[INFO] fetching crate bio-jtools 0.2.0...
[INFO] checking bio-jtools-0.2.0 against master#e6e4f7ed1589e03bc2f6c5931c1a72e7947e8682 for beta-170-4
[INFO] extracting crate bio-jtools 0.2.0 into /workspace/builds/worker-0-tc2/source
[INFO] validating manifest of crates.io crate bio-jtools 0.2.0 on toolchain e6e4f7ed1589e03bc2f6c5931c1a72e7947e8682
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+e6e4f7ed1589e03bc2f6c5931c1a72e7947e8682" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] started tweaking crates.io crate bio-jtools 0.2.0
[INFO] finished tweaking crates.io crate bio-jtools 0.2.0
[INFO] tweaked toml for crates.io crate bio-jtools 0.2.0 written to /workspace/builds/worker-0-tc2/source/Cargo.toml
[INFO] crate crates.io crate bio-jtools 0.2.0 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" "+e6e4f7ed1589e03bc2f6c5931c1a72e7947e8682" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc2/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:19e73879b68f455e41552ea35293514db52ea292d993f571636dbffedb77a1ee" "/opt/rustwide/cargo-home/bin/cargo" "+e6e4f7ed1589e03bc2f6c5931c1a72e7947e8682" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] a9404044280be58954990404ca46eed13d66555b0c0aa34c020407132fa7fc6e
[INFO] running `Command { std: "docker" "start" "-a" "a9404044280be58954990404ca46eed13d66555b0c0aa34c020407132fa7fc6e", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "a9404044280be58954990404ca46eed13d66555b0c0aa34c020407132fa7fc6e", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "a9404044280be58954990404ca46eed13d66555b0c0aa34c020407132fa7fc6e", kill_on_drop: false }`
[INFO] [stdout] a9404044280be58954990404ca46eed13d66555b0c0aa34c020407132fa7fc6e
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc2/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "RUSTDOCFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:19e73879b68f455e41552ea35293514db52ea292d993f571636dbffedb77a1ee" "/opt/rustwide/cargo-home/bin/cargo" "+e6e4f7ed1589e03bc2f6c5931c1a72e7947e8682" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] d4466ac53bc3bae40fd52e4e5e263f48311abc1b40da7c8e87a54c5b0e3c5412
[INFO] running `Command { std: "docker" "start" "-a" "d4466ac53bc3bae40fd52e4e5e263f48311abc1b40da7c8e87a54c5b0e3c5412", kill_on_drop: false }`
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[INFO] [stdout] warning: function `filter` is never used
[INFO] [stdout]   --> src/align/filter.rs:50:8
[INFO] [stdout]    |
[INFO] [stdout] 50 | pub fn filter<T: RecordReader, S: RecordWriter>(
[INFO] [stdout]    |        ^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(dead_code)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: fields `genome_depth` and `genome_support` are never read
[INFO] [stdout]    --> src/align/info_stats.rs:130:5
[INFO] [stdout]     |
[INFO] [stdout] 110 | pub struct SamBamCramStats {
[INFO] [stdout]     |            --------------- fields in this struct
[INFO] [stdout] ...
[INFO] [stdout] 130 |     genome_depth: (),
[INFO] [stdout]     |     ^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 133 |     genome_support: (),
[INFO] [stdout]     |     ^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `SamBamCramStats` has a derived impl for the trait `Debug`, but this is intentionally ignored during dead code analysis
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variant `Cram` is never constructed
[INFO] [stdout]  --> src/align/reader.rs:9:5
[INFO] [stdout]   |
[INFO] [stdout] 6 | pub enum SamBamCramReader<R1: BufRead, R2: Read> {
[INFO] [stdout]   |          ---------------- variant in this enum
[INFO] [stdout] ...
[INFO] [stdout] 9 |     Cram,
[INFO] [stdout]   |     ^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: constant `RESERVED_DIRNAMES` is never used
[INFO] [stdout]   --> src/data/mod.rs:18:7
[INFO] [stdout]    |
[INFO] [stdout] 18 | const RESERVED_DIRNAMES: [&'static str; 7] = [
[INFO] [stdout]    |       ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: constant `RESERVED_FILENAMES` is never used
[INFO] [stdout]   --> src/data/mod.rs:21:7
[INFO] [stdout]    |
[INFO] [stdout] 21 | const RESERVED_FILENAMES: [&'static str; 5] = [
[INFO] [stdout]    |       ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: multiple fields are never read
[INFO] [stdout]   --> src/data/mod.rs:31:5
[INFO] [stdout]    |
[INFO] [stdout] 30 | struct SeqDir {
[INFO] [stdout]    |        ------ fields in this struct
[INFO] [stdout] 31 |     path: PathBuf,
[INFO] [stdout]    |     ^^^^
[INFO] [stdout] 32 |     date: Date,
[INFO] [stdout]    |     ^^^^
[INFO] [stdout] 33 |     instrument: String,
[INFO] [stdout]    |     ^^^^^^^^^^
[INFO] [stdout] 34 |     run: u16,
[INFO] [stdout]    |     ^^^
[INFO] [stdout] 35 |     position: char,
[INFO] [stdout]    |     ^^^^^^^^
[INFO] [stdout] 36 |     flowcell: String,
[INFO] [stdout]    |     ^^^^^^^^
[INFO] [stdout] 37 |     description: String,
[INFO] [stdout]    |     ^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `SeqDir` has a derived impl for the trait `Debug`, but this is intentionally ignored during dead code analysis
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: multiple associated items are never used
[INFO] [stdout]    --> src/data/mod.rs:42:12
[INFO] [stdout]     |
[INFO] [stdout] 40  | impl SeqDir {
[INFO] [stdout]     | ----------- associated items in this implementation
[INFO] [stdout] 41  |     /// Construct a new SeqDir object from a path
[INFO] [stdout] 42  |     pub fn new(path: &Path) -> SeqDir {
[INFO] [stdout]     |            ^^^
[INFO] [stdout] ...
[INFO] [stdout] 104 |     pub fn path(&self) -> &Path {
[INFO] [stdout]     |            ^^^^
[INFO] [stdout] ...
[INFO] [stdout] 109 |     pub fn date(&self) -> Date {
[INFO] [stdout]     |            ^^^^
[INFO] [stdout] ...
[INFO] [stdout] 114 |     pub fn instrument(&self) -> &str {
[INFO] [stdout]     |            ^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 119 |     pub fn run(&self) -> u16 {
[INFO] [stdout]     |            ^^^
[INFO] [stdout] ...
[INFO] [stdout] 124 |     pub fn position(&self) -> char {
[INFO] [stdout]     |            ^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 129 |     pub fn flowcell(&self) -> &str {
[INFO] [stdout]     |            ^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 134 |     pub fn description(&self) -> &str {
[INFO] [stdout]     |            ^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 139 |     pub fn create_reserved_files(&self, verbose: bool, dryrun: bool) {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 158 |     pub fn create_reserved_dirs(&self, verbose: bool, dryrun: bool) {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 177 |     pub fn relocate_hts_files(&self, verbose: bool, dryrun: bool) {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `create_reserved_file` is never used
[INFO] [stdout]    --> src/data/mod.rs:248:4
[INFO] [stdout]     |
[INFO] [stdout] 248 | fn create_reserved_file(seq: &SeqDir, file: &str) {
[INFO] [stdout]     |    ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `create_reserved_dir` is never used
[INFO] [stdout]    --> src/data/mod.rs:258:4
[INFO] [stdout]     |
[INFO] [stdout] 258 | fn create_reserved_dir(p: PathBuf) {
[INFO] [stdout]     |    ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `create_readme` is never used
[INFO] [stdout]    --> src/data/mod.rs:263:4
[INFO] [stdout]     |
[INFO] [stdout] 263 | fn create_readme(seq: &SeqDir) {
[INFO] [stdout]     |    ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `create_cluster_yaml` is never used
[INFO] [stdout]    --> src/data/mod.rs:284:4
[INFO] [stdout]     |
[INFO] [stdout] 284 | fn create_cluster_yaml(seq: &SeqDir) {
[INFO] [stdout]     |    ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `create_snakefile` is never used
[INFO] [stdout]    --> src/data/mod.rs:302:4
[INFO] [stdout]     |
[INFO] [stdout] 302 | fn create_snakefile(seq: &SeqDir) {
[INFO] [stdout]     |    ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `update_sample` is never used
[INFO] [stdout]    --> src/data/mod.rs:407:4
[INFO] [stdout]     |
[INFO] [stdout] 407 | fn update_sample(s: &mut SeqSample, mate: String, lane: String) {
[INFO] [stdout]     |    ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `create_config` is never used
[INFO] [stdout]    --> src/data/mod.rs:416:4
[INFO] [stdout]     |
[INFO] [stdout] 416 | fn create_config(sd: &SeqDir, dryrun: bool) {
[INFO] [stdout]     |    ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `mv_to_dir` is never used
[INFO] [stdout]    --> src/data/mod.rs:505:4
[INFO] [stdout]     |
[INFO] [stdout] 505 | fn mv_to_dir(file: &Path, dir: &Path) {
[INFO] [stdout]     |    ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `organize` is never used
[INFO] [stdout]    --> src/data/mod.rs:510:8
[INFO] [stdout]     |
[INFO] [stdout] 510 | pub fn organize(indir: &Path, dryrun: bool, verbose: bool) {
[INFO] [stdout]     |        ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: multiple fields are never read
[INFO] [stdout]   --> src/record/header.rs:45:5
[INFO] [stdout]    |
[INFO] [stdout] 43 | pub(crate) struct CasavaV1_8Name {
[INFO] [stdout]    |                   -------------- fields in this struct
[INFO] [stdout] 44 |     /// Instrument name
[INFO] [stdout] 45 |     instrument: Option<String>,
[INFO] [stdout]    |     ^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 48 |     lane: Option<u8>,
[INFO] [stdout]    |     ^^^^
[INFO] [stdout] ...
[INFO] [stdout] 51 |     tile: Option<u8>,
[INFO] [stdout]    |     ^^^^
[INFO] [stdout] ...
[INFO] [stdout] 54 |     x: Option<u8>,
[INFO] [stdout]    |     ^
[INFO] [stdout] ...
[INFO] [stdout] 57 |     y: Option<u8>,
[INFO] [stdout]    |     ^
[INFO] [stdout] ...
[INFO] [stdout] 61 |     sample_index: Option<u8>,
[INFO] [stdout]    |     ^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 64 |     pair_member: Option<u8>,
[INFO] [stdout]    |     ^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `CasavaV1_8Name` has a derived impl for the trait `Debug`, but this is intentionally ignored during dead code analysis
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: fields `id`, `description`, and `length` are never read
[INFO] [stdout]   --> src/record/header.rs:71:5
[INFO] [stdout]    |
[INFO] [stdout] 69 | pub(crate) struct SraName<'id> {
[INFO] [stdout]    |                   ------- fields in this struct
[INFO] [stdout] 70 |     /// Clobbered record ID
[INFO] [stdout] 71 |     id: Cow<'id, [u8]>,
[INFO] [stdout]    |     ^^
[INFO] [stdout] ...
[INFO] [stdout] 74 |     description: Cow<'id, [u8]>,
[INFO] [stdout]    |     ^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 77 |     length: Cow<'id, [u8]>,
[INFO] [stdout]    |     ^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `SraName` has a derived impl for the trait `Debug`, but this is intentionally ignored during dead code analysis
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: 18 warnings emitted
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Checking guppy v0.15.2
[INFO] [stderr]     Checking nextest-filtering v0.3.0
[INFO] [stderr]     Checking hyper-rustls v0.23.2
[INFO] [stderr]     Checking reqwest v0.11.14
[INFO] [stderr]     Checking cargo-nextest v0.9.49
[INFO] [stdout] warning: function `filter` is never used
[INFO] [stdout]   --> src/align/filter.rs:50:8
[INFO] [stdout]    |
[INFO] [stdout] 50 | pub fn filter<T: RecordReader, S: RecordWriter>(
[INFO] [stdout]    |        ^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(dead_code)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: fields `genome_depth` and `genome_support` are never read
[INFO] [stdout]    --> src/align/info_stats.rs:130:5
[INFO] [stdout]     |
[INFO] [stdout] 110 | pub struct SamBamCramStats {
[INFO] [stdout]     |            --------------- fields in this struct
[INFO] [stdout] ...
[INFO] [stdout] 130 |     genome_depth: (),
[INFO] [stdout]     |     ^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 133 |     genome_support: (),
[INFO] [stdout]     |     ^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `SamBamCramStats` has a derived impl for the trait `Debug`, but this is intentionally ignored during dead code analysis
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variant `Cram` is never constructed
[INFO] [stdout]  --> src/align/reader.rs:9:5
[INFO] [stdout]   |
[INFO] [stdout] 6 | pub enum SamBamCramReader<R1: BufRead, R2: Read> {
[INFO] [stdout]   |          ---------------- variant in this enum
[INFO] [stdout] ...
[INFO] [stdout] 9 |     Cram,
[INFO] [stdout]   |     ^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: constant `RESERVED_DIRNAMES` is never used
[INFO] [stdout]   --> src/data/mod.rs:18:7
[INFO] [stdout]    |
[INFO] [stdout] 18 | const RESERVED_DIRNAMES: [&'static str; 7] = [
[INFO] [stdout]    |       ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: constant `RESERVED_FILENAMES` is never used
[INFO] [stdout]   --> src/data/mod.rs:21:7
[INFO] [stdout]    |
[INFO] [stdout] 21 | const RESERVED_FILENAMES: [&'static str; 5] = [
[INFO] [stdout]    |       ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: multiple fields are never read
[INFO] [stdout]   --> src/data/mod.rs:31:5
[INFO] [stdout]    |
[INFO] [stdout] 30 | struct SeqDir {
[INFO] [stdout]    |        ------ fields in this struct
[INFO] [stdout] 31 |     path: PathBuf,
[INFO] [stdout]    |     ^^^^
[INFO] [stdout] 32 |     date: Date,
[INFO] [stdout]    |     ^^^^
[INFO] [stdout] 33 |     instrument: String,
[INFO] [stdout]    |     ^^^^^^^^^^
[INFO] [stdout] 34 |     run: u16,
[INFO] [stdout]    |     ^^^
[INFO] [stdout] 35 |     position: char,
[INFO] [stdout]    |     ^^^^^^^^
[INFO] [stdout] 36 |     flowcell: String,
[INFO] [stdout]    |     ^^^^^^^^
[INFO] [stdout] 37 |     description: String,
[INFO] [stdout]    |     ^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `SeqDir` has a derived impl for the trait `Debug`, but this is intentionally ignored during dead code analysis
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: multiple associated items are never used
[INFO] [stdout]    --> src/data/mod.rs:42:12
[INFO] [stdout]     |
[INFO] [stdout] 40  | impl SeqDir {
[INFO] [stdout]     | ----------- associated items in this implementation
[INFO] [stdout] 41  |     /// Construct a new SeqDir object from a path
[INFO] [stdout] 42  |     pub fn new(path: &Path) -> SeqDir {
[INFO] [stdout]     |            ^^^
[INFO] [stdout] ...
[INFO] [stdout] 104 |     pub fn path(&self) -> &Path {
[INFO] [stdout]     |            ^^^^
[INFO] [stdout] ...
[INFO] [stdout] 109 |     pub fn date(&self) -> Date {
[INFO] [stdout]     |            ^^^^
[INFO] [stdout] ...
[INFO] [stdout] 114 |     pub fn instrument(&self) -> &str {
[INFO] [stdout]     |            ^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 119 |     pub fn run(&self) -> u16 {
[INFO] [stdout]     |            ^^^
[INFO] [stdout] ...
[INFO] [stdout] 124 |     pub fn position(&self) -> char {
[INFO] [stdout]     |            ^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 129 |     pub fn flowcell(&self) -> &str {
[INFO] [stdout]     |            ^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 134 |     pub fn description(&self) -> &str {
[INFO] [stdout]     |            ^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 139 |     pub fn create_reserved_files(&self, verbose: bool, dryrun: bool) {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 158 |     pub fn create_reserved_dirs(&self, verbose: bool, dryrun: bool) {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 177 |     pub fn relocate_hts_files(&self, verbose: bool, dryrun: bool) {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `create_reserved_file` is never used
[INFO] [stdout]    --> src/data/mod.rs:248:4
[INFO] [stdout]     |
[INFO] [stdout] 248 | fn create_reserved_file(seq: &SeqDir, file: &str) {
[INFO] [stdout]     |    ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `create_reserved_dir` is never used
[INFO] [stdout]    --> src/data/mod.rs:258:4
[INFO] [stdout]     |
[INFO] [stdout] 258 | fn create_reserved_dir(p: PathBuf) {
[INFO] [stdout]     |    ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `create_readme` is never used
[INFO] [stdout]    --> src/data/mod.rs:263:4
[INFO] [stdout]     |
[INFO] [stdout] 263 | fn create_readme(seq: &SeqDir) {
[INFO] [stdout]     |    ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `create_cluster_yaml` is never used
[INFO] [stdout]    --> src/data/mod.rs:284:4
[INFO] [stdout]     |
[INFO] [stdout] 284 | fn create_cluster_yaml(seq: &SeqDir) {
[INFO] [stdout]     |    ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `create_snakefile` is never used
[INFO] [stdout]    --> src/data/mod.rs:302:4
[INFO] [stdout]     |
[INFO] [stdout] 302 | fn create_snakefile(seq: &SeqDir) {
[INFO] [stdout]     |    ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `update_sample` is never used
[INFO] [stdout]    --> src/data/mod.rs:407:4
[INFO] [stdout]     |
[INFO] [stdout] 407 | fn update_sample(s: &mut SeqSample, mate: String, lane: String) {
[INFO] [stdout]     |    ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `create_config` is never used
[INFO] [stdout]    --> src/data/mod.rs:416:4
[INFO] [stdout]     |
[INFO] [stdout] 416 | fn create_config(sd: &SeqDir, dryrun: bool) {
[INFO] [stdout]     |    ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `mv_to_dir` is never used
[INFO] [stdout]    --> src/data/mod.rs:505:4
[INFO] [stdout]     |
[INFO] [stdout] 505 | fn mv_to_dir(file: &Path, dir: &Path) {
[INFO] [stdout]     |    ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `organize` is never used
[INFO] [stdout]    --> src/data/mod.rs:510:8
[INFO] [stdout]     |
[INFO] [stdout] 510 | pub fn organize(indir: &Path, dryrun: bool, verbose: bool) {
[INFO] [stdout]     |        ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: multiple fields are never read
[INFO] [stdout]   --> src/record/header.rs:45:5
[INFO] [stdout]    |
[INFO] [stdout] 43 | pub(crate) struct CasavaV1_8Name {
[INFO] [stdout]    |                   -------------- fields in this struct
[INFO] [stdout] 44 |     /// Instrument name
[INFO] [stdout] 45 |     instrument: Option<String>,
[INFO] [stdout]    |     ^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 48 |     lane: Option<u8>,
[INFO] [stdout]    |     ^^^^
[INFO] [stdout] ...
[INFO] [stdout] 51 |     tile: Option<u8>,
[INFO] [stdout]    |     ^^^^
[INFO] [stdout] ...
[INFO] [stdout] 54 |     x: Option<u8>,
[INFO] [stdout]    |     ^
[INFO] [stdout] ...
[INFO] [stdout] 57 |     y: Option<u8>,
[INFO] [stdout]    |     ^
[INFO] [stdout] ...
[INFO] [stdout] 61 |     sample_index: Option<u8>,
[INFO] [stdout]    |     ^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 64 |     pair_member: Option<u8>,
[INFO] [stdout]    |     ^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `CasavaV1_8Name` has a derived impl for the trait `Debug`, but this is intentionally ignored during dead code analysis
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: fields `id`, `description`, and `length` are never read
[INFO] [stdout]   --> src/record/header.rs:71:5
[INFO] [stdout]    |
[INFO] [stdout] 69 | pub(crate) struct SraName<'id> {
[INFO] [stdout]    |                   ------- fields in this struct
[INFO] [stdout] 70 |     /// Clobbered record ID
[INFO] [stdout] 71 |     id: Cow<'id, [u8]>,
[INFO] [stdout]    |     ^^
[INFO] [stdout] ...
[INFO] [stdout] 74 |     description: Cow<'id, [u8]>,
[INFO] [stdout]    |     ^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 77 |     length: Cow<'id, [u8]>,
[INFO] [stdout]    |     ^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `SraName` has a derived impl for the trait `Debug`, but this is intentionally ignored during dead code analysis
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: 18 warnings emitted
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished dev [unoptimized + debuginfo] target(s) in 16.97s
[INFO] [stderr] warning: the following packages contain code that will be rejected by a future version of Rust: buf_redux v0.8.4, nom v5.1.2, quick-xml v0.22.0
[INFO] [stderr] note: to see what the problems were, use the option `--future-incompat-report`, or run `cargo report future-incompatibilities --id 1`
[INFO] running `Command { std: "docker" "inspect" "d4466ac53bc3bae40fd52e4e5e263f48311abc1b40da7c8e87a54c5b0e3c5412", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "d4466ac53bc3bae40fd52e4e5e263f48311abc1b40da7c8e87a54c5b0e3c5412", kill_on_drop: false }`
[INFO] [stdout] d4466ac53bc3bae40fd52e4e5e263f48311abc1b40da7c8e87a54c5b0e3c5412
