[INFO] cloning repository https://github.com/juanfraitu1/Rustle
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/juanfraitu1/Rustle" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fjuanfraitu1%2FRustle", kill_on_drop: false }`
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[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fjuanfraitu1%2FRustle" "/workspace/builds/worker-1-tc1/source", kill_on_drop: false }`
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[INFO] removed 0 missing tests
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[INFO] validating manifest of git repo https://github.com/juanfraitu1/Rustle on toolchain 656ccbe796ff98def9b555c118e1620c5389e3b2
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+656ccbe796ff98def9b555c118e1620c5389e3b2" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate git repo https://github.com/juanfraitu1/Rustle 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" "+656ccbe796ff98def9b555c118e1620c5389e3b2" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
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[INFO] [stdout] warning: unused import: `crate::genome::GenomeIndex`
[INFO] [stdout]    --> src/rustle/vg_family/family_graph.rs:497:5
[INFO] [stdout]     |
[INFO] [stdout] 497 | use crate::genome::GenomeIndex;
[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: `pass1_skeletons`
[INFO] [stdout]   --> src/rustle/vg_family/denovo_pipeline.rs:30:20
[INFO] [stdout]    |
[INFO] [stdout] 30 |     assemble_gate, pass1_skeletons, pass1_skeletons_robust, primary_reads_from_bam, reads_in_region,
[INFO] [stdout]    |                    ^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `noodles_sam::alignment::record::Cigar`
[INFO] [stdout]   --> src/rustle/vg_family/asj_strand_bias.rs:44:5
[INFO] [stdout]    |
[INFO] [stdout] 44 | use noodles_sam::alignment::record::Cigar as _;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `noodles_sam::alignment::record::Cigar`
[INFO] [stdout]   --> src/rustle/vg_family/o2_materialize.rs:39:5
[INFO] [stdout]    |
[INFO] [stdout] 39 | use noodles_sam::alignment::record::Cigar as _;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `t_lap` is never read
[INFO] [stdout]     --> src/rustle/vg_family/denovo_pipeline.rs:1301:17
[INFO] [stdout]      |
[INFO] [stdout] 1301 |                 t_lap = std::time::Instant::now();
[INFO] [stdout]      |                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 1395 |     lap!("conflict-graph + POA homology diagnostic");
[INFO] [stdout]      |     ------------------------------------------------ in this macro invocation
[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]      = note: this warning originates in the macro `lap` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `ps_sideA` should have a snake case name
[INFO] [stdout]    --> src/rustle/vg_family/phasing.rs:388:13
[INFO] [stdout]     |
[INFO] [stdout] 388 |     let mut ps_sideA: HashMap<u32, Vec<u64>> = HashMap::new();
[INFO] [stdout]     |             ^^^^^^^^ help: convert the identifier to snake case: `ps_side_a`
[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 `ps_sideB` should have a snake case name
[INFO] [stdout]    --> src/rustle/vg_family/phasing.rs:389:13
[INFO] [stdout]     |
[INFO] [stdout] 389 |     let mut ps_sideB: HashMap<u32, Vec<u64>> = HashMap::new();
[INFO] [stdout]     |             ^^^^^^^^ help: convert the identifier to snake case: `ps_side_b`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `noodles_sam::alignment::record::Cigar`
[INFO] [stdout]   --> src/rustle/vg_family/asj_strand_bias.rs:44:5
[INFO] [stdout]    |
[INFO] [stdout] 44 | use noodles_sam::alignment::record::Cigar as _;
[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::Cigar`
[INFO] [stdout]   --> src/rustle/vg_family/o2_materialize.rs:39:5
[INFO] [stdout]    |
[INFO] [stdout] 39 | use noodles_sam::alignment::record::Cigar as _;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `t_lap` is never read
[INFO] [stdout]     --> src/rustle/vg_family/denovo_pipeline.rs:1301:17
[INFO] [stdout]      |
[INFO] [stdout] 1301 |                 t_lap = std::time::Instant::now();
[INFO] [stdout]      |                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 1395 |     lap!("conflict-graph + POA homology diagnostic");
[INFO] [stdout]      |     ------------------------------------------------ in this macro invocation
[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]      = note: this warning originates in the macro `lap` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]     --> src/rustle/vg_family/denovo_pipeline.rs:2812:13
[INFO] [stdout]      |
[INFO] [stdout] 2812 |         let mut place = |g: &mut Vec<u8>, base: usize, f1: u64, f2: u64| {
[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/rustle/vg_family/denovo_pipeline.rs:2866:13
[INFO] [stdout]      |
[INFO] [stdout] 2866 |         let mut put = |g: &mut Vec<u8>, at: usize, s: &[u8]| g[at..at + s.len()].copy_from_slice(s);
[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/rustle/vg_family/denovo_pipeline.rs:3506:13
[INFO] [stdout]      |
[INFO] [stdout] 3506 |         let mut put = |g: &mut Vec<u8>, at: usize, s: &[u8]| g[at..at + s.len()].copy_from_slice(s);
[INFO] [stdout]      |             ----^^^
[INFO] [stdout]      |             |
[INFO] [stdout]      |             help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `homolog_cluster` is never used
[INFO] [stdout]     --> src/rustle/vg_family/family_graph.rs:1149:8
[INFO] [stdout]      |
[INFO] [stdout] 1149 |     fn homolog_cluster(ancestor: &[u8], n: usize, snp: f64, indel: f64, ilen: usize,
[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 `make_two_copy_genome_3exon` is never used
[INFO] [stdout]     --> src/rustle/vg_family/family_graph.rs:1691:12
[INFO] [stdout]      |
[INFO] [stdout] 1691 |     pub fn make_two_copy_genome_3exon() -> GenomeIndex {
[INFO] [stdout]      |            ^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `ps_sideA` should have a snake case name
[INFO] [stdout]    --> src/rustle/vg_family/phasing.rs:388:13
[INFO] [stdout]     |
[INFO] [stdout] 388 |     let mut ps_sideA: HashMap<u32, Vec<u64>> = HashMap::new();
[INFO] [stdout]     |             ^^^^^^^^ help: convert the identifier to snake case: `ps_side_a`
[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 `ps_sideB` should have a snake case name
[INFO] [stdout]    --> src/rustle/vg_family/phasing.rs:389:13
[INFO] [stdout]     |
[INFO] [stdout] 389 |     let mut ps_sideB: HashMap<u32, Vec<u64>> = HashMap::new();
[INFO] [stdout]     |             ^^^^^^^^ help: convert the identifier to snake case: `ps_side_b`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 32.92s
[INFO] running `Command { std: "docker" "inspect" "bb2a38669ad120089a501e57bafaeb0945d29e8871ebaa186bc750e7fb58a2f7", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "bb2a38669ad120089a501e57bafaeb0945d29e8871ebaa186bc750e7fb58a2f7", kill_on_drop: false }`
[INFO] [stdout] bb2a38669ad120089a501e57bafaeb0945d29e8871ebaa186bc750e7fb58a2f7
