[INFO] cloning repository https://github.com/propenster/ERVCaller-rs
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/propenster/ERVCaller-rs" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fpropenster%2FERVCaller-rs", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fpropenster%2FERVCaller-rs'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] b463588e65ab7d025bbce9a688f61119f5db4c3b
[INFO] checking propenster/ERVCaller-rs against try#b28cc4eb48a6415b914e8ad0308be255ff8d73ed for pr-156508
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fpropenster%2FERVCaller-rs" "/workspace/builds/worker-2-tc2/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-2-tc2/source'...
[INFO] [stderr] done.
[INFO] started tweaking git repo https://github.com/propenster/ERVCaller-rs
[INFO] finished tweaking git repo https://github.com/propenster/ERVCaller-rs
[INFO] tweaked toml for git repo https://github.com/propenster/ERVCaller-rs written to /workspace/builds/worker-2-tc2/source/Cargo.toml
[INFO] validating manifest of git repo https://github.com/propenster/ERVCaller-rs on toolchain b28cc4eb48a6415b914e8ad0308be255ff8d73ed
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+b28cc4eb48a6415b914e8ad0308be255ff8d73ed" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate git repo https://github.com/propenster/ERVCaller-rs 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" "+b28cc4eb48a6415b914e8ad0308be255ff8d73ed" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Blocking waiting for file lock on package cache
[INFO] [stderr]     Blocking waiting for file lock on package cache
[INFO] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded clap_derive v4.4.0
[INFO] [stderr]   Downloaded clap v4.4.1
[INFO] [stderr]   Downloaded aho-corasick v1.0.5
[INFO] [stderr]   Downloaded memchr v2.6.1
[INFO] [stderr]   Downloaded clap_builder v4.4.1
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-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:d429b63d4308055ea97f60fb1d3dfca48854a00942f1bd2ad806beaf015945ec" "/opt/rustwide/cargo-home/bin/cargo" "+b28cc4eb48a6415b914e8ad0308be255ff8d73ed" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] 34ab383dfbaa740d9b85aa61454d0a2212862183e26223600fca3a84e5f1622a
[INFO] running `Command { std: "docker" "start" "-a" "34ab383dfbaa740d9b85aa61454d0a2212862183e26223600fca3a84e5f1622a", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "34ab383dfbaa740d9b85aa61454d0a2212862183e26223600fca3a84e5f1622a", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "34ab383dfbaa740d9b85aa61454d0a2212862183e26223600fca3a84e5f1622a", kill_on_drop: false }`
[INFO] [stdout] 34ab383dfbaa740d9b85aa61454d0a2212862183e26223600fca3a84e5f1622a
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-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:d429b63d4308055ea97f60fb1d3dfca48854a00942f1bd2ad806beaf015945ec" "/opt/rustwide/cargo-home/bin/cargo" "+b28cc4eb48a6415b914e8ad0308be255ff8d73ed" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] f6be123b38b4c012b035ef6b23c6848172d04541b972232704df6f6dbb34c31d
[INFO] running `Command { std: "docker" "start" "-a" "f6be123b38b4c012b035ef6b23c6848172d04541b972232704df6f6dbb34c31d", kill_on_drop: false }`
[INFO] [stderr]     Checking memchr v2.6.1
[INFO] [stderr]     Checking regex-syntax v0.7.5
[INFO] [stderr]    Compiling anyhow v1.0.75
[INFO] [stderr]    Compiling syn v2.0.29
[INFO] [stderr]     Checking clap_builder v4.4.1
[INFO] [stderr]     Checking aho-corasick v1.0.5
[INFO] [stderr]     Checking regex-automata v0.3.7
[INFO] [stderr]    Compiling clap_derive v4.4.0
[INFO] [stderr]     Checking clap v4.4.1
[INFO] [stderr]     Checking regex v1.9.4
[INFO] [stderr]     Checking ervcaller-rs v0.1.0 (/opt/rustwide/workdir)
[INFO] [stdout] warning: unused import: `anyhow`
[INFO] [stdout]  --> src/main.rs:1:14
[INFO] [stdout]   |
[INFO] [stdout] 1 | use anyhow::{anyhow, Error, Result};
[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: `command`
[INFO] [stdout]  --> src/main.rs:2:12
[INFO] [stdout]   |
[INFO] [stdout] 2 | use clap::{command, error::ErrorKind, Parser};
[INFO] [stdout]   |            ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::f32::consts::E`
[INFO] [stdout]  --> src/main.rs:4:5
[INFO] [stdout]   |
[INFO] [stdout] 4 | use std::f32::consts::E;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `PathBuf`
[INFO] [stdout]  --> src/main.rs:7:23
[INFO] [stdout]   |
[INFO] [stdout] 7 | use std::path::{Path, PathBuf};
[INFO] [stdout]   |                       ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `ExitStatus`
[INFO] [stdout]  --> src/main.rs:8:29
[INFO] [stdout]   |
[INFO] [stdout] 8 | use std::process::{Command, ExitStatus};
[INFO] [stdout]   |                             ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused doc comment
[INFO] [stdout]    --> src/main.rs:183:5
[INFO] [stdout]     |
[INFO] [stdout] 183 |       /// create output director passed from cli args if not exists
[INFO] [stdout]     |       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 184 | /     if let Err(err) = create_directory_if_not_exists(&args.output_directory) {
[INFO] [stdout] 185 | |         eprintln!("Failed to create directory: {}", err);
[INFO] [stdout] 186 | |     }
[INFO] [stdout]     | |_____- rustdoc does not generate documentation for expressions
[INFO] [stdout]     |
[INFO] [stdout]     = help: use `//` for a plain comment
[INFO] [stdout]     = note: `#[warn(unused_doc_comments)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `anyhow`
[INFO] [stdout]  --> src/main.rs:1:14
[INFO] [stdout]   |
[INFO] [stdout] 1 | use anyhow::{anyhow, Error, Result};
[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: `command`
[INFO] [stdout]  --> src/main.rs:2:12
[INFO] [stdout]   |
[INFO] [stdout] 2 | use clap::{command, error::ErrorKind, Parser};
[INFO] [stdout]   |            ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::f32::consts::E`
[INFO] [stdout]  --> src/main.rs:4:5
[INFO] [stdout]   |
[INFO] [stdout] 4 | use std::f32::consts::E;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `PathBuf`
[INFO] [stdout]  --> src/main.rs:7:23
[INFO] [stdout]   |
[INFO] [stdout] 7 | use std::path::{Path, PathBuf};
[INFO] [stdout]   |                       ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `ExitStatus`
[INFO] [stdout]  --> src/main.rs:8:29
[INFO] [stdout]   |
[INFO] [stdout] 8 | use std::process::{Command, ExitStatus};
[INFO] [stdout]   |                             ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused doc comment
[INFO] [stdout]    --> src/main.rs:183:5
[INFO] [stdout]     |
[INFO] [stdout] 183 |       /// create output director passed from cli args if not exists
[INFO] [stdout]     |       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 184 | /     if let Err(err) = create_directory_if_not_exists(&args.output_directory) {
[INFO] [stdout] 185 | |         eprintln!("Failed to create directory: {}", err);
[INFO] [stdout] 186 | |     }
[INFO] [stdout]     | |_____- rustdoc does not generate documentation for expressions
[INFO] [stdout]     |
[INFO] [stdout]     = help: use `//` for a plain comment
[INFO] [stdout]     = note: `#[warn(unused_doc_comments)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/main.rs:168:9
[INFO] [stdout]     |
[INFO] [stdout] 168 |     let mut tsd_min_len = 100;
[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/main.rs:169:9
[INFO] [stdout]     |
[INFO] [stdout] 169 |     let mut alignment_score = 30;
[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/main.rs:170:9
[INFO] [stdout]     |
[INFO] [stdout] 170 |     let mut human_genome = &args.human_reference_genome;
[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/main.rs:171:9
[INFO] [stdout]     |
[INFO] [stdout] 171 |     let mut human_genome_tophat = &args.human_reference_genome;
[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/main.rs:173:9
[INFO] [stdout]     |
[INFO] [stdout] 173 |     let mut genome: HashMap<String, String> = HashMap::new();
[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/main.rs:179:9
[INFO] [stdout]     |
[INFO] [stdout] 179 |     let mut bp1_tmp3: Vec<String> = Vec::new(); // Define the correct type
[INFO] [stdout]     |         ----^^^^^^^^
[INFO] [stdout]     |         |
[INFO] [stdout]     |         help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `std_insert_size` is assigned to, but never used
[INFO] [stdout]   --> src/main.rs:99:9
[INFO] [stdout]    |
[INFO] [stdout] 99 |     let mut std_insert_size: f32 = 0.0;
[INFO] [stdout]    |         ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: consider using `_std_insert_size` instead
[INFO] [stdout]    = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `bowtie2_d`
[INFO] [stdout]    --> src/main.rs:107:9
[INFO] [stdout]     |
[INFO] [stdout] 107 |     let bowtie2_d = "";
[INFO] [stdout]     |         ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_bowtie2_d`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `tophat_d`
[INFO] [stdout]    --> src/main.rs:108:9
[INFO] [stdout]     |
[INFO] [stdout] 108 |     let tophat_d = "";
[INFO] [stdout]     |         ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_tophat_d`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `se_mei_d`
[INFO] [stdout]    --> src/main.rs:111:9
[INFO] [stdout]     |
[INFO] [stdout] 111 |     let se_mei_d = "";
[INFO] [stdout]     |         ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_se_mei_d`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `tsd_min_len`
[INFO] [stdout]    --> src/main.rs:168:9
[INFO] [stdout]     |
[INFO] [stdout] 168 |     let mut tsd_min_len = 100;
[INFO] [stdout]     |         ^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_tsd_min_len`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `human_genome`
[INFO] [stdout]    --> src/main.rs:170:9
[INFO] [stdout]     |
[INFO] [stdout] 170 |     let mut human_genome = &args.human_reference_genome;
[INFO] [stdout]     |         ^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_human_genome`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `human_genome_tophat`
[INFO] [stdout]    --> src/main.rs:171:9
[INFO] [stdout]     |
[INFO] [stdout] 171 |     let mut human_genome_tophat = &args.human_reference_genome;
[INFO] [stdout]     |         ^^^^^^^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_human_genome_tophat`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `genome`
[INFO] [stdout]    --> src/main.rs:173:9
[INFO] [stdout]     |
[INFO] [stdout] 173 |     let mut genome: HashMap<String, String> = HashMap::new();
[INFO] [stdout]     |         ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_genome`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `order` is assigned to, but never used
[INFO] [stdout]    --> src/main.rs:174:9
[INFO] [stdout]     |
[INFO] [stdout] 174 |     let mut order = 0;
[INFO] [stdout]     |         ^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: consider using `_order` instead
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `min_insertsize`
[INFO] [stdout]    --> src/main.rs:175:9
[INFO] [stdout]     |
[INFO] [stdout] 175 |     let min_insertsize = 0;
[INFO] [stdout]     |         ^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_min_insertsize`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `thread_1`
[INFO] [stdout]    --> src/main.rs:176:9
[INFO] [stdout]     |
[INFO] [stdout] 176 |     let thread_1 = args.threads.unwrap() - 1;
[INFO] [stdout]     |         ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_thread_1`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `double_length_insertsize`
[INFO] [stdout]    --> src/main.rs:177:9
[INFO] [stdout]     |
[INFO] [stdout] 177 |     let double_length_insertsize = 0.0f64; // Define the correct type
[INFO] [stdout]     |         ^^^^^^^^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_double_length_insertsize`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `cmd`
[INFO] [stdout]    --> src/main.rs:178:9
[INFO] [stdout]     |
[INFO] [stdout] 178 |     let cmd = String::new(); // You can use String for dynamic strings
[INFO] [stdout]     |         ^^^ help: if this is intentional, prefix it with an underscore: `_cmd`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `bp1_tmp3`
[INFO] [stdout]    --> src/main.rs:179:9
[INFO] [stdout]     |
[INFO] [stdout] 179 |     let mut bp1_tmp3: Vec<String> = Vec::new(); // Define the correct type
[INFO] [stdout]     |         ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_bp1_tmp3`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `header3`
[INFO] [stdout]    --> src/main.rs:180:9
[INFO] [stdout]     |
[INFO] [stdout] 180 |     let header3 = "Sample_ID Is_Split_mode ... Genotype\n".to_string();
[INFO] [stdout]     |         ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_header3`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `order`
[INFO] [stdout]    --> src/main.rs:281:13
[INFO] [stdout]     |
[INFO] [stdout] 281 |         let order = 1;
[INFO] [stdout]     |             ^^^^^ help: if this is intentional, prefix it with an underscore: `_order`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `order`
[INFO] [stdout]    --> src/main.rs:285:17
[INFO] [stdout]     |
[INFO] [stdout] 285 |             let order = 2;
[INFO] [stdout]     |                 ^^^^^ help: if this is intentional, prefix it with an underscore: `_order`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `std_insert_size` is never read
[INFO] [stdout]    --> src/main.rs:117:9
[INFO] [stdout]     |
[INFO] [stdout] 117 |         std_insert_size = args.l_std_insert_size.unwrap();
[INFO] [stdout]     |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout]     = note: `#[warn(unused_assignments)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `order` is never read
[INFO] [stdout]    --> src/main.rs:360:9
[INFO] [stdout]     |
[INFO] [stdout] 360 |         order = 0;
[INFO] [stdout]     |         ^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/main.rs:168:9
[INFO] [stdout]     |
[INFO] [stdout] 168 |     let mut tsd_min_len = 100;
[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/main.rs:169:9
[INFO] [stdout]     |
[INFO] [stdout] 169 |     let mut alignment_score = 30;
[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/main.rs:170:9
[INFO] [stdout]     |
[INFO] [stdout] 170 |     let mut human_genome = &args.human_reference_genome;
[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/main.rs:171:9
[INFO] [stdout]     |
[INFO] [stdout] 171 |     let mut human_genome_tophat = &args.human_reference_genome;
[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/main.rs:173:9
[INFO] [stdout]     |
[INFO] [stdout] 173 |     let mut genome: HashMap<String, String> = HashMap::new();
[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/main.rs:179:9
[INFO] [stdout]     |
[INFO] [stdout] 179 |     let mut bp1_tmp3: Vec<String> = Vec::new(); // Define the correct type
[INFO] [stdout]     |         ----^^^^^^^^
[INFO] [stdout]     |         |
[INFO] [stdout]     |         help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `std_insert_size` is assigned to, but never used
[INFO] [stdout]   --> src/main.rs:99:9
[INFO] [stdout]    |
[INFO] [stdout] 99 |     let mut std_insert_size: f32 = 0.0;
[INFO] [stdout]    |         ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: consider using `_std_insert_size` instead
[INFO] [stdout]    = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `bowtie2_d`
[INFO] [stdout]    --> src/main.rs:107:9
[INFO] [stdout]     |
[INFO] [stdout] 107 |     let bowtie2_d = "";
[INFO] [stdout]     |         ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_bowtie2_d`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `tophat_d`
[INFO] [stdout]    --> src/main.rs:108:9
[INFO] [stdout]     |
[INFO] [stdout] 108 |     let tophat_d = "";
[INFO] [stdout]     |         ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_tophat_d`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `se_mei_d`
[INFO] [stdout]    --> src/main.rs:111:9
[INFO] [stdout]     |
[INFO] [stdout] 111 |     let se_mei_d = "";
[INFO] [stdout]     |         ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_se_mei_d`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `tsd_min_len`
[INFO] [stdout]    --> src/main.rs:168:9
[INFO] [stdout]     |
[INFO] [stdout] 168 |     let mut tsd_min_len = 100;
[INFO] [stdout]     |         ^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_tsd_min_len`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `human_genome`
[INFO] [stdout]    --> src/main.rs:170:9
[INFO] [stdout]     |
[INFO] [stdout] 170 |     let mut human_genome = &args.human_reference_genome;
[INFO] [stdout]     |         ^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_human_genome`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `human_genome_tophat`
[INFO] [stdout]    --> src/main.rs:171:9
[INFO] [stdout]     |
[INFO] [stdout] 171 |     let mut human_genome_tophat = &args.human_reference_genome;
[INFO] [stdout]     |         ^^^^^^^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_human_genome_tophat`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `genome`
[INFO] [stdout]    --> src/main.rs:173:9
[INFO] [stdout]     |
[INFO] [stdout] 173 |     let mut genome: HashMap<String, String> = HashMap::new();
[INFO] [stdout]     |         ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_genome`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `order` is assigned to, but never used
[INFO] [stdout]    --> src/main.rs:174:9
[INFO] [stdout]     |
[INFO] [stdout] 174 |     let mut order = 0;
[INFO] [stdout]     |         ^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: consider using `_order` instead
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `min_insertsize`
[INFO] [stdout]    --> src/main.rs:175:9
[INFO] [stdout]     |
[INFO] [stdout] 175 |     let min_insertsize = 0;
[INFO] [stdout]     |         ^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_min_insertsize`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `thread_1`
[INFO] [stdout]    --> src/main.rs:176:9
[INFO] [stdout]     |
[INFO] [stdout] 176 |     let thread_1 = args.threads.unwrap() - 1;
[INFO] [stdout]     |         ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_thread_1`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `double_length_insertsize`
[INFO] [stdout]    --> src/main.rs:177:9
[INFO] [stdout]     |
[INFO] [stdout] 177 |     let double_length_insertsize = 0.0f64; // Define the correct type
[INFO] [stdout]     |         ^^^^^^^^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_double_length_insertsize`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `cmd`
[INFO] [stdout]    --> src/main.rs:178:9
[INFO] [stdout]     |
[INFO] [stdout] 178 |     let cmd = String::new(); // You can use String for dynamic strings
[INFO] [stdout]     |         ^^^ help: if this is intentional, prefix it with an underscore: `_cmd`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `bp1_tmp3`
[INFO] [stdout]    --> src/main.rs:179:9
[INFO] [stdout]     |
[INFO] [stdout] 179 |     let mut bp1_tmp3: Vec<String> = Vec::new(); // Define the correct type
[INFO] [stdout]     |         ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_bp1_tmp3`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `header3`
[INFO] [stdout]    --> src/main.rs:180:9
[INFO] [stdout]     |
[INFO] [stdout] 180 |     let header3 = "Sample_ID Is_Split_mode ... Genotype\n".to_string();
[INFO] [stdout]     |         ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_header3`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `order`
[INFO] [stdout]    --> src/main.rs:281:13
[INFO] [stdout]     |
[INFO] [stdout] 281 |         let order = 1;
[INFO] [stdout]     |             ^^^^^ help: if this is intentional, prefix it with an underscore: `_order`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `order`
[INFO] [stdout]    --> src/main.rs:285:17
[INFO] [stdout]     |
[INFO] [stdout] 285 |             let order = 2;
[INFO] [stdout]     |                 ^^^^^ help: if this is intentional, prefix it with an underscore: `_order`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `std_insert_size` is never read
[INFO] [stdout]    --> src/main.rs:117:9
[INFO] [stdout]     |
[INFO] [stdout] 117 |         std_insert_size = args.l_std_insert_size.unwrap();
[INFO] [stdout]     |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout]     = note: `#[warn(unused_assignments)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `order` is never read
[INFO] [stdout]    --> src/main.rs:360:9
[INFO] [stdout]     |
[INFO] [stdout] 360 |         order = 0;
[INFO] [stdout]     |         ^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `format`
[INFO] [stdout]    --> src/main.rs:610:16
[INFO] [stdout]     |
[INFO] [stdout] 610 | fn align_to_hg(format: &str, arg: &str) {
[INFO] [stdout]     |                ^^^^^^ help: if this is intentional, prefix it with an underscore: `_format`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `arg`
[INFO] [stdout]    --> src/main.rs:610:30
[INFO] [stdout]     |
[INFO] [stdout] 610 | fn align_to_hg(format: &str, arg: &str) {
[INFO] [stdout]     |                              ^^^ help: if this is intentional, prefix it with an underscore: `_arg`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `input_sample_id`
[INFO] [stdout]    --> src/main.rs:614:23
[INFO] [stdout]     |
[INFO] [stdout] 614 | fn convert_bamtofastq(input_sample_id: &str) {
[INFO] [stdout]     |                       ^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_input_sample_id`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `parse_as_xs` is never used
[INFO] [stdout]    --> src/main.rs:566:4
[INFO] [stdout]     |
[INFO] [stdout] 566 | fn parse_as_xs(line: &str) -> (&str, &str) {
[INFO] [stdout]     |    ^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `format`
[INFO] [stdout]    --> src/main.rs:610:16
[INFO] [stdout]     |
[INFO] [stdout] 610 | fn align_to_hg(format: &str, arg: &str) {
[INFO] [stdout]     |                ^^^^^^ help: if this is intentional, prefix it with an underscore: `_format`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `arg`
[INFO] [stdout]    --> src/main.rs:610:30
[INFO] [stdout]     |
[INFO] [stdout] 610 | fn align_to_hg(format: &str, arg: &str) {
[INFO] [stdout]     |                              ^^^ help: if this is intentional, prefix it with an underscore: `_arg`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `aS` should have a snake case name
[INFO] [stdout]    --> src/main.rs:528:17
[INFO] [stdout]     |
[INFO] [stdout] 528 |         let mut aS = "NA";
[INFO] [stdout]     |                 ^^ help: convert the identifier to snake case: `a_s`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(non_snake_case)]` (part of `#[warn(nonstandard_style)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `aS` should have a snake case name
[INFO] [stdout]    --> src/main.rs:567:13
[INFO] [stdout]     |
[INFO] [stdout] 567 |     let mut aS = "NA";
[INFO] [stdout]     |             ^^ help: convert the identifier to snake case: `a_s`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `input_sample_id`
[INFO] [stdout]    --> src/main.rs:614:23
[INFO] [stdout]     |
[INFO] [stdout] 614 | fn convert_bamtofastq(input_sample_id: &str) {
[INFO] [stdout]     |                       ^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_input_sample_id`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `parse_as_xs` is never used
[INFO] [stdout]    --> src/main.rs:566:4
[INFO] [stdout]     |
[INFO] [stdout] 566 | fn parse_as_xs(line: &str) -> (&str, &str) {
[INFO] [stdout]     |    ^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `aS` should have a snake case name
[INFO] [stdout]    --> src/main.rs:528:17
[INFO] [stdout]     |
[INFO] [stdout] 528 |         let mut aS = "NA";
[INFO] [stdout]     |                 ^^ help: convert the identifier to snake case: `a_s`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(non_snake_case)]` (part of `#[warn(nonstandard_style)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `aS` should have a snake case name
[INFO] [stdout]    --> src/main.rs:567:13
[INFO] [stdout]     |
[INFO] [stdout] 567 |     let mut aS = "NA";
[INFO] [stdout]     |             ^^ help: convert the identifier to snake case: `a_s`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 7.63s
[INFO] running `Command { std: "docker" "inspect" "f6be123b38b4c012b035ef6b23c6848172d04541b972232704df6f6dbb34c31d", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "f6be123b38b4c012b035ef6b23c6848172d04541b972232704df6f6dbb34c31d", kill_on_drop: false }`
[INFO] [stdout] f6be123b38b4c012b035ef6b23c6848172d04541b972232704df6f6dbb34c31d
