[INFO] fetching crate bamnado 0.3.6...
[INFO] checking bamnado-0.3.6 against master#779e19d8baa3e3625bd4fc5c85cbb2ad47b43155 for pr-147589-1
[INFO] extracting crate bamnado 0.3.6 into /workspace/builds/worker-7-tc1/source
[INFO] started tweaking crates.io crate bamnado 0.3.6
[INFO] finished tweaking crates.io crate bamnado 0.3.6
[INFO] tweaked toml for crates.io crate bamnado 0.3.6 written to /workspace/builds/worker-7-tc1/source/Cargo.toml
[INFO] validating manifest of crates.io crate bamnado 0.3.6 on toolchain 779e19d8baa3e3625bd4fc5c85cbb2ad47b43155
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+779e19d8baa3e3625bd4fc5c85cbb2ad47b43155" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate crates.io crate bamnado 0.3.6 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" "+779e19d8baa3e3625bd4fc5c85cbb2ad47b43155" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Updating crates.io index
[INFO] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded polars-error v0.49.1
[INFO] [stderr]   Downloaded polars-time v0.49.1
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[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc1/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+779e19d8baa3e3625bd4fc5c85cbb2ad47b43155" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] 478ec474cf7b3a22ba9a1afa1412a92e847d9fc75c11781da50d498a7551ab87
[INFO] running `Command { std: "docker" "start" "-a" "478ec474cf7b3a22ba9a1afa1412a92e847d9fc75c11781da50d498a7551ab87", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "478ec474cf7b3a22ba9a1afa1412a92e847d9fc75c11781da50d498a7551ab87", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "478ec474cf7b3a22ba9a1afa1412a92e847d9fc75c11781da50d498a7551ab87", kill_on_drop: false }`
[INFO] [stdout] 478ec474cf7b3a22ba9a1afa1412a92e847d9fc75c11781da50d498a7551ab87
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc1/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "RUSTDOCFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+779e19d8baa3e3625bd4fc5c85cbb2ad47b43155" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] a8113f2cfe95c51e3c7b64445f8e6c1bab24bc5d105394264db450210aa66b67
[INFO] running `Command { std: "docker" "start" "-a" "a8113f2cfe95c51e3c7b64445f8e6c1bab24bc5d105394264db450210aa66b67", kill_on_drop: false }`
[INFO] [stderr]     Checking either v1.15.0
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[INFO] [stderr]     Checking fs4 v0.13.1
[INFO] [stderr]     Checking tempfile v3.20.0
[INFO] [stderr]     Checking attohttpc v0.25.0
[INFO] [stderr]     Checking petgraph v0.8.2
[INFO] [stderr]     Checking lz4 v1.28.1
[INFO] [stderr]     Checking now v0.1.3
[INFO] [stderr]     Checking nalgebra v0.33.2
[INFO] [stderr]     Checking tokio-util v0.7.15
[INFO] [stderr]     Checking tower v0.5.2
[INFO] [stderr]     Checking tokio-rustls v0.26.2
[INFO] [stderr]     Checking async-compression v0.4.25
[INFO] [stderr]     Checking bigtools v0.5.6
[INFO] [stderr]     Checking h2 v0.4.11
[INFO] [stderr]     Checking noodles-bgzf v0.41.0
[INFO] [stderr]     Checking tower-http v0.6.6
[INFO] [stderr]     Checking noodles-csi v0.49.0
[INFO] [stderr]     Checking noodles-fasta v0.54.0
[INFO] [stderr]     Checking noodles-sam v0.77.0
[INFO] [stderr]     Checking noodles-tabix v0.55.0
[INFO] [stderr]     Checking noodles-bed v0.26.0
[INFO] [stderr]     Checking hyper v1.6.0
[INFO] [stderr]     Checking noodles-bam v0.81.0
[INFO] [stderr]     Checking hyper-util v0.1.15
[INFO] [stderr]     Checking noodles-cram v0.84.0
[INFO] [stderr]     Checking hyper-rustls v0.27.7
[INFO] [stderr]     Checking statrs v0.18.0
[INFO] [stderr]     Checking reqwest v0.12.22
[INFO] [stderr]     Checking object_store v0.12.2
[INFO] [stderr]     Checking bio v2.3.0
[INFO] [stderr]     Checking noodles v0.99.0
[INFO] [stderr]     Checking polars-error v0.49.1
[INFO] [stderr]     Checking polars-row v0.49.1
[INFO] [stderr]     Checking polars-parquet v0.49.1
[INFO] [stderr]     Checking polars-time v0.49.1
[INFO] [stderr]     Checking polars-io v0.49.1
[INFO] [stderr]     Checking polars-expr v0.49.1
[INFO] [stderr]     Checking polars-mem-engine v0.49.1
[INFO] [stderr]     Checking bamnado v0.3.6 (/opt/rustwide/workdir)
[INFO] [stdout] warning: unused import: `warn`
[INFO] [stdout]  --> src/bam_utils.rs:6:24
[INFO] [stdout]   |
[INFO] [stdout] 6 | use log::{debug, info, warn};
[INFO] [stdout]   |                        ^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `noodles::sam::alignment::record::data::field::tag::Tag`
[INFO] [stdout]   --> src/bam_utils.rs:10:5
[INFO] [stdout]    |
[INFO] [stdout] 10 | use noodles::sam::alignment::record::data::field::tag::Tag;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `BufRead`
[INFO] [stdout]   --> src/bam_utils.rs:14:15
[INFO] [stdout]    |
[INFO] [stdout] 14 | use std::io::{BufRead, Write};
[INFO] [stdout]    |               ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `regex::Regex`
[INFO] [stdout]   --> src/bam_utils.rs:17:5
[INFO] [stdout]    |
[INFO] [stdout] 17 | use regex::Regex;
[INFO] [stdout]    |     ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `HashSet`
[INFO] [stdout]  --> src/spike_in_analysis.rs:1:22
[INFO] [stdout]   |
[INFO] [stdout] 1 | use ahash::{HashMap, HashSet, HashSetExt};
[INFO] [stdout]   |                      ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `error`
[INFO] [stdout]   --> src/spike_in_analysis.rs:10:11
[INFO] [stdout]    |
[INFO] [stdout] 10 | use log::{error, info};
[INFO] [stdout]    |           ^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `record::Record`
[INFO] [stdout]   --> src/spike_in_analysis.rs:11:33
[INFO] [stdout]    |
[INFO] [stdout] 11 | use noodles::bam::{self as bam, record::Record};
[INFO] [stdout]    |                                 ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `alignment::RecordBuf` and `header::Header`
[INFO] [stdout]   --> src/spike_in_analysis.rs:12:33
[INFO] [stdout]    |
[INFO] [stdout] 12 | use noodles::sam::{self as sam, alignment::RecordBuf, header::Header};
[INFO] [stdout]    |                                 ^^^^^^^^^^^^^^^^^^^^  ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::ops::Deref`
[INFO] [stdout]  --> src/coverage_analysis.rs:6:5
[INFO] [stdout]   |
[INFO] [stdout] 6 | use std::ops::Deref;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `core`
[INFO] [stdout]   --> src/coverage_analysis.rs:14:20
[INFO] [stdout]    |
[INFO] [stdout] 14 | use noodles::{bam, core};
[INFO] [stdout]    |                    ^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `cols`, `mean_horizontal`, and `sum_horizontal`
[INFO] [stdout]   --> src/coverage_analysis.rs:15:30
[INFO] [stdout]    |
[INFO] [stdout] 15 | use polars::lazy::dsl::{col, cols, mean_horizontal, sum_horizontal};
[INFO] [stdout]    |                              ^^^^  ^^^^^^^^^^^^^^^  ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `debug`, `info`, and `warn`
[INFO] [stdout]  --> src/bam_splitter.rs:6:11
[INFO] [stdout]   |
[INFO] [stdout] 6 | use log::{debug, info, warn};
[INFO] [stdout]   |           ^^^^^  ^^^^  ^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `sam`
[INFO] [stdout]   --> src/bam_splitter.rs:11:20
[INFO] [stdout]    |
[INFO] [stdout] 11 | use noodles::{bam, sam};
[INFO] [stdout]    |                    ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `Map` and `map::ReferenceSequence`
[INFO] [stdout]   --> src/bam_splitter.rs:13:43
[INFO] [stdout]    |
[INFO] [stdout] 13 | use noodles::sam::header::record::value::{map::ReferenceSequence, Map};
[INFO] [stdout]    |                                           ^^^^^^^^^^^^^^^^^^^^^^  ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::bam_utils::BamStats`
[INFO] [stdout]  --> src/bam_modifier.rs:1:5
[INFO] [stdout]   |
[INFO] [stdout] 1 | use crate::bam_utils::BamStats;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::genomic_intervals`
[INFO] [stdout]  --> src/bam_modifier.rs:3:5
[INFO] [stdout]   |
[INFO] [stdout] 3 | use crate::genomic_intervals;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `IntervalMaker` and `Shift`
[INFO] [stdout]  --> src/bam_modifier.rs:4:32
[INFO] [stdout]   |
[INFO] [stdout] 4 | use crate::genomic_intervals::{IntervalMaker, Shift};
[INFO] [stdout]   |                                ^^^^^^^^^^^^^  ^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crossbeam::channel::unbounded`
[INFO] [stdout]  --> src/bam_modifier.rs:8:5
[INFO] [stdout]   |
[INFO] [stdout] 8 | use crossbeam::channel::unbounded;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `debug` and `info`
[INFO] [stdout]   --> src/bam_modifier.rs:10:11
[INFO] [stdout]    |
[INFO] [stdout] 10 | use log::{debug, info, warn};
[INFO] [stdout]    |           ^^^^^  ^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `Map` and `map::ReferenceSequence`
[INFO] [stdout]   --> src/bam_modifier.rs:15:43
[INFO] [stdout]    |
[INFO] [stdout] 15 | use noodles::sam::header::record::value::{Map, map::ReferenceSequence};
[INFO] [stdout]    |                                           ^^^  ^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `bam` and `sam`
[INFO] [stdout]   --> src/bam_modifier.rs:16:15
[INFO] [stdout]    |
[INFO] [stdout] 16 | use noodles::{bam, sam};
[INFO] [stdout]    |               ^^^  ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `IntoParallelIterator`
[INFO] [stdout]   --> src/bam_modifier.rs:17:19
[INFO] [stdout]    |
[INFO] [stdout] 17 | use rayon::iter::{IntoParallelIterator, ParallelIterator};
[INFO] [stdout]    |                   ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `warn`
[INFO] [stdout]  --> src/bam_utils.rs:6:24
[INFO] [stdout]   |
[INFO] [stdout] 6 | use log::{debug, info, warn};
[INFO] [stdout]   |                        ^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `noodles::sam::alignment::record::data::field::tag::Tag`
[INFO] [stdout]   --> src/bam_utils.rs:10:5
[INFO] [stdout]    |
[INFO] [stdout] 10 | use noodles::sam::alignment::record::data::field::tag::Tag;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `BufRead`
[INFO] [stdout]   --> src/bam_utils.rs:14:15
[INFO] [stdout]    |
[INFO] [stdout] 14 | use std::io::{BufRead, Write};
[INFO] [stdout]    |               ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `regex::Regex`
[INFO] [stdout]   --> src/bam_utils.rs:17:5
[INFO] [stdout]    |
[INFO] [stdout] 17 | use regex::Regex;
[INFO] [stdout]    |     ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `HashSet`
[INFO] [stdout]  --> src/spike_in_analysis.rs:1:22
[INFO] [stdout]   |
[INFO] [stdout] 1 | use ahash::{HashMap, HashSet, HashSetExt};
[INFO] [stdout]   |                      ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `error`
[INFO] [stdout]   --> src/spike_in_analysis.rs:10:11
[INFO] [stdout]    |
[INFO] [stdout] 10 | use log::{error, info};
[INFO] [stdout]    |           ^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `record::Record`
[INFO] [stdout]   --> src/spike_in_analysis.rs:11:33
[INFO] [stdout]    |
[INFO] [stdout] 11 | use noodles::bam::{self as bam, record::Record};
[INFO] [stdout]    |                                 ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `alignment::RecordBuf` and `header::Header`
[INFO] [stdout]   --> src/spike_in_analysis.rs:12:33
[INFO] [stdout]    |
[INFO] [stdout] 12 | use noodles::sam::{self as sam, alignment::RecordBuf, header::Header};
[INFO] [stdout]    |                                 ^^^^^^^^^^^^^^^^^^^^  ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::ops::Deref`
[INFO] [stdout]  --> src/coverage_analysis.rs:6:5
[INFO] [stdout]   |
[INFO] [stdout] 6 | use std::ops::Deref;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `core`
[INFO] [stdout]   --> src/coverage_analysis.rs:14:20
[INFO] [stdout]    |
[INFO] [stdout] 14 | use noodles::{bam, core};
[INFO] [stdout]    |                    ^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `cols`, `mean_horizontal`, and `sum_horizontal`
[INFO] [stdout]   --> src/coverage_analysis.rs:15:30
[INFO] [stdout]    |
[INFO] [stdout] 15 | use polars::lazy::dsl::{col, cols, mean_horizontal, sum_horizontal};
[INFO] [stdout]    |                              ^^^^  ^^^^^^^^^^^^^^^  ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `bigtools::BigWigRead`
[INFO] [stdout]   --> src/coverage_analysis.rs:21:5
[INFO] [stdout]    |
[INFO] [stdout] 21 | use bigtools::BigWigRead;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `debug`, `info`, and `warn`
[INFO] [stdout]  --> src/bam_splitter.rs:6:11
[INFO] [stdout]   |
[INFO] [stdout] 6 | use log::{debug, info, warn};
[INFO] [stdout]   |           ^^^^^  ^^^^  ^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `sam`
[INFO] [stdout]   --> src/bam_splitter.rs:11:20
[INFO] [stdout]    |
[INFO] [stdout] 11 | use noodles::{bam, sam};
[INFO] [stdout]    |                    ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `Map` and `map::ReferenceSequence`
[INFO] [stdout]   --> src/bam_splitter.rs:13:43
[INFO] [stdout]    |
[INFO] [stdout] 13 | use noodles::sam::header::record::value::{map::ReferenceSequence, Map};
[INFO] [stdout]    |                                           ^^^^^^^^^^^^^^^^^^^^^^  ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::bam_utils::BamStats`
[INFO] [stdout]  --> src/bam_modifier.rs:1:5
[INFO] [stdout]   |
[INFO] [stdout] 1 | use crate::bam_utils::BamStats;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::genomic_intervals`
[INFO] [stdout]  --> src/bam_modifier.rs:3:5
[INFO] [stdout]   |
[INFO] [stdout] 3 | use crate::genomic_intervals;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `IntervalMaker` and `Shift`
[INFO] [stdout]  --> src/bam_modifier.rs:4:32
[INFO] [stdout]   |
[INFO] [stdout] 4 | use crate::genomic_intervals::{IntervalMaker, Shift};
[INFO] [stdout]   |                                ^^^^^^^^^^^^^  ^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crossbeam::channel::unbounded`
[INFO] [stdout]  --> src/bam_modifier.rs:8:5
[INFO] [stdout]   |
[INFO] [stdout] 8 | use crossbeam::channel::unbounded;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `debug` and `info`
[INFO] [stdout]   --> src/bam_modifier.rs:10:11
[INFO] [stdout]    |
[INFO] [stdout] 10 | use log::{debug, info, warn};
[INFO] [stdout]    |           ^^^^^  ^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `Map` and `map::ReferenceSequence`
[INFO] [stdout]   --> src/bam_modifier.rs:15:43
[INFO] [stdout]    |
[INFO] [stdout] 15 | use noodles::sam::header::record::value::{Map, map::ReferenceSequence};
[INFO] [stdout]    |                                           ^^^  ^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `bam` and `sam`
[INFO] [stdout]   --> src/bam_modifier.rs:16:15
[INFO] [stdout]    |
[INFO] [stdout] 16 | use noodles::{bam, sam};
[INFO] [stdout]    |               ^^^  ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `IntoParallelIterator`
[INFO] [stdout]   --> src/bam_modifier.rs:17:19
[INFO] [stdout]    |
[INFO] [stdout] 17 | use rayon::iter::{IntoParallelIterator, ParallelIterator};
[INFO] [stdout]    |                   ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `Write`
[INFO] [stdout]   --> src/bam_utils.rs:14:24
[INFO] [stdout]    |
[INFO] [stdout] 14 | use std::io::{BufRead, Write};
[INFO] [stdout]    |                        ^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `bio_types::annot::loc::Loc`
[INFO] [stdout]  --> src/bam_utils.rs:4:5
[INFO] [stdout]   |
[INFO] [stdout] 4 | use bio_types::annot::loc::Loc;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `ParallelIterator`
[INFO] [stdout]   --> src/bam_modifier.rs:17:41
[INFO] [stdout]    |
[INFO] [stdout] 17 | use rayon::iter::{IntoParallelIterator, ParallelIterator};
[INFO] [stdout]    |                                         ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `HashSetExt`
[INFO] [stdout]  --> src/spike_in_analysis.rs:1:31
[INFO] [stdout]   |
[INFO] [stdout] 1 | use ahash::{HashMap, HashSet, HashSetExt};
[INFO] [stdout]   |                               ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `i`
[INFO] [stdout]    --> src/bam_utils.rs:153:14
[INFO] [stdout]     |
[INFO] [stdout] 153 |         for (i, column) in df.iter().enumerate() {
[INFO] [stdout]     |              ^ help: if this is intentional, prefix it with an underscore: `_i`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `Write`
[INFO] [stdout]   --> src/bam_utils.rs:14:24
[INFO] [stdout]    |
[INFO] [stdout] 14 | use std::io::{BufRead, Write};
[INFO] [stdout]    |                        ^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `bio_types::annot::loc::Loc`
[INFO] [stdout]  --> src/bam_utils.rs:4:5
[INFO] [stdout]   |
[INFO] [stdout] 4 | use bio_types::annot::loc::Loc;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `ParallelIterator`
[INFO] [stdout]   --> src/bam_modifier.rs:17:41
[INFO] [stdout]    |
[INFO] [stdout] 17 | use rayon::iter::{IntoParallelIterator, ParallelIterator};
[INFO] [stdout]    |                                         ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `HashSetExt`
[INFO] [stdout]  --> src/spike_in_analysis.rs:1:31
[INFO] [stdout]   |
[INFO] [stdout] 1 | use ahash::{HashMap, HashSet, HashSetExt};
[INFO] [stdout]   |                               ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/bam_utils.rs:528:9
[INFO] [stdout]     |
[INFO] [stdout] 528 |     let mut buf_reader = std::io::BufReader::new(reader);
[INFO] [stdout]     |         ----^^^^^^^^^^
[INFO] [stdout]     |         |
[INFO] [stdout]     |         help: remove this `mut`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_mut)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `i`
[INFO] [stdout]    --> src/bam_utils.rs:153:14
[INFO] [stdout]     |
[INFO] [stdout] 153 |         for (i, column) in df.iter().enumerate() {
[INFO] [stdout]     |              ^ help: if this is intentional, prefix it with an underscore: `_i`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/bam_utils.rs:528:9
[INFO] [stdout]     |
[INFO] [stdout] 528 |     let mut buf_reader = std::io::BufReader::new(reader);
[INFO] [stdout]     |         ----^^^^^^^^^^
[INFO] [stdout]     |         |
[INFO] [stdout]     |         help: remove this `mut`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_mut)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]   --> src/coverage_analysis.rs:29:19
[INFO] [stdout]    |
[INFO] [stdout] 29 | fn write_bedgraph(mut df: DataFrame, outfile: PathBuf, ignore_scaffold_chromosomes: bool) -> Result<()> {
[INFO] [stdout]    |                   ----^^
[INFO] [stdout]    |                   |
[INFO] [stdout]    |                   help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]   --> src/coverage_analysis.rs:29:19
[INFO] [stdout]    |
[INFO] [stdout] 29 | fn write_bedgraph(mut df: DataFrame, outfile: PathBuf, ignore_scaffold_chromosomes: bool) -> Result<()> {
[INFO] [stdout]    |                   ----^^
[INFO] [stdout]    |                   |
[INFO] [stdout]    |                   help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `e`
[INFO] [stdout]   --> src/bam_splitter.rs:45:17
[INFO] [stdout]    |
[INFO] [stdout] 45 |             Err(e) => {
[INFO] [stdout]    |                 ^ help: if this is intentional, prefix it with an underscore: `_e`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `reader`
[INFO] [stdout]    --> src/bam_splitter.rs:121:17
[INFO] [stdout]     |
[INFO] [stdout] 121 |             let reader = bam::io::indexed_reader::Builder::default()
[INFO] [stdout]     |                 ^^^^^^ help: if this is intentional, prefix it with an underscore: `_reader`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `chromsizes_refid`
[INFO] [stdout]    --> src/bam_splitter.rs:106:13
[INFO] [stdout]     |
[INFO] [stdout] 106 |         let chromsizes_refid = bam_stats
[INFO] [stdout]     |             ^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_chromsizes_refid`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `n_total_chunks`
[INFO] [stdout]    --> src/bam_splitter.rs:111:13
[INFO] [stdout]     |
[INFO] [stdout] 111 |         let n_total_chunks = genomic_chunks.len();
[INFO] [stdout]     |             ^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_n_total_chunks`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `e`
[INFO] [stdout]   --> src/bam_modifier.rs:49:17
[INFO] [stdout]    |
[INFO] [stdout] 49 |             Err(e) => get_bam_header(&filepath)?,
[INFO] [stdout]    |                 ^ help: if this is intentional, prefix it with an underscore: `_e`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: field `chrom` is never read
[INFO] [stdout]    --> src/bam_utils.rs:170:5
[INFO] [stdout]     |
[INFO] [stdout] 169 | struct ChromosomeStats {
[INFO] [stdout]     |        --------------- field in this struct
[INFO] [stdout] 170 |     chrom: String,
[INFO] [stdout]     |     ^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `ChromosomeStats` has a derived impl for the trait `Debug`, but this is intentionally ignored during dead code analysis
[INFO] [stdout]     = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: fields `file_path` and `contigs` are never read
[INFO] [stdout]    --> src/bam_utils.rs:232:5
[INFO] [stdout]     |
[INFO] [stdout] 228 | pub struct BamStats {
[INFO] [stdout]     |            -------- fields in this struct
[INFO] [stdout] ...
[INFO] [stdout] 232 |     file_path: PathBuf,
[INFO] [stdout]     |     ^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 238 |     contigs: Vec<Contig<String, ReqStrand>>,
[INFO] [stdout]     |     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: field `input_header` is never read
[INFO] [stdout]    --> src/spike_in_analysis.rs:107:5
[INFO] [stdout]     |
[INFO] [stdout] 104 | pub struct BamSplitter {
[INFO] [stdout]     |            ----------- field in this struct
[INFO] [stdout] ...
[INFO] [stdout] 107 |     input_header: sam::Header,
[INFO] [stdout]     |     ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `convert_bedgraph_to_bigwig` is never used
[INFO] [stdout]    --> src/coverage_analysis.rs:110:4
[INFO] [stdout]     |
[INFO] [stdout] 110 | fn convert_bedgraph_to_bigwig(
[INFO] [stdout]     |    ^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `e`
[INFO] [stdout]   --> src/bam_splitter.rs:45:17
[INFO] [stdout]    |
[INFO] [stdout] 45 |             Err(e) => {
[INFO] [stdout]    |                 ^ help: if this is intentional, prefix it with an underscore: `_e`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `reader`
[INFO] [stdout]    --> src/bam_splitter.rs:121:17
[INFO] [stdout]     |
[INFO] [stdout] 121 |             let reader = bam::io::indexed_reader::Builder::default()
[INFO] [stdout]     |                 ^^^^^^ help: if this is intentional, prefix it with an underscore: `_reader`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `chromsizes_refid`
[INFO] [stdout]    --> src/bam_splitter.rs:106:13
[INFO] [stdout]     |
[INFO] [stdout] 106 |         let chromsizes_refid = bam_stats
[INFO] [stdout]     |             ^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_chromsizes_refid`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `n_total_chunks`
[INFO] [stdout]    --> src/bam_splitter.rs:111:13
[INFO] [stdout]     |
[INFO] [stdout] 111 |         let n_total_chunks = genomic_chunks.len();
[INFO] [stdout]     |             ^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_n_total_chunks`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `e`
[INFO] [stdout]   --> src/bam_modifier.rs:49:17
[INFO] [stdout]    |
[INFO] [stdout] 49 |             Err(e) => get_bam_header(&filepath)?,
[INFO] [stdout]    |                 ^ help: if this is intentional, prefix it with an underscore: `_e`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: field `chrom` is never read
[INFO] [stdout]    --> src/bam_utils.rs:170:5
[INFO] [stdout]     |
[INFO] [stdout] 169 | struct ChromosomeStats {
[INFO] [stdout]     |        --------------- field in this struct
[INFO] [stdout] 170 |     chrom: String,
[INFO] [stdout]     |     ^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `ChromosomeStats` has a derived impl for the trait `Debug`, but this is intentionally ignored during dead code analysis
[INFO] [stdout]     = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: fields `file_path` and `contigs` are never read
[INFO] [stdout]    --> src/bam_utils.rs:232:5
[INFO] [stdout]     |
[INFO] [stdout] 228 | pub struct BamStats {
[INFO] [stdout]     |            -------- fields in this struct
[INFO] [stdout] ...
[INFO] [stdout] 232 |     file_path: PathBuf,
[INFO] [stdout]     |     ^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 238 |     contigs: Vec<Contig<String, ReqStrand>>,
[INFO] [stdout]     |     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: field `input_header` is never read
[INFO] [stdout]    --> src/spike_in_analysis.rs:107:5
[INFO] [stdout]     |
[INFO] [stdout] 104 | pub struct BamSplitter {
[INFO] [stdout]     |            ----------- field in this struct
[INFO] [stdout] ...
[INFO] [stdout] 107 |     input_header: sam::Header,
[INFO] [stdout]     |     ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `error`
[INFO] [stdout]  --> src/main.rs:3:11
[INFO] [stdout]   |
[INFO] [stdout] 3 | use log::{error, info};
[INFO] [stdout]   |           ^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `error`
[INFO] [stdout]  --> src/main.rs:3:11
[INFO] [stdout]   |
[INFO] [stdout] 3 | use log::{error, info};
[INFO] [stdout]   |           ^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::str::FromStr`
[INFO] [stdout]  --> src/main.rs:8:5
[INFO] [stdout]   |
[INFO] [stdout] 8 | use std::str::FromStr;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::str::FromStr`
[INFO] [stdout]  --> src/main.rs:8:5
[INFO] [stdout]   |
[INFO] [stdout] 8 | use std::str::FromStr;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `blacklist`
[INFO] [stdout]    --> src/main.rs:278:15
[INFO] [stdout]     |
[INFO] [stdout] 278 |         (Some(blacklist), None) => {
[INFO] [stdout]     |               ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_blacklist`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `blacklist`
[INFO] [stdout]    --> src/main.rs:278:15
[INFO] [stdout]     |
[INFO] [stdout] 278 |         (Some(blacklist), None) => {
[INFO] [stdout]     |               ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_blacklist`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `allow_unknown_mapq`
[INFO] [stdout]    --> src/main.rs:503:13
[INFO] [stdout]     |
[INFO] [stdout] 503 |             allow_unknown_mapq,
[INFO] [stdout]     |             ^^^^^^^^^^^^^^^^^^ help: try ignoring the field: `allow_unknown_mapq: _`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `filter`
[INFO] [stdout]    --> src/main.rs:510:17
[INFO] [stdout]     |
[INFO] [stdout] 510 |             let filter = create_filter_from_options(filter_options, None)?;
[INFO] [stdout]     |                 ^^^^^^ help: if this is intentional, prefix it with an underscore: `_filter`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `allow_unknown_mapq`
[INFO] [stdout]    --> src/main.rs:503:13
[INFO] [stdout]     |
[INFO] [stdout] 503 |             allow_unknown_mapq,
[INFO] [stdout]     |             ^^^^^^^^^^^^^^^^^^ help: try ignoring the field: `allow_unknown_mapq: _`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `filter`
[INFO] [stdout]    --> src/main.rs:510:17
[INFO] [stdout]     |
[INFO] [stdout] 510 |             let filter = create_filter_from_options(filter_options, None)?;
[INFO] [stdout]     |                 ^^^^^^ help: if this is intentional, prefix it with an underscore: `_filter`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `check_bedgraph_to_bigwig_tool` is never used
[INFO] [stdout]    --> src/main.rs:310:4
[INFO] [stdout]     |
[INFO] [stdout] 310 | fn check_bedgraph_to_bigwig_tool() -> Result<()> {
[INFO] [stdout]     |    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `check_bedgraph_to_bigwig_tool` is never used
[INFO] [stdout]    --> src/main.rs:310:4
[INFO] [stdout]     |
[INFO] [stdout] 310 | fn check_bedgraph_to_bigwig_tool() -> Result<()> {
[INFO] [stdout]     |    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 2m 00s
[INFO] running `Command { std: "docker" "inspect" "a8113f2cfe95c51e3c7b64445f8e6c1bab24bc5d105394264db450210aa66b67", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "a8113f2cfe95c51e3c7b64445f8e6c1bab24bc5d105394264db450210aa66b67", kill_on_drop: false }`
[INFO] [stdout] a8113f2cfe95c51e3c7b64445f8e6c1bab24bc5d105394264db450210aa66b67
