(...).alignment(PathBuf::from("alignment.paf"));
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout] help: use `..` for an exclusive range
[INFO] [stdout]     |
[INFO] [stdout] 518 - let builder = ScrubbyBuilder::new(...).alignment(PathBuf::from("alignment.paf"));
[INFO] [stdout] 518 + let builder = ScrubbyBuilder::new(..).alignment(PathBuf::from("alignment.paf"));
[INFO] [stdout]     |
[INFO] [stdout] help: or `..=` for an inclusive range
[INFO] [stdout]     |
[INFO] [stdout] 518 - let builder = ScrubbyBuilder::new(...).alignment(PathBuf::from("alignment.paf"));
[INFO] [stdout] 518 + let builder = ScrubbyBuilder::new(..=).alignment(PathBuf::from("alignment.paf"));
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0586]: inclusive range with no end
[INFO] [stdout]    --> src/scrubby.rs:518:35
[INFO] [stdout]     |
[INFO] [stdout] 518 | let builder = ScrubbyBuilder::new(...).alignment(PathBuf::from("alignment.paf"));
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`)
[INFO] [stdout] help: use `..` instead
[INFO] [stdout]     |
[INFO] [stdout] 518 - let builder = ScrubbyBuilder::new(...).alignment(PathBuf::from("alignment.paf"));
[INFO] [stdout] 518 + let builder = ScrubbyBuilder::new(..).alignment(PathBuf::from("alignment.paf"));
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder`
[INFO] [stdout]    --> src/scrubby.rs:515:5
[INFO] [stdout]     |
[INFO] [stdout] 515 | use scrubby::ScrubbyBuilder;
[INFO] [stdout]     |     ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 3 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0432, E0586.
[INFO] [stdout] For more information about an error, try `rustc --explain E0432`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::aligner_index (line 638) stdout ----
[INFO] [stdout] error: unexpected token: `...`
[INFO] [stdout]    --> src/scrubby.rs:643:35
[INFO] [stdout]     |
[INFO] [stdout] 643 | let builder = ScrubbyBuilder::new(...).aligner_index(PathBuf::from("aligner_index"));
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout] help: use `..` for an exclusive range
[INFO] [stdout]     |
[INFO] [stdout] 643 - let builder = ScrubbyBuilder::new(...).aligner_index(PathBuf::from("aligner_index"));
[INFO] [stdout] 643 + let builder = ScrubbyBuilder::new(..).aligner_index(PathBuf::from("aligner_index"));
[INFO] [stdout]     |
[INFO] [stdout] help: or `..=` for an inclusive range
[INFO] [stdout]     |
[INFO] [stdout] 643 - let builder = ScrubbyBuilder::new(...).aligner_index(PathBuf::from("aligner_index"));
[INFO] [stdout] 643 + let builder = ScrubbyBuilder::new(..=).aligner_index(PathBuf::from("aligner_index"));
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0586]: inclusive range with no end
[INFO] [stdout]    --> src/scrubby.rs:643:35
[INFO] [stdout]     |
[INFO] [stdout] 643 | let builder = ScrubbyBuilder::new(...).aligner_index(PathBuf::from("aligner_index"));
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`)
[INFO] [stdout] help: use `..` instead
[INFO] [stdout]     |
[INFO] [stdout] 643 - let builder = ScrubbyBuilder::new(...).aligner_index(PathBuf::from("aligner_index"));
[INFO] [stdout] 643 + let builder = ScrubbyBuilder::new(..).aligner_index(PathBuf::from("aligner_index"));
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder`
[INFO] [stdout]    --> src/scrubby.rs:640:5
[INFO] [stdout]     |
[INFO] [stdout] 640 | use scrubby::ScrubbyBuilder;
[INFO] [stdout]     |     ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 3 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0432, E0586.
[INFO] [stdout] For more information about an error, try `rustc --explain E0432`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/download.rs - download::ScrubbyIndex::classifier_name (line 44) stdout ----
[INFO] [stdout] error[E0433]: cannot find type `ScrubbyIndex` in this scope
[INFO] [stdout]   --> src/download.rs:45:13
[INFO] [stdout]    |
[INFO] [stdout] 45 | let index = ScrubbyIndex::Chm13v2;
[INFO] [stdout]    |             ^^^^^^^^^^^^ use of undeclared type `ScrubbyIndex`
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `Classifier` in this scope
[INFO] [stdout]   --> src/download.rs:46:18
[INFO] [stdout]    |
[INFO] [stdout] 46 | let classifier = Classifier::new();
[INFO] [stdout]    |                  ^^^^^^^^^^ use of undeclared type `Classifier`
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 2 previous errors
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0433`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::aligner (line 500) stdout ----
[INFO] [stdout] error: unexpected token: `...`
[INFO] [stdout]    --> src/scrubby.rs:504:35
[INFO] [stdout]     |
[INFO] [stdout] 504 | let builder = ScrubbyBuilder::new(...).aligner(Aligner::Minimap2);
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout] help: use `..` for an exclusive range
[INFO] [stdout]     |
[INFO] [stdout] 504 - let builder = ScrubbyBuilder::new(...).aligner(Aligner::Minimap2);
[INFO] [stdout] 504 + let builder = ScrubbyBuilder::new(..).aligner(Aligner::Minimap2);
[INFO] [stdout]     |
[INFO] [stdout] help: or `..=` for an inclusive range
[INFO] [stdout]     |
[INFO] [stdout] 504 - let builder = ScrubbyBuilder::new(...).aligner(Aligner::Minimap2);
[INFO] [stdout] 504 + let builder = ScrubbyBuilder::new(..=).aligner(Aligner::Minimap2);
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0586]: inclusive range with no end
[INFO] [stdout]    --> src/scrubby.rs:504:35
[INFO] [stdout]     |
[INFO] [stdout] 504 | let builder = ScrubbyBuilder::new(...).aligner(Aligner::Minimap2);
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`)
[INFO] [stdout] help: use `..` instead
[INFO] [stdout]     |
[INFO] [stdout] 504 - let builder = ScrubbyBuilder::new(...).aligner(Aligner::Minimap2);
[INFO] [stdout] 504 + let builder = ScrubbyBuilder::new(..).aligner(Aligner::Minimap2);
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0432]: unresolved imports `scrubby::ScrubbyBuilder`, `scrubby::Aligner`
[INFO] [stdout]    --> src/scrubby.rs:502:15
[INFO] [stdout]     |
[INFO] [stdout] 502 | use scrubby::{ScrubbyBuilder, Aligner};
[INFO] [stdout]     |               ^^^^^^^^^^^^^^  ^^^^^^^ no `Aligner` in the root
[INFO] [stdout]     |               |
[INFO] [stdout]     |               no `ScrubbyBuilder` in the root
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 3 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0432, E0586.
[INFO] [stdout] For more information about an error, try `rustc --explain E0432`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::build_alignment (line 1008) stdout ----
[INFO] [stdout] error: unexpected token: `...`
[INFO] [stdout]     --> src/scrubby.rs:1012:35
[INFO] [stdout]      |
[INFO] [stdout] 1012 | let scrubby = ScrubbyBuilder::new(...).build_alignment().unwrap();
[INFO] [stdout]      |                                   ^^^
[INFO] [stdout]      |
[INFO] [stdout] help: use `..` for an exclusive range
[INFO] [stdout]      |
[INFO] [stdout] 1012 - let scrubby = ScrubbyBuilder::new(...).build_alignment().unwrap();
[INFO] [stdout] 1012 + let scrubby = ScrubbyBuilder::new(..).build_alignment().unwrap();
[INFO] [stdout]      |
[INFO] [stdout] help: or `..=` for an inclusive range
[INFO] [stdout]      |
[INFO] [stdout] 1012 - let scrubby = ScrubbyBuilder::new(...).build_alignment().unwrap();
[INFO] [stdout] 1012 + let scrubby = ScrubbyBuilder::new(..=).build_alignment().unwrap();
[INFO] [stdout]      |
[INFO] [stdout] 
[INFO] [stdout] error[E0586]: inclusive range with no end
[INFO] [stdout]     --> src/scrubby.rs:1012:35
[INFO] [stdout]      |
[INFO] [stdout] 1012 | let scrubby = ScrubbyBuilder::new(...).build_alignment().unwrap();
[INFO] [stdout]      |                                   ^^^
[INFO] [stdout]      |
[INFO] [stdout]      = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`)
[INFO] [stdout] help: use `..` instead
[INFO] [stdout]      |
[INFO] [stdout] 1012 - let scrubby = ScrubbyBuilder::new(...).build_alignment().unwrap();
[INFO] [stdout] 1012 + let scrubby = ScrubbyBuilder::new(..).build_alignment().unwrap();
[INFO] [stdout]      |
[INFO] [stdout] 
[INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder`
[INFO] [stdout]     --> src/scrubby.rs:1010:5
[INFO] [stdout]      |
[INFO] [stdout] 1010 | use scrubby::ScrubbyBuilder;
[INFO] [stdout]      |     ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 3 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0432, E0586.
[INFO] [stdout] For more information about an error, try `rustc --explain E0432`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::build (line 802) stdout ----
[INFO] [stdout] error: unexpected token: `...`
[INFO] [stdout]    --> src/scrubby.rs:806:35
[INFO] [stdout]     |
[INFO] [stdout] 806 | let scrubby = ScrubbyBuilder::new(...).build().unwrap();
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout] help: use `..` for an exclusive range
[INFO] [stdout]     |
[INFO] [stdout] 806 - let scrubby = ScrubbyBuilder::new(...).build().unwrap();
[INFO] [stdout] 806 + let scrubby = ScrubbyBuilder::new(..).build().unwrap();
[INFO] [stdout]     |
[INFO] [stdout] help: or `..=` for an inclusive range
[INFO] [stdout]     |
[INFO] [stdout] 806 - let scrubby = ScrubbyBuilder::new(...).build().unwrap();
[INFO] [stdout] 806 + let scrubby = ScrubbyBuilder::new(..=).build().unwrap();
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0586]: inclusive range with no end
[INFO] [stdout]    --> src/scrubby.rs:806:35
[INFO] [stdout]     |
[INFO] [stdout] 806 | let scrubby = ScrubbyBuilder::new(...).build().unwrap();
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`)
[INFO] [stdout] help: use `..` instead
[INFO] [stdout]     |
[INFO] [stdout] 806 - let scrubby = ScrubbyBuilder::new(...).build().unwrap();
[INFO] [stdout] 806 + let scrubby = ScrubbyBuilder::new(..).build().unwrap();
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder`
[INFO] [stdout]    --> src/scrubby.rs:804:5
[INFO] [stdout]     |
[INFO] [stdout] 804 | use scrubby::ScrubbyBuilder;
[INFO] [stdout]     |     ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 3 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0432, E0586.
[INFO] [stdout] For more information about an error, try `rustc --explain E0432`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::alignment_format (line 527) stdout ----
[INFO] [stdout] error: unexpected token: `...`
[INFO] [stdout]    --> src/scrubby.rs:532:35
[INFO] [stdout]     |
[INFO] [stdout] 532 | let builder = ScrubbyBuilder::new(...).alignment_format(AlignmentFormat::Bam);
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout] help: use `..` for an exclusive range
[INFO] [stdout]     |
[INFO] [stdout] 532 - let builder = ScrubbyBuilder::new(...).alignment_format(AlignmentFormat::Bam);
[INFO] [stdout] 532 + let builder = ScrubbyBuilder::new(..).alignment_format(AlignmentFormat::Bam);
[INFO] [stdout]     |
[INFO] [stdout] help: or `..=` for an inclusive range
[INFO] [stdout]     |
[INFO] [stdout] 532 - let builder = ScrubbyBuilder::new(...).alignment_format(AlignmentFormat::Bam);
[INFO] [stdout] 532 + let builder = ScrubbyBuilder::new(..=).alignment_format(AlignmentFormat::Bam);
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0586]: inclusive range with no end
[INFO] [stdout]    --> src/scrubby.rs:532:35
[INFO] [stdout]     |
[INFO] [stdout] 532 | let builder = ScrubbyBuilder::new(...).alignment_format(AlignmentFormat::Bam);
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`)
[INFO] [stdout] help: use `..` instead
[INFO] [stdout]     |
[INFO] [stdout] 532 - let builder = ScrubbyBuilder::new(...).alignment_format(AlignmentFormat::Bam);
[INFO] [stdout] 532 + let builder = ScrubbyBuilder::new(..).alignment_format(AlignmentFormat::Bam);
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0432]: unresolved imports `scrubby::ScrubbyBuilder`, `scrubby::AlignmentFormat`
[INFO] [stdout]    --> src/scrubby.rs:529:15
[INFO] [stdout]     |
[INFO] [stdout] 529 | use scrubby::{ScrubbyBuilder, AlignmentFormat};
[INFO] [stdout]     |               ^^^^^^^^^^^^^^  ^^^^^^^^^^^^^^^ no `AlignmentFormat` in the root
[INFO] [stdout]     |               |
[INFO] [stdout]     |               no `ScrubbyBuilder` in the root
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 3 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0432, E0586.
[INFO] [stdout] For more information about an error, try `rustc --explain E0432`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::classifier (line 583) stdout ----
[INFO] [stdout] error: unexpected token: `...`
[INFO] [stdout]    --> src/scrubby.rs:587:35
[INFO] [stdout]     |
[INFO] [stdout] 587 | let builder = ScrubbyBuilder::new(...).classifier(Classifier::Kraken2);
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout] help: use `..` for an exclusive range
[INFO] [stdout]     |
[INFO] [stdout] 587 - let builder = ScrubbyBuilder::new(...).classifier(Classifier::Kraken2);
[INFO] [stdout] 587 + let builder = ScrubbyBuilder::new(..).classifier(Classifier::Kraken2);
[INFO] [stdout]     |
[INFO] [stdout] help: or `..=` for an inclusive range
[INFO] [stdout]     |
[INFO] [stdout] 587 - let builder = ScrubbyBuilder::new(...).classifier(Classifier::Kraken2);
[INFO] [stdout] 587 + let builder = ScrubbyBuilder::new(..=).classifier(Classifier::Kraken2);
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0586]: inclusive range with no end
[INFO] [stdout]    --> src/scrubby.rs:587:35
[INFO] [stdout]     |
[INFO] [stdout] 587 | let builder = ScrubbyBuilder::new(...).classifier(Classifier::Kraken2);
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`)
[INFO] [stdout] help: use `..` instead
[INFO] [stdout]     |
[INFO] [stdout] 587 - let builder = ScrubbyBuilder::new(...).classifier(Classifier::Kraken2);
[INFO] [stdout] 587 + let builder = ScrubbyBuilder::new(..).classifier(Classifier::Kraken2);
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0432]: unresolved imports `scrubby::ScrubbyBuilder`, `scrubby::Classifier`
[INFO] [stdout]    --> src/scrubby.rs:585:15
[INFO] [stdout]     |
[INFO] [stdout] 585 | use scrubby::{ScrubbyBuilder, Classifier};
[INFO] [stdout]     |               ^^^^^^^^^^^^^^  ^^^^^^^^^^ no `Classifier` in the root
[INFO] [stdout]     |               |
[INFO] [stdout]     |               no `ScrubbyBuilder` in the root
[INFO] [stdout]     |
[INFO] [stdout] help: a similar name exists in the module (notice the capitalization)
[INFO] [stdout]     |
[INFO] [stdout] 585 - use scrubby::{ScrubbyBuilder, Classifier};
[INFO] [stdout] 585 + use scrubby::{ScrubbyBuilder, classifier};
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 3 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0432, E0586.
[INFO] [stdout] For more information about an error, try `rustc --explain E0432`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::build_classifier (line 967) stdout ----
[INFO] [stdout] error: unexpected token: `...`
[INFO] [stdout]    --> src/scrubby.rs:971:35
[INFO] [stdout]     |
[INFO] [stdout] 971 | let scrubby = ScrubbyBuilder::new(...).build_classifier().unwrap();
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout] help: use `..` for an exclusive range
[INFO] [stdout]     |
[INFO] [stdout] 971 - let scrubby = ScrubbyBuilder::new(...).build_classifier().unwrap();
[INFO] [stdout] 971 + let scrubby = ScrubbyBuilder::new(..).build_classifier().unwrap();
[INFO] [stdout]     |
[INFO] [stdout] help: or `..=` for an inclusive range
[INFO] [stdout]     |
[INFO] [stdout] 971 - let scrubby = ScrubbyBuilder::new(...).build_classifier().unwrap();
[INFO] [stdout] 971 + let scrubby = ScrubbyBuilder::new(..=).build_classifier().unwrap();
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0586]: inclusive range with no end
[INFO] [stdout]    --> src/scrubby.rs:971:35
[INFO] [stdout]     |
[INFO] [stdout] 971 | let scrubby = ScrubbyBuilder::new(...).build_classifier().unwrap();
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`)
[INFO] [stdout] help: use `..` instead
[INFO] [stdout]     |
[INFO] [stdout] 971 - let scrubby = ScrubbyBuilder::new(...).build_classifier().unwrap();
[INFO] [stdout] 971 + let scrubby = ScrubbyBuilder::new(..).build_classifier().unwrap();
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder`
[INFO] [stdout]    --> src/scrubby.rs:969:5
[INFO] [stdout]     |
[INFO] [stdout] 969 | use scrubby::ScrubbyBuilder;
[INFO] [stdout]     |     ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 3 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0432, E0586.
[INFO] [stdout] For more information about an error, try `rustc --explain E0432`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::classifier_args (line 692) stdout ----
[INFO] [stdout] error: unexpected token: `...`
[INFO] [stdout]    --> src/scrubby.rs:696:35
[INFO] [stdout]     |
[INFO] [stdout] 696 | let builder = ScrubbyBuilder::new(...).classifier_args("classifier_args".to_string());
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout] help: use `..` for an exclusive range
[INFO] [stdout]     |
[INFO] [stdout] 696 - let builder = ScrubbyBuilder::new(...).classifier_args("classifier_args".to_string());
[INFO] [stdout] 696 + let builder = ScrubbyBuilder::new(..).classifier_args("classifier_args".to_string());
[INFO] [stdout]     |
[INFO] [stdout] help: or `..=` for an inclusive range
[INFO] [stdout]     |
[INFO] [stdout] 696 - let builder = ScrubbyBuilder::new(...).classifier_args("classifier_args".to_string());
[INFO] [stdout] 696 + let builder = ScrubbyBuilder::new(..=).classifier_args("classifier_args".to_string());
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0586]: inclusive range with no end
[INFO] [stdout]    --> src/scrubby.rs:696:35
[INFO] [stdout]     |
[INFO] [stdout] 696 | let builder = ScrubbyBuilder::new(...).classifier_args("classifier_args".to_string());
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`)
[INFO] [stdout] help: use `..` instead
[INFO] [stdout]     |
[INFO] [stdout] 696 - let builder = ScrubbyBuilder::new(...).classifier_args("classifier_args".to_string());
[INFO] [stdout] 696 + let builder = ScrubbyBuilder::new(..).classifier_args("classifier_args".to_string());
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder`
[INFO] [stdout]    --> src/scrubby.rs:694:5
[INFO] [stdout]     |
[INFO] [stdout] 694 | use scrubby::ScrubbyBuilder;
[INFO] [stdout]     |     ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 3 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0432, E0586.
[INFO] [stdout] For more information about an error, try `rustc --explain E0432`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::classifier_index (line 652) stdout ----
[INFO] [stdout] error: unexpected token: `...`
[INFO] [stdout]    --> src/scrubby.rs:657:35
[INFO] [stdout]     |
[INFO] [stdout] 657 | let builder = ScrubbyBuilder::new(...).classifier_index(PathBuf::from("classifier_index"));
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout] help: use `..` for an exclusive range
[INFO] [stdout]     |
[INFO] [stdout] 657 - let builder = ScrubbyBuilder::new(...).classifier_index(PathBuf::from("classifier_index"));
[INFO] [stdout] 657 + let builder = ScrubbyBuilder::new(..).classifier_index(PathBuf::from("classifier_index"));
[INFO] [stdout]     |
[INFO] [stdout] help: or `..=` for an inclusive range
[INFO] [stdout]     |
[INFO] [stdout] 657 - let builder = ScrubbyBuilder::new(...).classifier_index(PathBuf::from("classifier_index"));
[INFO] [stdout] 657 + let builder = ScrubbyBuilder::new(..=).classifier_index(PathBuf::from("classifier_index"));
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0586]: inclusive range with no end
[INFO] [stdout]    --> src/scrubby.rs:657:35
[INFO] [stdout]     |
[INFO] [stdout] 657 | let builder = ScrubbyBuilder::new(...).classifier_index(PathBuf::from("classifier_index"));
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`)
[INFO] [stdout] help: use `..` instead
[INFO] [stdout]     |
[INFO] [stdout] 657 - let builder = ScrubbyBuilder::new(...).classifier_index(PathBuf::from("classifier_index"));
[INFO] [stdout] 657 + let builder = ScrubbyBuilder::new(..).classifier_index(PathBuf::from("classifier_index"));
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder`
[INFO] [stdout]    --> src/scrubby.rs:654:5
[INFO] [stdout]     |
[INFO] [stdout] 654 | use scrubby::ScrubbyBuilder;
[INFO] [stdout]     |     ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 3 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0432, E0586.
[INFO] [stdout] For more information about an error, try `rustc --explain E0432`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::command (line 420) stdout ----
[INFO] [stdout] error: unexpected token: `...`
[INFO] [stdout]    --> src/scrubby.rs:425:35
[INFO] [stdout]     |
[INFO] [stdout] 425 | let builder = ScrubbyBuilder::new(...).command("scrubby clean ...");
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout] help: use `..` for an exclusive range
[INFO] [stdout]     |
[INFO] [stdout] 425 - let builder = ScrubbyBuilder::new(...).command("scrubby clean ...");
[INFO] [stdout] 425 + let builder = ScrubbyBuilder::new(..).command("scrubby clean ...");
[INFO] [stdout]     |
[INFO] [stdout] help: or `..=` for an inclusive range
[INFO] [stdout]     |
[INFO] [stdout] 425 - let builder = ScrubbyBuilder::new(...).command("scrubby clean ...");
[INFO] [stdout] 425 + let builder = ScrubbyBuilder::new(..=).command("scrubby clean ...");
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0586]: inclusive range with no end
[INFO] [stdout]    --> src/scrubby.rs:425:35
[INFO] [stdout]     |
[INFO] [stdout] 425 | let builder = ScrubbyBuilder::new(...).command("scrubby clean ...");
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`)
[INFO] [stdout] help: use `..` instead
[INFO] [stdout]     |
[INFO] [stdout] 425 - let builder = ScrubbyBuilder::new(...).command("scrubby clean ...");
[INFO] [stdout] 425 + let builder = ScrubbyBuilder::new(..).command("scrubby clean ...");
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder`
[INFO] [stdout]    --> src/scrubby.rs:422:5
[INFO] [stdout]     |
[INFO] [stdout] 422 | use scrubby::ScrubbyBuilder;
[INFO] [stdout]     |     ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 3 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0432, E0586.
[INFO] [stdout] For more information about an error, try `rustc --explain E0432`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::new (line 337) stdout ----
[INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder`
[INFO] [stdout]    --> src/scrubby.rs:339:5
[INFO] [stdout]     |
[INFO] [stdout] 339 | use scrubby::ScrubbyBuilder;
[INFO] [stdout]     |     ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 1 previous error
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0432`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::keep (line 461) stdout ----
[INFO] [stdout] error: unexpected token: `...`
[INFO] [stdout]    --> src/scrubby.rs:465:35
[INFO] [stdout]     |
[INFO] [stdout] 465 | let builder = ScrubbyBuilder::new(...).keep(true);
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout] help: use `..` for an exclusive range
[INFO] [stdout]     |
[INFO] [stdout] 465 - let builder = ScrubbyBuilder::new(...).keep(true);
[INFO] [stdout] 465 + let builder = ScrubbyBuilder::new(..).keep(true);
[INFO] [stdout]     |
[INFO] [stdout] help: or `..=` for an inclusive range
[INFO] [stdout]     |
[INFO] [stdout] 465 - let builder = ScrubbyBuilder::new(...).keep(true);
[INFO] [stdout] 465 + let builder = ScrubbyBuilder::new(..=).keep(true);
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0586]: inclusive range with no end
[INFO] [stdout]    --> src/scrubby.rs:465:35
[INFO] [stdout]     |
[INFO] [stdout] 465 | let builder = ScrubbyBuilder::new(...).keep(true);
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`)
[INFO] [stdout] help: use `..` instead
[INFO] [stdout]     |
[INFO] [stdout] 465 - let builder = ScrubbyBuilder::new(...).keep(true);
[INFO] [stdout] 465 + let builder = ScrubbyBuilder::new(..).keep(true);
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder`
[INFO] [stdout]    --> src/scrubby.rs:463:5
[INFO] [stdout]     |
[INFO] [stdout] 463 | use scrubby::ScrubbyBuilder;
[INFO] [stdout]     |     ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 3 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0432, E0586.
[INFO] [stdout] For more information about an error, try `rustc --explain E0432`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::index (line 624) stdout ----
[INFO] [stdout] error: unexpected token: `...`
[INFO] [stdout]    --> src/scrubby.rs:629:35
[INFO] [stdout]     |
[INFO] [stdout] 629 | let builder = ScrubbyBuilder::new(...).index(PathBuf::from("index"));
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout] help: use `..` for an exclusive range
[INFO] [stdout]     |
[INFO] [stdout] 629 - let builder = ScrubbyBuilder::new(...).index(PathBuf::from("index"));
[INFO] [stdout] 629 + let builder = ScrubbyBuilder::new(..).index(PathBuf::from("index"));
[INFO] [stdout]     |
[INFO] [stdout] help: or `..=` for an inclusive range
[INFO] [stdout]     |
[INFO] [stdout] 629 - let builder = ScrubbyBuilder::new(...).index(PathBuf::from("index"));
[INFO] [stdout] 629 + let builder = ScrubbyBuilder::new(..=).index(PathBuf::from("index"));
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0586]: inclusive range with no end
[INFO] [stdout]    --> src/scrubby.rs:629:35
[INFO] [stdout]     |
[INFO] [stdout] 629 | let builder = ScrubbyBuilder::new(...).index(PathBuf::from("index"));
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`)
[INFO] [stdout] help: use `..` instead
[INFO] [stdout]     |
[INFO] [stdout] 629 - let builder = ScrubbyBuilder::new(...).index(PathBuf::from("index"));
[INFO] [stdout] 629 + let builder = ScrubbyBuilder::new(..).index(PathBuf::from("index"));
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder`
[INFO] [stdout]    --> src/scrubby.rs:626:5
[INFO] [stdout]     |
[INFO] [stdout] 626 | use scrubby::ScrubbyBuilder;
[INFO] [stdout]     |     ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 3 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0432, E0586.
[INFO] [stdout] For more information about an error, try `rustc --explain E0432`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::extract (line 448) stdout ----
[INFO] [stdout] error: unexpected token: `...`
[INFO] [stdout]    --> src/scrubby.rs:452:35
[INFO] [stdout]     |
[INFO] [stdout] 452 | let builder = ScrubbyBuilder::new(...).extract(true);
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout] help: use `..` for an exclusive range
[INFO] [stdout]     |
[INFO] [stdout] 452 - let builder = ScrubbyBuilder::new(...).extract(true);
[INFO] [stdout] 452 + let builder = ScrubbyBuilder::new(..).extract(true);
[INFO] [stdout]     |
[INFO] [stdout] help: or `..=` for an inclusive range
[INFO] [stdout]     |
[INFO] [stdout] 452 - let builder = ScrubbyBuilder::new(...).extract(true);
[INFO] [stdout] 452 + let builder = ScrubbyBuilder::new(..=).extract(true);
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0586]: inclusive range with no end
[INFO] [stdout]    --> src/scrubby.rs:452:35
[INFO] [stdout]     |
[INFO] [stdout] 452 | let builder = ScrubbyBuilder::new(...).extract(true);
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`)
[INFO] [stdout] help: use `..` instead
[INFO] [stdout]     |
[INFO] [stdout] 452 - let builder = ScrubbyBuilder::new(...).extract(true);
[INFO] [stdout] 452 + let builder = ScrubbyBuilder::new(..).extract(true);
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder`
[INFO] [stdout]    --> src/scrubby.rs:450:5
[INFO] [stdout]     |
[INFO] [stdout] 450 | use scrubby::ScrubbyBuilder;
[INFO] [stdout]     |     ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 3 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0432, E0586.
[INFO] [stdout] For more information about an error, try `rustc --explain E0432`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::json (line 406) stdout ----
[INFO] [stdout] error: unexpected token: `...`
[INFO] [stdout]    --> src/scrubby.rs:411:35
[INFO] [stdout]     |
[INFO] [stdout] 411 | let builder = ScrubbyBuilder::new(...).json(PathBuf::from("report.json"));
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout] help: use `..` for an exclusive range
[INFO] [stdout]     |
[INFO] [stdout] 411 - let builder = ScrubbyBuilder::new(...).json(PathBuf::from("report.json"));
[INFO] [stdout] 411 + let builder = ScrubbyBuilder::new(..).json(PathBuf::from("report.json"));
[INFO] [stdout]     |
[INFO] [stdout] help: or `..=` for an inclusive range
[INFO] [stdout]     |
[INFO] [stdout] 411 - let builder = ScrubbyBuilder::new(...).json(PathBuf::from("report.json"));
[INFO] [stdout] 411 + let builder = ScrubbyBuilder::new(..=).json(PathBuf::from("report.json"));
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0586]: inclusive range with no end
[INFO] [stdout]    --> src/scrubby.rs:411:35
[INFO] [stdout]     |
[INFO] [stdout] 411 | let builder = ScrubbyBuilder::new(...).json(PathBuf::from("report.json"));
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`)
[INFO] [stdout] help: use `..` instead
[INFO] [stdout]     |
[INFO] [stdout] 411 - let builder = ScrubbyBuilder::new(...).json(PathBuf::from("report.json"));
[INFO] [stdout] 411 + let builder = ScrubbyBuilder::new(..).json(PathBuf::from("report.json"));
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder`
[INFO] [stdout]    --> src/scrubby.rs:408:5
[INFO] [stdout]     |
[INFO] [stdout] 408 | use scrubby::ScrubbyBuilder;
[INFO] [stdout]     |     ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 3 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0432, E0586.
[INFO] [stdout] For more information about an error, try `rustc --explain E0432`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::min_query_coverage (line 555) stdout ----
[INFO] [stdout] error: unexpected token: `...`
[INFO] [stdout]    --> src/scrubby.rs:560:35
[INFO] [stdout]     |
[INFO] [stdout] 560 | let builder = ScrubbyBuilder::new(...).min_query_coverage(0.5);
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout] help: use `..` for an exclusive range
[INFO] [stdout]     |
[INFO] [stdout] 560 - let builder = ScrubbyBuilder::new(...).min_query_coverage(0.5);
[INFO] [stdout] 560 + let builder = ScrubbyBuilder::new(..).min_query_coverage(0.5);
[INFO] [stdout]     |
[INFO] [stdout] help: or `..=` for an inclusive range
[INFO] [stdout]     |
[INFO] [stdout] 560 - let builder = ScrubbyBuilder::new(...).min_query_coverage(0.5);
[INFO] [stdout] 560 + let builder = ScrubbyBuilder::new(..=).min_query_coverage(0.5);
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0586]: inclusive range with no end
[INFO] [stdout]    --> src/scrubby.rs:560:35
[INFO] [stdout]     |
[INFO] [stdout] 560 | let builder = ScrubbyBuilder::new(...).min_query_coverage(0.5);
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`)
[INFO] [stdout] help: use `..` instead
[INFO] [stdout]     |
[INFO] [stdout] 560 - let builder = ScrubbyBuilder::new(...).min_query_coverage(0.5);
[INFO] [stdout] 560 + let builder = ScrubbyBuilder::new(..).min_query_coverage(0.5);
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder`
[INFO] [stdout]    --> src/scrubby.rs:557:5
[INFO] [stdout]     |
[INFO] [stdout] 557 | use scrubby::ScrubbyBuilder;
[INFO] [stdout]     |     ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 3 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0432, E0586.
[INFO] [stdout] For more information about an error, try `rustc --explain E0432`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::min_mapq (line 569) stdout ----
[INFO] [stdout] error: unexpected token: `...`
[INFO] [stdout]    --> src/scrubby.rs:574:35
[INFO] [stdout]     |
[INFO] [stdout] 574 | let builder = ScrubbyBuilder::new(...).min_mapq(50);
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout] help: use `..` for an exclusive range
[INFO] [stdout]     |
[INFO] [stdout] 574 - let builder = ScrubbyBuilder::new(...).min_mapq(50);
[INFO] [stdout] 574 + let builder = ScrubbyBuilder::new(..).min_mapq(50);
[INFO] [stdout]     |
[INFO] [stdout] help: or `..=` for an inclusive range
[INFO] [stdout]     |
[INFO] [stdout] 574 - let builder = ScrubbyBuilder::new(...).min_mapq(50);
[INFO] [stdout] 574 + let builder = ScrubbyBuilder::new(..=).min_mapq(50);
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0586]: inclusive range with no end
[INFO] [stdout]    --> src/scrubby.rs:574:35
[INFO] [stdout]     |
[INFO] [stdout] 574 | let builder = ScrubbyBuilder::new(...).min_mapq(50);
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`)
[INFO] [stdout] help: use `..` instead
[INFO] [stdout]     |
[INFO] [stdout] 574 - let builder = ScrubbyBuilder::new(...).min_mapq(50);
[INFO] [stdout] 574 + let builder = ScrubbyBuilder::new(..).min_mapq(50);
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder`
[INFO] [stdout]    --> src/scrubby.rs:571:5
[INFO] [stdout]     |
[INFO] [stdout] 571 | use scrubby::ScrubbyBuilder;
[INFO] [stdout]     |     ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 3 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0432, E0586.
[INFO] [stdout] For more information about an error, try `rustc --explain E0432`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::preset (line 744) stdout ----
[INFO] [stdout] error: unexpected token: `...`
[INFO] [stdout]    --> src/scrubby.rs:749:35
[INFO] [stdout]     |
[INFO] [stdout] 749 | let builder = ScrubbyBuilder::new(...).preset(Preset::MapOnt);
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout] help: use `..` for an exclusive range
[INFO] [stdout]     |
[INFO] [stdout] 749 - let builder = ScrubbyBuilder::new(...).preset(Preset::MapOnt);
[INFO] [stdout] 749 + let builder = ScrubbyBuilder::new(..).preset(Preset::MapOnt);
[INFO] [stdout]     |
[INFO] [stdout] help: or `..=` for an inclusive range
[INFO] [stdout]     |
[INFO] [stdout] 749 - let builder = ScrubbyBuilder::new(...).preset(Preset::MapOnt);
[INFO] [stdout] 749 + let builder = ScrubbyBuilder::new(..=).preset(Preset::MapOnt);
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0586]: inclusive range with no end
[INFO] [stdout]    --> src/scrubby.rs:749:35
[INFO] [stdout]     |
[INFO] [stdout] 749 | let builder = ScrubbyBuilder::new(...).preset(Preset::MapOnt);
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`)
[INFO] [stdout] help: use `..` instead
[INFO] [stdout]     |
[INFO] [stdout] 749 - let builder = ScrubbyBuilder::new(...).preset(Preset::MapOnt);
[INFO] [stdout] 749 + let builder = ScrubbyBuilder::new(..).preset(Preset::MapOnt);
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder`
[INFO] [stdout]    --> src/scrubby.rs:746:5
[INFO] [stdout]     |
[INFO] [stdout] 746 | use scrubby::ScrubbyBuilder;
[INFO] [stdout]     |     ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root
[INFO] [stdout] 
[INFO] [stdout] error[E0432]: unresolved import `scrubby::Preset`
[INFO] [stdout]    --> src/scrubby.rs:747:5
[INFO] [stdout]     |
[INFO] [stdout] 747 | use scrubby::Preset;
[INFO] [stdout]     |     ^^^^^^^^^^^^^^^ no `Preset` in the root
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 4 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0432, E0586.
[INFO] [stdout] For more information about an error, try `rustc --explain E0432`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::min_query_length (line 541) stdout ----
[INFO] [stdout] error: unexpected token: `...`
[INFO] [stdout]    --> src/scrubby.rs:546:35
[INFO] [stdout]     |
[INFO] [stdout] 546 | let builder = ScrubbyBuilder::new(...).min_query_length(50);
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout] help: use `..` for an exclusive range
[INFO] [stdout]     |
[INFO] [stdout] 546 - let builder = ScrubbyBuilder::new(...).min_query_length(50);
[INFO] [stdout] 546 + let builder = ScrubbyBuilder::new(..).min_query_length(50);
[INFO] [stdout]     |
[INFO] [stdout] help: or `..=` for an inclusive range
[INFO] [stdout]     |
[INFO] [stdout] 546 - let builder = ScrubbyBuilder::new(...).min_query_length(50);
[INFO] [stdout] 546 + let builder = ScrubbyBuilder::new(..=).min_query_length(50);
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0586]: inclusive range with no end
[INFO] [stdout]    --> src/scrubby.rs:546:35
[INFO] [stdout]     |
[INFO] [stdout] 546 | let builder = ScrubbyBuilder::new(...).min_query_length(50);
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`)
[INFO] [stdout] help: use `..` instead
[INFO] [stdout]     |
[INFO] [stdout] 546 - let builder = ScrubbyBuilder::new(...).min_query_length(50);
[INFO] [stdout] 546 + let builder = ScrubbyBuilder::new(..).min_query_length(50);
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder`
[INFO] [stdout]    --> src/scrubby.rs:543:5
[INFO] [stdout]     |
[INFO] [stdout] 543 | use scrubby::ScrubbyBuilder;
[INFO] [stdout]     |     ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 3 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0432, E0586.
[INFO] [stdout] For more information about an error, try `rustc --explain E0432`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::needletail_parallel (line 731) stdout ----
[INFO] [stdout] error: unexpected token: `...`
[INFO] [stdout]    --> src/scrubby.rs:735:35
[INFO] [stdout]     |
[INFO] [stdout] 735 | let builder = ScrubbyBuilder::new(...).needletail_parallel(true);
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout] help: use `..` for an exclusive range
[INFO] [stdout]     |
[INFO] [stdout] 735 - let builder = ScrubbyBuilder::new(...).needletail_parallel(true);
[INFO] [stdout] 735 + let builder = ScrubbyBuilder::new(..).needletail_parallel(true);
[INFO] [stdout]     |
[INFO] [stdout] help: or `..=` for an inclusive range
[INFO] [stdout]     |
[INFO] [stdout] 735 - let builder = ScrubbyBuilder::new(...).needletail_parallel(true);
[INFO] [stdout] 735 + let builder = ScrubbyBuilder::new(..=).needletail_parallel(true);
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0586]: inclusive range with no end
[INFO] [stdout]    --> src/scrubby.rs:735:35
[INFO] [stdout]     |
[INFO] [stdout] 735 | let builder = ScrubbyBuilder::new(...).needletail_parallel(true);
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`)
[INFO] [stdout] help: use `..` instead
[INFO] [stdout]     |
[INFO] [stdout] 735 - let builder = ScrubbyBuilder::new(...).needletail_parallel(true);
[INFO] [stdout] 735 + let builder = ScrubbyBuilder::new(..).needletail_parallel(true);
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder`
[INFO] [stdout]    --> src/scrubby.rs:733:5
[INFO] [stdout]     |
[INFO] [stdout] 733 | use scrubby::ScrubbyBuilder;
[INFO] [stdout]     |     ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 3 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0432, E0586.
[INFO] [stdout] For more information about an error, try `rustc --explain E0432`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::read_ids (line 392) stdout ----
[INFO] [stdout] error: unexpected token: `...`
[INFO] [stdout]    --> src/scrubby.rs:397:35
[INFO] [stdout]     |
[INFO] [stdout] 397 | let builder = ScrubbyBuilder::new(...).read_ids(PathBuf::from("depleted_reads.fastq"));
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout] help: use `..` for an exclusive range
[INFO] [stdout]     |
[INFO] [stdout] 397 - let builder = ScrubbyBuilder::new(...).read_ids(PathBuf::from("depleted_reads.fastq"));
[INFO] [stdout] 397 + let builder = ScrubbyBuilder::new(..).read_ids(PathBuf::from("depleted_reads.fastq"));
[INFO] [stdout]     |
[INFO] [stdout] help: or `..=` for an inclusive range
[INFO] [stdout]     |
[INFO] [stdout] 397 - let builder = ScrubbyBuilder::new(...).read_ids(PathBuf::from("depleted_reads.fastq"));
[INFO] [stdout] 397 + let builder = ScrubbyBuilder::new(..=).read_ids(PathBuf::from("depleted_reads.fastq"));
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0586]: inclusive range with no end
[INFO] [stdout]    --> src/scrubby.rs:397:35
[INFO] [stdout]     |
[INFO] [stdout] 397 | let builder = ScrubbyBuilder::new(...).read_ids(PathBuf::from("depleted_reads.fastq"));
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`)
[INFO] [stdout] help: use `..` instead
[INFO] [stdout]     |
[INFO] [stdout] 397 - let builder = ScrubbyBuilder::new(...).read_ids(PathBuf::from("depleted_reads.fastq"));
[INFO] [stdout] 397 + let builder = ScrubbyBuilder::new(..).read_ids(PathBuf::from("depleted_reads.fastq"));
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder`
[INFO] [stdout]    --> src/scrubby.rs:394:5
[INFO] [stdout]     |
[INFO] [stdout] 394 | use scrubby::ScrubbyBuilder;
[INFO] [stdout]     |     ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 3 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0432, E0586.
[INFO] [stdout] For more information about an error, try `rustc --explain E0432`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::reads (line 596) stdout ----
[INFO] [stdout] error: unexpected token: `...`
[INFO] [stdout]    --> src/scrubby.rs:601:35
[INFO] [stdout]     |
[INFO] [stdout] 601 | let builder = ScrubbyBuilder::new(...).reads(PathBuf::from("read_classifications.tsv"));
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout] help: use `..` for an exclusive range
[INFO] [stdout]     |
[INFO] [stdout] 601 - let builder = ScrubbyBuilder::new(...).reads(PathBuf::from("read_classifications.tsv"));
[INFO] [stdout] 601 + let builder = ScrubbyBuilder::new(..).reads(PathBuf::from("read_classifications.tsv"));
[INFO] [stdout]     |
[INFO] [stdout] help: or `..=` for an inclusive range
[INFO] [stdout]     |
[INFO] [stdout] 601 - let builder = ScrubbyBuilder::new(...).reads(PathBuf::from("read_classifications.tsv"));
[INFO] [stdout] 601 + let builder = ScrubbyBuilder::new(..=).reads(PathBuf::from("read_classifications.tsv"));
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0586]: inclusive range with no end
[INFO] [stdout]    --> src/scrubby.rs:601:35
[INFO] [stdout]     |
[INFO] [stdout] 601 | let builder = ScrubbyBuilder::new(...).reads(PathBuf::from("read_classifications.tsv"));
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`)
[INFO] [stdout] help: use `..` instead
[INFO] [stdout]     |
[INFO] [stdout] 601 - let builder = ScrubbyBuilder::new(...).reads(PathBuf::from("read_classifications.tsv"));
[INFO] [stdout] 601 + let builder = ScrubbyBuilder::new(..).reads(PathBuf::from("read_classifications.tsv"));
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder`
[INFO] [stdout]    --> src/scrubby.rs:598:5
[INFO] [stdout]     |
[INFO] [stdout] 598 | use scrubby::ScrubbyBuilder;
[INFO] [stdout]     |     ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 3 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0432, E0586.
[INFO] [stdout] For more information about an error, try `rustc --explain E0432`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::report (line 610) stdout ----
[INFO] [stdout] error: unexpected token: `...`
[INFO] [stdout]    --> src/scrubby.rs:615:35
[INFO] [stdout]     |
[INFO] [stdout] 615 | let builder = ScrubbyBuilder::new(...).report(PathBuf::from("classifier_report.tsv"));
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout] help: use `..` for an exclusive range
[INFO] [stdout]     |
[INFO] [stdout] 615 - let builder = ScrubbyBuilder::new(...).report(PathBuf::from("classifier_report.tsv"));
[INFO] [stdout] 615 + let builder = ScrubbyBuilder::new(..).report(PathBuf::from("classifier_report.tsv"));
[INFO] [stdout]     |
[INFO] [stdout] help: or `..=` for an inclusive range
[INFO] [stdout]     |
[INFO] [stdout] 615 - let builder = ScrubbyBuilder::new(...).report(PathBuf::from("classifier_report.tsv"));
[INFO] [stdout] 615 + let builder = ScrubbyBuilder::new(..=).report(PathBuf::from("classifier_report.tsv"));
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0586]: inclusive range with no end
[INFO] [stdout]    --> src/scrubby.rs:615:35
[INFO] [stdout]     |
[INFO] [stdout] 615 | let builder = ScrubbyBuilder::new(...).report(PathBuf::from("classifier_report.tsv"));
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`)
[INFO] [stdout] help: use `..` instead
[INFO] [stdout]     |
[INFO] [stdout] 615 - let builder = ScrubbyBuilder::new(...).report(PathBuf::from("classifier_report.tsv"));
[INFO] [stdout] 615 + let builder = ScrubbyBuilder::new(..).report(PathBuf::from("classifier_report.tsv"));
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder`
[INFO] [stdout]    --> src/scrubby.rs:612:5
[INFO] [stdout]     |
[INFO] [stdout] 612 | use scrubby::ScrubbyBuilder;
[INFO] [stdout]     |     ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 3 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0432, E0586.
[INFO] [stdout] For more information about an error, try `rustc --explain E0432`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::samtools_threads (line 718) stdout ----
[INFO] [stderr] error: doctest failed, to rerun pass `--doc`
[INFO] [stdout] error: unexpected token: `...`
[INFO] [stdout]    --> src/scrubby.rs:722:35
[INFO] [stdout]     |
[INFO] [stdout] 722 | let builder = ScrubbyBuilder::new(...).samtools_threads(4);
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout] help: use `..` for an exclusive range
[INFO] [stdout]     |
[INFO] [stdout] 722 - let builder = ScrubbyBuilder::new(...).samtools_threads(4);
[INFO] [stdout] 722 + let builder = ScrubbyBuilder::new(..).samtools_threads(4);
[INFO] [stdout]     |
[INFO] [stdout] help: or `..=` for an inclusive range
[INFO] [stdout]     |
[INFO] [stdout] 722 - let builder = ScrubbyBuilder::new(...).samtools_threads(4);
[INFO] [stdout] 722 + let builder = ScrubbyBuilder::new(..=).samtools_threads(4);
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0586]: inclusive range with no end
[INFO] [stdout]    --> src/scrubby.rs:722:35
[INFO] [stdout]     |
[INFO] [stdout] 722 | let builder = ScrubbyBuilder::new(...).samtools_threads(4);
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`)
[INFO] [stdout] help: use `..` instead
[INFO] [stdout]     |
[INFO] [stdout] 722 - let builder = ScrubbyBuilder::new(...).samtools_threads(4);
[INFO] [stdout] 722 + let builder = ScrubbyBuilder::new(..).samtools_threads(4);
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder`
[INFO] [stdout]    --> src/scrubby.rs:720:5
[INFO] [stdout]     |
[INFO] [stdout] 720 | use scrubby::ScrubbyBuilder;
[INFO] [stdout]     |     ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 3 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0432, E0586.
[INFO] [stdout] For more information about an error, try `rustc --explain E0432`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::taxa (line 666) stdout ----
[INFO] [stdout] error: unexpected token: `...`
[INFO] [stdout]    --> src/scrubby.rs:670:35
[INFO] [stdout]     |
[INFO] [stdout] 670 | let builder = ScrubbyBuilder::new(...).taxa(vec!["taxon1", "taxon2"]);
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout] help: use `..` for an exclusive range
[INFO] [stdout]     |
[INFO] [stdout] 670 - let builder = ScrubbyBuilder::new(...).taxa(vec!["taxon1", "taxon2"]);
[INFO] [stdout] 670 + let builder = ScrubbyBuilder::new(..).taxa(vec!["taxon1", "taxon2"]);
[INFO] [stdout]     |
[INFO] [stdout] help: or `..=` for an inclusive range
[INFO] [stdout]     |
[INFO] [stdout] 670 - let builder = ScrubbyBuilder::new(...).taxa(vec!["taxon1", "taxon2"]);
[INFO] [stdout] 670 + let builder = ScrubbyBuilder::new(..=).taxa(vec!["taxon1", "taxon2"]);
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0586]: inclusive range with no end
[INFO] [stdout]    --> src/scrubby.rs:670:35
[INFO] [stdout]     |
[INFO] [stdout] 670 | let builder = ScrubbyBuilder::new(...).taxa(vec!["taxon1", "taxon2"]);
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`)
[INFO] [stdout] help: use `..` instead
[INFO] [stdout]     |
[INFO] [stdout] 670 - let builder = ScrubbyBuilder::new(...).taxa(vec!["taxon1", "taxon2"]);
[INFO] [stdout] 670 + let builder = ScrubbyBuilder::new(..).taxa(vec!["taxon1", "taxon2"]);
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder`
[INFO] [stdout]    --> src/scrubby.rs:668:5
[INFO] [stdout]     |
[INFO] [stdout] 668 | use scrubby::ScrubbyBuilder;
[INFO] [stdout]     |     ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 3 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0432, E0586.
[INFO] [stdout] For more information about an error, try `rustc --explain E0432`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::workdir (line 434) stdout ----
[INFO] [stdout] error: unexpected token: `...`
[INFO] [stdout]    --> src/scrubby.rs:439:35
[INFO] [stdout]     |
[INFO] [stdout] 439 | let builder = ScrubbyBuilder::new(...).workdir(PathBuf::from("workdir"));
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout] help: use `..` for an exclusive range
[INFO] [stdout]     |
[INFO] [stdout] 439 - let builder = ScrubbyBuilder::new(...).workdir(PathBuf::from("workdir"));
[INFO] [stdout] 439 + let builder = ScrubbyBuilder::new(..).workdir(PathBuf::from("workdir"));
[INFO] [stdout]     |
[INFO] [stdout] help: or `..=` for an inclusive range
[INFO] [stdout]     |
[INFO] [stdout] 439 - let builder = ScrubbyBuilder::new(...).workdir(PathBuf::from("workdir"));
[INFO] [stdout] 439 + let builder = ScrubbyBuilder::new(..=).workdir(PathBuf::from("workdir"));
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0586]: inclusive range with no end
[INFO] [stdout]    --> src/scrubby.rs:439:35
[INFO] [stdout]     |
[INFO] [stdout] 439 | let builder = ScrubbyBuilder::new(...).workdir(PathBuf::from("workdir"));
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`)
[INFO] [stdout] help: use `..` instead
[INFO] [stdout]     |
[INFO] [stdout] 439 - let builder = ScrubbyBuilder::new(...).workdir(PathBuf::from("workdir"));
[INFO] [stdout] 439 + let builder = ScrubbyBuilder::new(..).workdir(PathBuf::from("workdir"));
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder`
[INFO] [stdout]    --> src/scrubby.rs:436:5
[INFO] [stdout]     |
[INFO] [stdout] 436 | use scrubby::ScrubbyBuilder;
[INFO] [stdout]     |     ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 3 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0432, E0586.
[INFO] [stdout] For more information about an error, try `rustc --explain E0432`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/terminal.rs - terminal::AlignmentArgs::validate_and_build (line 406) stdout ----
[INFO] [stdout] error[E0433]: cannot find type `AlignmentArgs` in this scope
[INFO] [stdout]    --> src/terminal.rs:410:16
[INFO] [stdout]     |
[INFO] [stdout] 410 | let aln_args = AlignmentArgs::parse();
[INFO] [stdout]     |                ^^^^^^^^^^^^^ use of undeclared type `AlignmentArgs`
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 1 previous error
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0433`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::threads (line 487) stdout ----
[INFO] [stdout] error: unexpected token: `...`
[INFO] [stdout]    --> src/scrubby.rs:491:35
[INFO] [stdout]     |
[INFO] [stdout] 491 | let builder = ScrubbyBuilder::new(...).threads(8);
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout] help: use `..` for an exclusive range
[INFO] [stdout]     |
[INFO] [stdout] 491 - let builder = ScrubbyBuilder::new(...).threads(8);
[INFO] [stdout] 491 + let builder = ScrubbyBuilder::new(..).threads(8);
[INFO] [stdout]     |
[INFO] [stdout] help: or `..=` for an inclusive range
[INFO] [stdout]     |
[INFO] [stdout] 491 - let builder = ScrubbyBuilder::new(...).threads(8);
[INFO] [stdout] 491 + let builder = ScrubbyBuilder::new(..=).threads(8);
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0586]: inclusive range with no end
[INFO] [stdout]    --> src/scrubby.rs:491:35
[INFO] [stdout]     |
[INFO] [stdout] 491 | let builder = ScrubbyBuilder::new(...).threads(8);
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`)
[INFO] [stdout] help: use `..` instead
[INFO] [stdout]     |
[INFO] [stdout] 491 - let builder = ScrubbyBuilder::new(...).threads(8);
[INFO] [stdout] 491 + let builder = ScrubbyBuilder::new(..).threads(8);
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder`
[INFO] [stdout]    --> src/scrubby.rs:489:5
[INFO] [stdout]     |
[INFO] [stdout] 489 | use scrubby::ScrubbyBuilder;
[INFO] [stdout]     |     ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 3 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0432, E0586.
[INFO] [stdout] For more information about an error, try `rustc --explain E0432`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::taxa_direct (line 679) stdout ----
[INFO] [stdout] error: unexpected token: `...`
[INFO] [stdout]    --> src/scrubby.rs:683:35
[INFO] [stdout]     |
[INFO] [stdout] 683 | let builder = ScrubbyBuilder::new(...).taxa_direct(vec!["taxon_direct1", "taxon_direct2"]);
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout] help: use `..` for an exclusive range
[INFO] [stdout]     |
[INFO] [stdout] 683 - let builder = ScrubbyBuilder::new(...).taxa_direct(vec!["taxon_direct1", "taxon_direct2"]);
[INFO] [stdout] 683 + let builder = ScrubbyBuilder::new(..).taxa_direct(vec!["taxon_direct1", "taxon_direct2"]);
[INFO] [stdout]     |
[INFO] [stdout] help: or `..=` for an inclusive range
[INFO] [stdout]     |
[INFO] [stdout] 683 - let builder = ScrubbyBuilder::new(...).taxa_direct(vec!["taxon_direct1", "taxon_direct2"]);
[INFO] [stdout] 683 + let builder = ScrubbyBuilder::new(..=).taxa_direct(vec!["taxon_direct1", "taxon_direct2"]);
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0586]: inclusive range with no end
[INFO] [stdout]    --> src/scrubby.rs:683:35
[INFO] [stdout]     |
[INFO] [stdout] 683 | let builder = ScrubbyBuilder::new(...).taxa_direct(vec!["taxon_direct1", "taxon_direct2"]);
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`)
[INFO] [stdout] help: use `..` instead
[INFO] [stdout]     |
[INFO] [stdout] 683 - let builder = ScrubbyBuilder::new(...).taxa_direct(vec!["taxon_direct1", "taxon_direct2"]);
[INFO] [stdout] 683 + let builder = ScrubbyBuilder::new(..).taxa_direct(vec!["taxon_direct1", "taxon_direct2"]);
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder`
[INFO] [stdout]    --> src/scrubby.rs:681:5
[INFO] [stdout]     |
[INFO] [stdout] 681 | use scrubby::ScrubbyBuilder;
[INFO] [stdout]     |     ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 3 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0432, E0586.
[INFO] [stdout] For more information about an error, try `rustc --explain E0432`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/utils.rs - utils::get_fastx_writer (line 53) stdout ----
[INFO] [stdout] error[E0425]: cannot find value `output_path` in this scope
[INFO] [stdout]   --> src/utils.rs:54:57
[INFO] [stdout]    |
[INFO] [stdout] 54 | let (reader, writer) = get_niffler_fastx_reader_writer(&output_path, niffler::compression::Level::Six, None).unwrap();
[INFO] [stdout]    |                                                         ^^^^^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find function `get_niffler_fastx_reader_writer` in this scope
[INFO] [stdout]   --> src/utils.rs:54:24
[INFO] [stdout]    |
[INFO] [stdout] 54 | let (reader, writer) = get_niffler_fastx_reader_writer(&output_path, niffler::compression::Level::Six, None).unwrap();
[INFO] [stdout]    |                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 2 previous errors
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0425`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::unpaired (line 474) stdout ----
[INFO] [stdout] error: unexpected token: `...`
[INFO] [stdout]    --> src/scrubby.rs:478:35
[INFO] [stdout]     |
[INFO] [stdout] 478 | let builder = ScrubbyBuilder::new(...).unpaired(true);
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout] help: use `..` for an exclusive range
[INFO] [stdout]     |
[INFO] [stdout] 478 - let builder = ScrubbyBuilder::new(...).unpaired(true);
[INFO] [stdout] 478 + let builder = ScrubbyBuilder::new(..).unpaired(true);
[INFO] [stdout]     |
[INFO] [stdout] help: or `..=` for an inclusive range
[INFO] [stdout]     |
[INFO] [stdout] 478 - let builder = ScrubbyBuilder::new(...).unpaired(true);
[INFO] [stdout] 478 + let builder = ScrubbyBuilder::new(..=).unpaired(true);
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0586]: inclusive range with no end
[INFO] [stdout]    --> src/scrubby.rs:478:35
[INFO] [stdout]     |
[INFO] [stdout] 478 | let builder = ScrubbyBuilder::new(...).unpaired(true);
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`)
[INFO] [stdout] help: use `..` instead
[INFO] [stdout]     |
[INFO] [stdout] 478 - let builder = ScrubbyBuilder::new(...).unpaired(true);
[INFO] [stdout] 478 + let builder = ScrubbyBuilder::new(..).unpaired(true);
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder`
[INFO] [stdout]    --> src/scrubby.rs:476:5
[INFO] [stdout]     |
[INFO] [stdout] 476 | use scrubby::ScrubbyBuilder;
[INFO] [stdout]     |     ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 3 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0432, E0586.
[INFO] [stdout] For more information about an error, try `rustc --explain E0432`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/terminal.rs - terminal::DownloadArgs::validate_and_build (line 475) stdout ----
[INFO] [stdout] error[E0433]: cannot find type `Download` in this scope
[INFO] [stdout]    --> src/terminal.rs:478:15
[INFO] [stdout]     |
[INFO] [stdout] 478 | let dl_args = Download::parse();
[INFO] [stdout]     |               ^^^^^^^^ use of undeclared type `Download`
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 1 previous error
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0433`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/terminal.rs - terminal::ClassifierArgs::validate_and_build (line 294) stdout ----
[INFO] [stdout] error[E0433]: cannot find type `ClassifierArgs` in this scope
[INFO] [stdout]    --> src/terminal.rs:298:18
[INFO] [stdout]     |
[INFO] [stdout] 298 | let class_args = ClassifierArgs::parse();
[INFO] [stdout]     |                  ^^^^^^^^^^^^^^ use of undeclared type `ClassifierArgs`
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 1 previous error
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0433`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/terminal.rs - terminal::DiffArgs::validate_and_build (line 540) stdout ----
[INFO] [stdout] error[E0433]: cannot find type `DifferenceArgs` in this scope
[INFO] [stdout]    --> src/terminal.rs:543:17
[INFO] [stdout]     |
[INFO] [stdout] 543 | let diff_args = DifferenceArgs::parse();
[INFO] [stdout]     |                 ^^^^^^^^^^^^^^ use of undeclared type `DifferenceArgs`
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 1 previous error
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0433`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/utils.rs - utils::ReadDifferenceBuilder::read_ids (line 309) stdout ----
[INFO] [stdout] error: unexpected token: `...`
[INFO] [stdout]    --> src/utils.rs:314:42
[INFO] [stdout]     |
[INFO] [stdout] 314 | let builder = ReadDifferenceBuilder::new(...).read_ids(PathBuf::from("depleted_reads.fastq"));
[INFO] [stdout]     |                                          ^^^
[INFO] [stdout]     |
[INFO] [stdout] help: use `..` for an exclusive range
[INFO] [stdout]     |
[INFO] [stdout] 314 - let builder = ReadDifferenceBuilder::new(...).read_ids(PathBuf::from("depleted_reads.fastq"));
[INFO] [stdout] 314 + let builder = ReadDifferenceBuilder::new(..).read_ids(PathBuf::from("depleted_reads.fastq"));
[INFO] [stdout]     |
[INFO] [stdout] help: or `..=` for an inclusive range
[INFO] [stdout]     |
[INFO] [stdout] 314 - let builder = ReadDifferenceBuilder::new(...).read_ids(PathBuf::from("depleted_reads.fastq"));
[INFO] [stdout] 314 + let builder = ReadDifferenceBuilder::new(..=).read_ids(PathBuf::from("depleted_reads.fastq"));
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0586]: inclusive range with no end
[INFO] [stdout]    --> src/utils.rs:314:42
[INFO] [stdout]     |
[INFO] [stdout] 314 | let builder = ReadDifferenceBuilder::new(...).read_ids(PathBuf::from("depleted_reads.fastq"));
[INFO] [stdout]     |                                          ^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`)
[INFO] [stdout] help: use `..` instead
[INFO] [stdout]     |
[INFO] [stdout] 314 - let builder = ReadDifferenceBuilder::new(...).read_ids(PathBuf::from("depleted_reads.fastq"));
[INFO] [stdout] 314 + let builder = ReadDifferenceBuilder::new(..).read_ids(PathBuf::from("depleted_reads.fastq"));
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0432]: unresolved import `scrubby::ReadDifferenceBuilder`
[INFO] [stdout]    --> src/utils.rs:311:5
[INFO] [stdout]     |
[INFO] [stdout] 311 | use scrubby::ReadDifferenceBuilder;
[INFO] [stdout]     |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ no `ReadDifferenceBuilder` in the root
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 3 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0432, E0586.
[INFO] [stdout] For more information about an error, try `rustc --explain E0432`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/terminal.rs - terminal::ReadsArgs::validate_and_build (line 172) stdout ----
[INFO] [stdout] error[E0433]: cannot find type `ReadsArgs` in this scope
[INFO] [stdout]    --> src/terminal.rs:176:18
[INFO] [stdout]     |
[INFO] [stdout] 176 | let reads_Args = ReadsArgs::parse();
[INFO] [stdout]     |                  ^^^^^^^^^ use of undeclared type `ReadsArgs`
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 1 previous error
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0433`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/utils.rs - utils::ReadDifferenceBuilder::json (line 323) stdout ----
[INFO] [stdout] error: unexpected token: `...`
[INFO] [stdout]    --> src/utils.rs:328:42
[INFO] [stdout]     |
[INFO] [stdout] 328 | let builder = ReadDifferenceBuilder::new(...).json(PathBuf::from("report.json"));
[INFO] [stdout]     |                                          ^^^
[INFO] [stdout]     |
[INFO] [stdout] help: use `..` for an exclusive range
[INFO] [stdout]     |
[INFO] [stdout] 328 - let builder = ReadDifferenceBuilder::new(...).json(PathBuf::from("report.json"));
[INFO] [stdout] 328 + let builder = ReadDifferenceBuilder::new(..).json(PathBuf::from("report.json"));
[INFO] [stdout]     |
[INFO] [stdout] help: or `..=` for an inclusive range
[INFO] [stdout]     |
[INFO] [stdout] 328 - let builder = ReadDifferenceBuilder::new(...).json(PathBuf::from("report.json"));
[INFO] [stdout] 328 + let builder = ReadDifferenceBuilder::new(..=).json(PathBuf::from("report.json"));
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0586]: inclusive range with no end
[INFO] [stdout]    --> src/utils.rs:328:42
[INFO] [stdout]     |
[INFO] [stdout] 328 | let builder = ReadDifferenceBuilder::new(...).json(PathBuf::from("report.json"));
[INFO] [stdout]     |                                          ^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`)
[INFO] [stdout] help: use `..` instead
[INFO] [stdout]     |
[INFO] [stdout] 328 - let builder = ReadDifferenceBuilder::new(...).json(PathBuf::from("report.json"));
[INFO] [stdout] 328 + let builder = ReadDifferenceBuilder::new(..).json(PathBuf::from("report.json"));
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] error[E0432]: unresolved import `scrubby::ReadDifferenceBuilder`
[INFO] [stdout]    --> src/utils.rs:325:5
[INFO] [stdout]     |
[INFO] [stdout] 325 | use scrubby::ReadDifferenceBuilder;
[INFO] [stdout]     |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ no `ReadDifferenceBuilder` in the root
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 3 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0432, E0586.
[INFO] [stdout] For more information about an error, try `rustc --explain E0432`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/utils.rs - utils::get_id (line 88) stdout ----
[INFO] [stdout] error[E0425]: cannot find function `get_id` in this scope
[INFO] [stdout]   --> src/utils.rs:89:10
[INFO] [stdout]    |
[INFO] [stdout] 89 | let id = get_id(b"@read1 description").unwrap();
[INFO] [stdout]    |          ^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 1 previous error
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0425`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/utils.rs - utils::niffler::compression::Format::from_path (line 24) stdout ----
[INFO] [stdout] error[E0432]: unresolved import `scrubby::CompressionExt`
[INFO] [stdout]   --> src/utils.rs:26:5
[INFO] [stdout]    |
[INFO] [stdout] 26 | use scrubby::CompressionExt;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^ no `CompressionExt` in the root
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no variant or associated item named `from_path` found for enum `niffler::Format` in the current scope
[INFO] [stdout]   --> src/utils.rs:27:44
[INFO] [stdout]    |
[INFO] [stdout] 27 | let format = niffler::compression::Format::from_path("file.gz");
[INFO] [stdout]    |                                            ^^^^^^^^^ variant or associated item not found in `niffler::Format`
[INFO] [stdout]    |
[INFO] [stdout]    = help: items from traits can only be used if the trait is in scope
[INFO] [stdout] help: trait `CompressionExt` which provides `from_path` is implemented but not in scope; perhaps you want to import it
[INFO] [stdout]    |
[INFO] [stdout] 23 + use crate::scrubby::utils::CompressionExt;
[INFO] [stdout]    |
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 2 previous errors
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0432, E0599.
[INFO] [stdout] For more information about an error, try `rustc --explain E0432`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] 
[INFO] [stdout] failures:
[INFO] [stdout]     src/classifier.rs - classifier::KrakenReadRecord::from_str (line 398)
[INFO] [stdout]     src/classifier.rs - classifier::KrakenReportRecord::from_str (line 446)
[INFO] [stdout]     src/classifier.rs - classifier::MetabuliReadRecord::from_str (line 494)
[INFO] [stdout]     src/classifier.rs - classifier::TaxonCounts::new (line 68)
[INFO] [stdout]     src/classifier.rs - classifier::TaxonCounts::update (line 88)
[INFO] [stdout]     src/classifier.rs - classifier::get_tax_level (line 342)
[INFO] [stdout]     src/classifier.rs - classifier::get_taxid_reads_kraken (line 267)
[INFO] [stdout]     src/classifier.rs - classifier::get_taxid_reads_metabuli (line 305)
[INFO] [stdout]     src/classifier.rs - classifier::get_taxids_from_report (line 121)
[INFO] [stdout]     src/cleaner.rs - cleaner::Cleaner::clean_reads (line 230)
[INFO] [stdout]     src/cleaner.rs - cleaner::Cleaner::from_scrubby (line 102)
[INFO] [stdout]     src/cleaner.rs - cleaner::Cleaner::run_aligner (line 129)
[INFO] [stdout]     src/cleaner.rs - cleaner::Cleaner::run_aligner_output (line 201)
[INFO] [stdout]     src/cleaner.rs - cleaner::Cleaner::run_classifier (line 153)
[INFO] [stdout]     src/cleaner.rs - cleaner::Cleaner::run_classifier_output (line 172)
[INFO] [stdout]     src/cleaner.rs - cleaner::FastqCleaner::clean_reads (line 727)
[INFO] [stdout]     src/cleaner.rs - cleaner::FastqCleaner::from (line 706)
[INFO] [stdout]     src/cleaner.rs - cleaner::SamtoolsConfig::from_scrubby (line 43)
[INFO] [stdout]     src/cleaner.rs - cleaner::SamtoolsConfig::get_pipeline (line 75)
[INFO] [stdout]     src/download.rs - download::ScrubbyDownloader::builder (line 118)
[INFO] [stdout]     src/download.rs - download::ScrubbyDownloader::download (line 237)
[INFO] [stdout]     src/download.rs - download::ScrubbyDownloader::download_index (line 160)
[INFO] [stdout]     src/download.rs - download::ScrubbyDownloader::list (line 130)
[INFO] [stdout]     src/download.rs - download::ScrubbyDownloader::new (line 101)
[INFO] [stdout]     src/download.rs - download::ScrubbyDownloader::unpack (line 206)
[INFO] [stdout]     src/download.rs - download::ScrubbyDownloaderBuilder::aligner (line 307)
[INFO] [stdout]     src/download.rs - download::ScrubbyDownloaderBuilder::base_url (line 352)
[INFO] [stdout]     src/download.rs - download::ScrubbyDownloaderBuilder::build (line 397)
[INFO] [stdout]     src/download.rs - download::ScrubbyDownloaderBuilder::classifier (line 322)
[INFO] [stdout]     src/download.rs - download::ScrubbyDownloaderBuilder::new (line 282)
[INFO] [stdout]     src/download.rs - download::ScrubbyDownloaderBuilder::password (line 382)
[INFO] [stdout]     src/download.rs - download::ScrubbyDownloaderBuilder::timeout (line 337)
[INFO] [stdout]     src/download.rs - download::ScrubbyDownloaderBuilder::username (line 367)
[INFO] [stdout]     src/download.rs - download::ScrubbyIndex::aligner_name (line 28)
[INFO] [stdout]     src/download.rs - download::ScrubbyIndex::classifier_name (line 44)
[INFO] [stdout]     src/download.rs - download::ScrubbyIndex::fmt (line 63)
[INFO] [stdout]     src/scrubby.rs - scrubby::Scrubby::builder (line 228)
[INFO] [stdout]     src/scrubby.rs - scrubby::Scrubby::clean (line 249)
[INFO] [stdout]     src/scrubby.rs - scrubby::Scrubby::new (line 193)
[INFO] [stdout]     src/scrubby.rs - scrubby::ScrubbyBuilder::aligner (line 500)
[INFO] [stdout]     src/scrubby.rs - scrubby::ScrubbyBuilder::aligner_args (line 705)
[INFO] [stdout]     src/scrubby.rs - scrubby::ScrubbyBuilder::aligner_index (line 638)
[INFO] [stdout]     src/scrubby.rs - scrubby::ScrubbyBuilder::alignment (line 513)
[INFO] [stdout]     src/scrubby.rs - scrubby::ScrubbyBuilder::alignment_format (line 527)
[INFO] [stdout]     src/scrubby.rs - scrubby::ScrubbyBuilder::build (line 802)
[INFO] [stdout]     src/scrubby.rs - scrubby::ScrubbyBuilder::build_alignment (line 1008)
[INFO] [stdout]     src/scrubby.rs - scrubby::ScrubbyBuilder::build_classifier (line 967)
[INFO] [stdout]     src/scrubby.rs - scrubby::ScrubbyBuilder::classifier (line 583)
[INFO] [stdout]     src/scrubby.rs - scrubby::ScrubbyBuilder::classifier_args (line 692)
[INFO] [stdout]     src/scrubby.rs - scrubby::ScrubbyBuilder::classifier_index (line 652)
[INFO] [stdout]     src/scrubby.rs - scrubby::ScrubbyBuilder::command (line 420)
[INFO] [stdout]     src/scrubby.rs - scrubby::ScrubbyBuilder::extract (line 448)
[INFO] [stdout]     src/scrubby.rs - scrubby::ScrubbyBuilder::index (line 624)
[INFO] [stdout]     src/scrubby.rs - scrubby::ScrubbyBuilder::json (line 406)
[INFO] [stdout]     src/scrubby.rs - scrubby::ScrubbyBuilder::keep (line 461)
[INFO] [stdout]     src/scrubby.rs - scrubby::ScrubbyBuilder::min_mapq (line 569)
[INFO] [stdout]     src/scrubby.rs - scrubby::ScrubbyBuilder::min_query_coverage (line 555)
[INFO] [stdout]     src/scrubby.rs - scrubby::ScrubbyBuilder::min_query_length (line 541)
[INFO] [stdout]     src/scrubby.rs - scrubby::ScrubbyBuilder::needletail_parallel (line 731)
[INFO] [stdout]     src/scrubby.rs - scrubby::ScrubbyBuilder::new (line 337)
[INFO] [stdout]     src/scrubby.rs - scrubby::ScrubbyBuilder::preset (line 744)
[INFO] [stdout]     src/scrubby.rs - scrubby::ScrubbyBuilder::read_ids (line 392)
[INFO] [stdout]     src/scrubby.rs - scrubby::ScrubbyBuilder::reads (line 596)
[INFO] [stdout]     src/scrubby.rs - scrubby::ScrubbyBuilder::report (line 610)
[INFO] [stdout]     src/scrubby.rs - scrubby::ScrubbyBuilder::samtools_threads (line 718)
[INFO] [stdout]     src/scrubby.rs - scrubby::ScrubbyBuilder::taxa (line 666)
[INFO] [stdout]     src/scrubby.rs - scrubby::ScrubbyBuilder::taxa_direct (line 679)
[INFO] [stdout]     src/scrubby.rs - scrubby::ScrubbyBuilder::threads (line 487)
[INFO] [stdout]     src/scrubby.rs - scrubby::ScrubbyBuilder::unpaired (line 474)
[INFO] [stdout]     src/scrubby.rs - scrubby::ScrubbyBuilder::workdir (line 434)
[INFO] [stdout]     src/terminal.rs - terminal::AlignmentArgs::validate_and_build (line 406)
[INFO] [stdout]     src/terminal.rs - terminal::ClassifierArgs::validate_and_build (line 294)
[INFO] [stdout]     src/terminal.rs - terminal::DiffArgs::validate_and_build (line 540)
[INFO] [stdout]     src/terminal.rs - terminal::DownloadArgs::validate_and_build (line 475)
[INFO] [stdout]     src/terminal.rs - terminal::ReadsArgs::validate_and_build (line 172)
[INFO] [stdout]     src/utils.rs - utils::ReadDifferenceBuilder::json (line 323)
[INFO] [stdout]     src/utils.rs - utils::ReadDifferenceBuilder::read_ids (line 309)
[INFO] [stdout]     src/utils.rs - utils::get_fastx_writer (line 53)
[INFO] [stdout]     src/utils.rs - utils::get_id (line 88)
[INFO] [stdout]     src/utils.rs - utils::niffler::compression::Format::from_path (line 24)
[INFO] [stdout] 
[INFO] [stdout] test result: FAILED. 0 passed; 80 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.61s
[INFO] [stdout] 
[INFO] running `Command { std: "docker" "inspect" "7a4020379f8d6b051095055db7e993ee6ff3d94df86c82bd026edccccaebe5a1", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "7a4020379f8d6b051095055db7e993ee6ff3d94df86c82bd026edccccaebe5a1", kill_on_drop: false }`
[INFO] [stdout] 7a4020379f8d6b051095055db7e993ee6ff3d94df86c82bd026edccccaebe5a1
