[INFO] cloning repository https://github.com/yvlaere/OLC_assembler
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/yvlaere/OLC_assembler" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fyvlaere%2FOLC_assembler", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fyvlaere%2FOLC_assembler'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] bcc27e45b638f261a3602d728b077faa69b01c3c
[INFO] checking yvlaere/OLC_assembler against try#a7b168ac4977e8e93a43448b44847adaa305d5a9 for pr-150557
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fyvlaere%2FOLC_assembler" "/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/yvlaere/OLC_assembler
[INFO] finished tweaking git repo https://github.com/yvlaere/OLC_assembler
[INFO] tweaked toml for git repo https://github.com/yvlaere/OLC_assembler written to /workspace/builds/worker-2-tc2/source/Cargo.toml
[INFO] validating manifest of git repo https://github.com/yvlaere/OLC_assembler on toolchain a7b168ac4977e8e93a43448b44847adaa305d5a9
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+a7b168ac4977e8e93a43448b44847adaa305d5a9" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate git repo https://github.com/yvlaere/OLC_assembler 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" "+a7b168ac4977e8e93a43448b44847adaa305d5a9" "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
[ERROR] error running command: no output for 300 seconds
[INFO] checking yvlaere/OLC_assembler against try#a7b168ac4977e8e93a43448b44847adaa305d5a9 for pr-150557
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fyvlaere%2FOLC_assembler" "/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/yvlaere/OLC_assembler
[INFO] finished tweaking git repo https://github.com/yvlaere/OLC_assembler
[INFO] tweaked toml for git repo https://github.com/yvlaere/OLC_assembler written to /workspace/builds/worker-2-tc2/source/Cargo.toml
[INFO] validating manifest of git repo https://github.com/yvlaere/OLC_assembler on toolchain a7b168ac4977e8e93a43448b44847adaa305d5a9
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+a7b168ac4977e8e93a43448b44847adaa305d5a9" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate git repo https://github.com/yvlaere/OLC_assembler 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" "+a7b168ac4977e8e93a43448b44847adaa305d5a9" "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] 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@sha256:98afbf2d16093dec2546ff8915fddc74e65664aa03fc460b3712b1c2c54a33e4" "/opt/rustwide/cargo-home/bin/cargo" "+a7b168ac4977e8e93a43448b44847adaa305d5a9" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] 184d1e49fe47e466b61fd42c252f2df6041f9d1ad6b320a1d34dbfe221e930f5
[INFO] running `Command { std: "docker" "start" "-a" "184d1e49fe47e466b61fd42c252f2df6041f9d1ad6b320a1d34dbfe221e930f5", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "184d1e49fe47e466b61fd42c252f2df6041f9d1ad6b320a1d34dbfe221e930f5", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "184d1e49fe47e466b61fd42c252f2df6041f9d1ad6b320a1d34dbfe221e930f5", kill_on_drop: false }`
[INFO] [stdout] 184d1e49fe47e466b61fd42c252f2df6041f9d1ad6b320a1d34dbfe221e930f5
[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@sha256:98afbf2d16093dec2546ff8915fddc74e65664aa03fc460b3712b1c2c54a33e4" "/opt/rustwide/cargo-home/bin/cargo" "+a7b168ac4977e8e93a43448b44847adaa305d5a9" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 992a80c9330688a3d1883d6d580e479780eb3745fbccd34d338543a88ef9cb94
[INFO] running `Command { std: "docker" "start" "-a" "992a80c9330688a3d1883d6d580e479780eb3745fbccd34d338543a88ef9cb94", kill_on_drop: false }`
[INFO] [stderr]    Compiling proc-macro2 v1.0.104
[INFO] [stderr]    Compiling quote v1.0.42
[INFO] [stderr]    Compiling serde_core v1.0.228
[INFO] [stderr]    Compiling serde v1.0.228
[INFO] [stderr]    Compiling syn v2.0.111
[INFO] [stderr]    Compiling serde_derive v1.0.228
[INFO] [stderr]     Checking bincode v1.3.3
[INFO] [stderr]     Checking OLC_assembler v0.1.0 (/opt/rustwide/workdir)
[INFO] [stdout] warning: unused import: `Write`
[INFO] [stdout]   --> src/alignment_filtering.rs:10:41
[INFO] [stdout]    |
[INFO] [stdout] 10 | use std::io::{self, BufRead, BufReader, Write};
[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::fs::File`
[INFO] [stdout]  --> src/create_overlap_graph.rs:5:5
[INFO] [stdout]   |
[INFO] [stdout] 5 | use std::fs::File;
[INFO] [stdout]   |     ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `Write`
[INFO] [stdout]   --> src/alignment_filtering.rs:10:41
[INFO] [stdout]    |
[INFO] [stdout] 10 | use std::io::{self, BufRead, BufReader, Write};
[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 imports: `BufRead` and `BufReader`
[INFO] [stdout]  --> src/create_overlap_graph.rs:6:15
[INFO] [stdout]   |
[INFO] [stdout] 6 | use std::io::{BufRead, BufReader};
[INFO] [stdout]   |               ^^^^^^^  ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::fs::File`
[INFO] [stdout]  --> src/create_overlap_graph.rs:5:5
[INFO] [stdout]   |
[INFO] [stdout] 5 | use std::fs::File;
[INFO] [stdout]   |     ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `BufRead` and `BufReader`
[INFO] [stdout]  --> src/create_overlap_graph.rs:6:15
[INFO] [stdout]   |
[INFO] [stdout] 6 | use std::io::{BufRead, BufReader};
[INFO] [stdout]   |               ^^^^^^^  ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `max_overhang`
[INFO] [stdout]   --> src/alignment_filtering.rs:99:122
[INFO] [stdout]    |
[INFO] [stdout] 99 | ..., usize), Overlap>, max_overhang: u32, overhang_ratio: f64, reads: &Vec<Read>, min_overlap_length: u32) -> AlignmentType {
[INFO] [stdout]    |                        ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_max_overhang`
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `overlap_len`
[INFO] [stdout]    --> src/alignment_filtering.rs:207:13
[INFO] [stdout]     |
[INFO] [stdout] 207 |         let overlap_len = r.alignment_block_length as u32;
[INFO] [stdout]     |             ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_overlap_len`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `overlap_len`
[INFO] [stdout]    --> src/alignment_filtering.rs:252:13
[INFO] [stdout]     |
[INFO] [stdout] 252 |         let overlap_len = r.alignment_block_length as u32;
[INFO] [stdout]     |             ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_overlap_len`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `max_overhang`
[INFO] [stdout]    --> src/alignment_filtering.rs:281:112
[INFO] [stdout]     |
[INFO] [stdout] 281 | ...ent_identity: &f32, max_overhang: &u32, overhang_ratio: &f64) -> Result<HashMap<(usize, usize), Overlap>, io::Error> {
[INFO] [stdout]     |                        ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_max_overhang`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `alignment_type`
[INFO] [stdout]    --> src/alignment_filtering.rs:443:13
[INFO] [stdout]     |
[INFO] [stdout] 443 | ...   let alignment_type = match classify_alignment(alignment, *query_id, *target_id, &mut overlaps, 4000000000, *overhang_ratio, &...
[INFO] [stdout]     |           ^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_alignment_type`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `max_overhang`
[INFO] [stdout]   --> src/alignment_filtering.rs:99:122
[INFO] [stdout]    |
[INFO] [stdout] 99 | ..., usize), Overlap>, max_overhang: u32, overhang_ratio: f64, reads: &Vec<Read>, min_overlap_length: u32) -> AlignmentType {
[INFO] [stdout]    |                        ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_max_overhang`
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `overlap_len`
[INFO] [stdout]    --> src/alignment_filtering.rs:207:13
[INFO] [stdout]     |
[INFO] [stdout] 207 |         let overlap_len = r.alignment_block_length as u32;
[INFO] [stdout]     |             ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_overlap_len`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `overlap_len`
[INFO] [stdout]    --> src/alignment_filtering.rs:252:13
[INFO] [stdout]     |
[INFO] [stdout] 252 |         let overlap_len = r.alignment_block_length as u32;
[INFO] [stdout]     |             ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_overlap_len`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `max_overhang`
[INFO] [stdout]   --> src/filter_paf.rs:57:127
[INFO] [stdout]    |
[INFO] [stdout] 57 | ...ent_identity: &f32, max_overhang: &u32, overhang_ratio: &f64) -> io::Result<()> {
[INFO] [stdout]    |                        ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_max_overhang`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `overhang_ratio`
[INFO] [stdout]   --> src/filter_paf.rs:57:147
[INFO] [stdout]    |
[INFO] [stdout] 57 | ...x_overhang: &u32, overhang_ratio: &f64) -> io::Result<()> {
[INFO] [stdout]    |                      ^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_overhang_ratio`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `max_overhang`
[INFO] [stdout]    --> src/alignment_filtering.rs:281:112
[INFO] [stdout]     |
[INFO] [stdout] 281 | ...ent_identity: &f32, max_overhang: &u32, overhang_ratio: &f64) -> Result<HashMap<(usize, usize), Overlap>, io::Error> {
[INFO] [stdout]     |                        ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_max_overhang`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `alignment_type`
[INFO] [stdout]    --> src/alignment_filtering.rs:443:13
[INFO] [stdout]     |
[INFO] [stdout] 443 | ...   let alignment_type = match classify_alignment(alignment, *query_id, *target_id, &mut overlaps, 4000000000, *overhang_ratio, &...
[INFO] [stdout]     |           ^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_alignment_type`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `max_overhang`
[INFO] [stdout]   --> src/filter_paf.rs:57:127
[INFO] [stdout]    |
[INFO] [stdout] 57 | ...ent_identity: &f32, max_overhang: &u32, overhang_ratio: &f64) -> io::Result<()> {
[INFO] [stdout]    |                        ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_max_overhang`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `overhang_ratio`
[INFO] [stdout]   --> src/filter_paf.rs:57:147
[INFO] [stdout]    |
[INFO] [stdout] 57 | ...x_overhang: &u32, overhang_ratio: &f64) -> io::Result<()> {
[INFO] [stdout]    |                      ^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_overhang_ratio`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `source_id`
[INFO] [stdout]   --> src/compress_graph.rs:43:10
[INFO] [stdout]    |
[INFO] [stdout] 43 |     for (source_id, node) in &graph.nodes {
[INFO] [stdout]    |          ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_source_id`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `node`
[INFO] [stdout]    --> src/compress_graph.rs:239:17
[INFO] [stdout]     |
[INFO] [stdout] 239 |             let node = graph.nodes.get(node_id)
[INFO] [stdout]     |                 ^^^^ help: if this is intentional, prefix it with an underscore: `_node`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `n` is never read
[INFO] [stdout]    --> src/tip_trimming.rs:100:9
[INFO] [stdout]     |
[INFO] [stdout] 100 |         n = next;
[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: unused variable: `next`
[INFO] [stdout]    --> src/tip_trimming.rs:121:24
[INFO] [stdout]     |
[INFO] [stdout] 121 |         let (tip_type, next) = node_classification(graph, &n);
[INFO] [stdout]     |                        ^^^^ help: if this is intentional, prefix it with an underscore: `_next`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `source_id`
[INFO] [stdout]   --> src/compress_graph.rs:43:10
[INFO] [stdout]    |
[INFO] [stdout] 43 |     for (source_id, node) in &graph.nodes {
[INFO] [stdout]    |          ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_source_id`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `node`
[INFO] [stdout]    --> src/compress_graph.rs:239:17
[INFO] [stdout]     |
[INFO] [stdout] 239 |             let node = graph.nodes.get(node_id)
[INFO] [stdout]     |                 ^^^^ help: if this is intentional, prefix it with an underscore: `_node`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `n` is never read
[INFO] [stdout]    --> src/tip_trimming.rs:100:9
[INFO] [stdout]     |
[INFO] [stdout] 100 |         n = next;
[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: unused variable: `next`
[INFO] [stdout]    --> src/tip_trimming.rs:121:24
[INFO] [stdout]     |
[INFO] [stdout] 121 |         let (tip_type, next) = node_classification(graph, &n);
[INFO] [stdout]     |                        ^^^^ help: if this is intentional, prefix it with an underscore: `_next`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `min_overlap_length`
[INFO] [stdout]   --> src/main.rs:37:9
[INFO] [stdout]    |
[INFO] [stdout] 37 |     let min_overlap_length: u32 = 2000;
[INFO] [stdout]    |         ^^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_min_overlap_length`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `min_overlap_count`
[INFO] [stdout]   --> src/main.rs:38:9
[INFO] [stdout]    |
[INFO] [stdout] 38 |     let min_overlap_count: u32 = 3;
[INFO] [stdout]    |         ^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_min_overlap_count`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `min_percent_identity`
[INFO] [stdout]   --> src/main.rs:39:9
[INFO] [stdout]    |
[INFO] [stdout] 39 |     let min_percent_identity: f32 = 5.0; // 100/2000 = 5%
[INFO] [stdout]    |         ^^^^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_min_percent_identity`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `max_overhang`
[INFO] [stdout]   --> src/main.rs:40:9
[INFO] [stdout]    |
[INFO] [stdout] 40 |     let max_overhang = 0;
[INFO] [stdout]    |         ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_max_overhang`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `overhang_ratio`
[INFO] [stdout]   --> src/main.rs:41:9
[INFO] [stdout]    |
[INFO] [stdout] 41 |     let overhang_ratio = 0.8;
[INFO] [stdout]    |         ^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_overhang_ratio`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `prev_node_count` is assigned to, but never used
[INFO] [stdout]   --> src/main.rs:69:9
[INFO] [stdout]    |
[INFO] [stdout] 69 |     let mut prev_node_count = graph.nodes.len() + 1;  // Ensure first iteration runs
[INFO] [stdout]    |         ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: consider using `_prev_node_count` instead
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `i`
[INFO] [stdout]   --> src/main.rs:71:9
[INFO] [stdout]    |
[INFO] [stdout] 71 |     for i in 0..10 {
[INFO] [stdout]    |         ^ help: if this is intentional, prefix it with an underscore: `_i`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `prev_node_count` is never read
[INFO] [stdout]   --> src/main.rs:72:9
[INFO] [stdout]    |
[INFO] [stdout] 72 |         prev_node_count = graph.nodes.len();
[INFO] [stdout]    |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `Read` is never constructed
[INFO] [stdout]   --> src/alignment_filtering.rs:17:8
[INFO] [stdout]    |
[INFO] [stdout] 17 | struct Read {
[INFO] [stdout]    |        ^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `Alignment` is never constructed
[INFO] [stdout]   --> src/alignment_filtering.rs:28:8
[INFO] [stdout]    |
[INFO] [stdout] 28 | struct Alignment {
[INFO] [stdout]    |        ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: enum `AlignmentType` is never used
[INFO] [stdout]   --> src/alignment_filtering.rs:59:6
[INFO] [stdout]    |
[INFO] [stdout] 59 | enum AlignmentType {
[INFO] [stdout]    |      ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: associated items `from_line`, `is_self_alignment`, and `percent_identity` are never used
[INFO] [stdout]   --> src/alignment_filtering.rs:69:8
[INFO] [stdout]    |
[INFO] [stdout] 68 | impl Alignment {
[INFO] [stdout]    | -------------- associated items in this implementation
[INFO] [stdout] 69 |     fn from_line(line: &str) -> Option<Self> {
[INFO] [stdout]    |        ^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 89 |     fn is_self_alignment(&self) -> bool {
[INFO] [stdout]    |        ^^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 93 |     fn percent_identity(&self) -> f32 {
[INFO] [stdout]    |        ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `classify_alignment` is never used
[INFO] [stdout]   --> src/alignment_filtering.rs:99:4
[INFO] [stdout]    |
[INFO] [stdout] 99 | fn classify_alignment(r: &Alignment, query_id: usize, target_id: usize, overlaps: &mut HashMap<(usize, usize), Overlap>, max_overhan...
[INFO] [stdout]    |    ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `filter_paf` is never used
[INFO] [stdout]    --> src/alignment_filtering.rs:281:8
[INFO] [stdout]     |
[INFO] [stdout] 281 | pub fn filter_paf(paf_in: &str, min_overlap_length: &u32, min_overlap_count: &u32, min_percent_identity: &f32, max_overhang: &u32, ...
[INFO] [stdout]     |        ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `PafRecord` is never constructed
[INFO] [stdout]   --> src/filter_paf.rs:12:8
[INFO] [stdout]    |
[INFO] [stdout] 12 | struct PafRecord {
[INFO] [stdout]    |        ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: associated items `from_line`, `is_self_alignment`, and `percent_identity` are never used
[INFO] [stdout]   --> src/filter_paf.rs:28:8
[INFO] [stdout]    |
[INFO] [stdout] 27 | impl PafRecord {
[INFO] [stdout]    | -------------- associated items in this implementation
[INFO] [stdout] 28 |     fn from_line(line: &str) -> Option<Self> {
[INFO] [stdout]    |        ^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 47 |     fn is_self_alignment(&self) -> bool {
[INFO] [stdout]    |        ^^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 51 |     fn percent_identity(&self) -> f32 {
[INFO] [stdout]    |        ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `filter_paf` is never used
[INFO] [stdout]   --> src/filter_paf.rs:57:8
[INFO] [stdout]    |
[INFO] [stdout] 57 | pub fn filter_paf(paf_in: &str, paf_out: &str, min_overlap_length: &u32, min_overlap_count: &u32, min_percent_identity: &f32, max_ov...
[INFO] [stdout]    |        ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `component_sizes_sorted` is never used
[INFO] [stdout]   --> src/graph_analysis.rs:93:8
[INFO] [stdout]    |
[INFO] [stdout] 93 | pub fn component_sizes_sorted(graph: &OverlapGraph) -> Vec<usize> {
[INFO] [stdout]    |        ^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `compressible_node_stats` is never used
[INFO] [stdout]    --> src/graph_analysis.rs:128:8
[INFO] [stdout]     |
[INFO] [stdout] 128 | pub fn compressible_node_stats(graph: &OverlapGraph) -> (usize, usize, f64) {
[INFO] [stdout]     |        ^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `tip_length_distribution` is never used
[INFO] [stdout]    --> src/graph_analysis.rs:155:8
[INFO] [stdout]     |
[INFO] [stdout] 155 | pub fn tip_length_distribution(graph: &OverlapGraph, max_walk: usize) -> Vec<usize> {
[INFO] [stdout]     |        ^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `branching_summary` is never used
[INFO] [stdout]    --> src/graph_analysis.rs:207:8
[INFO] [stdout]     |
[INFO] [stdout] 207 | pub fn branching_summary(graph: &OverlapGraph, top_k: usize) -> Vec<(String, usize, usize)> {
[INFO] [stdout]     |        ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `N50` should have a snake case name
[INFO] [stdout]    --> src/main.rs:158:9
[INFO] [stdout]     |
[INFO] [stdout] 158 |     let N50 = {
[INFO] [stdout]     |         ^^^ help: convert the identifier to snake case: `n50`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(non_snake_case)]` (part of `#[warn(nonstandard_style)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: using `.clone()` on a double reference, which returns `&std::string::String` instead of cloning the inner type
[INFO] [stdout]    --> src/bubble_removal.rs:155:40
[INFO] [stdout]     |
[INFO] [stdout] 155 |                     meetings.push((node.clone(), d));
[INFO] [stdout]     |                                        ^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(suspicious_double_ref_op)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `min_overlap_length`
[INFO] [stdout]   --> src/main.rs:37:9
[INFO] [stdout]    |
[INFO] [stdout] 37 |     let min_overlap_length: u32 = 2000;
[INFO] [stdout]    |         ^^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_min_overlap_length`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `min_overlap_count`
[INFO] [stdout]   --> src/main.rs:38:9
[INFO] [stdout]    |
[INFO] [stdout] 38 |     let min_overlap_count: u32 = 3;
[INFO] [stdout]    |         ^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_min_overlap_count`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `min_percent_identity`
[INFO] [stdout]   --> src/main.rs:39:9
[INFO] [stdout]    |
[INFO] [stdout] 39 |     let min_percent_identity: f32 = 5.0; // 100/2000 = 5%
[INFO] [stdout]    |         ^^^^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_min_percent_identity`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `max_overhang`
[INFO] [stdout]   --> src/main.rs:40:9
[INFO] [stdout]    |
[INFO] [stdout] 40 |     let max_overhang = 0;
[INFO] [stdout]    |         ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_max_overhang`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `overhang_ratio`
[INFO] [stdout]   --> src/main.rs:41:9
[INFO] [stdout]    |
[INFO] [stdout] 41 |     let overhang_ratio = 0.8;
[INFO] [stdout]    |         ^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_overhang_ratio`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `prev_node_count` is assigned to, but never used
[INFO] [stdout]   --> src/main.rs:69:9
[INFO] [stdout]    |
[INFO] [stdout] 69 |     let mut prev_node_count = graph.nodes.len() + 1;  // Ensure first iteration runs
[INFO] [stdout]    |         ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: consider using `_prev_node_count` instead
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `i`
[INFO] [stdout]   --> src/main.rs:71:9
[INFO] [stdout]    |
[INFO] [stdout] 71 |     for i in 0..10 {
[INFO] [stdout]    |         ^ help: if this is intentional, prefix it with an underscore: `_i`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `prev_node_count` is never read
[INFO] [stdout]   --> src/main.rs:72:9
[INFO] [stdout]    |
[INFO] [stdout] 72 |         prev_node_count = graph.nodes.len();
[INFO] [stdout]    |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `Read` is never constructed
[INFO] [stdout]   --> src/alignment_filtering.rs:17:8
[INFO] [stdout]    |
[INFO] [stdout] 17 | struct Read {
[INFO] [stdout]    |        ^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `Alignment` is never constructed
[INFO] [stdout]   --> src/alignment_filtering.rs:28:8
[INFO] [stdout]    |
[INFO] [stdout] 28 | struct Alignment {
[INFO] [stdout]    |        ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: enum `AlignmentType` is never used
[INFO] [stdout]   --> src/alignment_filtering.rs:59:6
[INFO] [stdout]    |
[INFO] [stdout] 59 | enum AlignmentType {
[INFO] [stdout]    |      ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: associated items `from_line`, `is_self_alignment`, and `percent_identity` are never used
[INFO] [stdout]   --> src/alignment_filtering.rs:69:8
[INFO] [stdout]    |
[INFO] [stdout] 68 | impl Alignment {
[INFO] [stdout]    | -------------- associated items in this implementation
[INFO] [stdout] 69 |     fn from_line(line: &str) -> Option<Self> {
[INFO] [stdout]    |        ^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 89 |     fn is_self_alignment(&self) -> bool {
[INFO] [stdout]    |        ^^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 93 |     fn percent_identity(&self) -> f32 {
[INFO] [stdout]    |        ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `classify_alignment` is never used
[INFO] [stdout]   --> src/alignment_filtering.rs:99:4
[INFO] [stdout]    |
[INFO] [stdout] 99 | fn classify_alignment(r: &Alignment, query_id: usize, target_id: usize, overlaps: &mut HashMap<(usize, usize), Overlap>, max_overhan...
[INFO] [stdout]    |    ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `filter_paf` is never used
[INFO] [stdout]    --> src/alignment_filtering.rs:281:8
[INFO] [stdout]     |
[INFO] [stdout] 281 | pub fn filter_paf(paf_in: &str, min_overlap_length: &u32, min_overlap_count: &u32, min_percent_identity: &f32, max_overhang: &u32, ...
[INFO] [stdout]     |        ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `PafRecord` is never constructed
[INFO] [stdout]   --> src/filter_paf.rs:12:8
[INFO] [stdout]    |
[INFO] [stdout] 12 | struct PafRecord {
[INFO] [stdout]    |        ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: associated items `from_line`, `is_self_alignment`, and `percent_identity` are never used
[INFO] [stdout]   --> src/filter_paf.rs:28:8
[INFO] [stdout]    |
[INFO] [stdout] 27 | impl PafRecord {
[INFO] [stdout]    | -------------- associated items in this implementation
[INFO] [stdout] 28 |     fn from_line(line: &str) -> Option<Self> {
[INFO] [stdout]    |        ^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 47 |     fn is_self_alignment(&self) -> bool {
[INFO] [stdout]    |        ^^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 51 |     fn percent_identity(&self) -> f32 {
[INFO] [stdout]    |        ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `filter_paf` is never used
[INFO] [stdout]   --> src/filter_paf.rs:57:8
[INFO] [stdout]    |
[INFO] [stdout] 57 | pub fn filter_paf(paf_in: &str, paf_out: &str, min_overlap_length: &u32, min_overlap_count: &u32, min_percent_identity: &f32, max_ov...
[INFO] [stdout]    |        ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `component_sizes_sorted` is never used
[INFO] [stdout]   --> src/graph_analysis.rs:93:8
[INFO] [stdout]    |
[INFO] [stdout] 93 | pub fn component_sizes_sorted(graph: &OverlapGraph) -> Vec<usize> {
[INFO] [stdout]    |        ^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `compressible_node_stats` is never used
[INFO] [stdout]    --> src/graph_analysis.rs:128:8
[INFO] [stdout]     |
[INFO] [stdout] 128 | pub fn compressible_node_stats(graph: &OverlapGraph) -> (usize, usize, f64) {
[INFO] [stdout]     |        ^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `tip_length_distribution` is never used
[INFO] [stdout]    --> src/graph_analysis.rs:155:8
[INFO] [stdout]     |
[INFO] [stdout] 155 | pub fn tip_length_distribution(graph: &OverlapGraph, max_walk: usize) -> Vec<usize> {
[INFO] [stdout]     |        ^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `branching_summary` is never used
[INFO] [stdout]    --> src/graph_analysis.rs:207:8
[INFO] [stdout]     |
[INFO] [stdout] 207 | pub fn branching_summary(graph: &OverlapGraph, top_k: usize) -> Vec<(String, usize, usize)> {
[INFO] [stdout]     |        ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `N50` should have a snake case name
[INFO] [stdout]    --> src/main.rs:158:9
[INFO] [stdout]     |
[INFO] [stdout] 158 |     let N50 = {
[INFO] [stdout]     |         ^^^ help: convert the identifier to snake case: `n50`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(non_snake_case)]` (part of `#[warn(nonstandard_style)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: using `.clone()` on a double reference, which returns `&std::string::String` instead of cloning the inner type
[INFO] [stdout]    --> src/bubble_removal.rs:155:40
[INFO] [stdout]     |
[INFO] [stdout] 155 |                     meetings.push((node.clone(), d));
[INFO] [stdout]     |                                        ^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(suspicious_double_ref_op)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 7.77s
[INFO] running `Command { std: "docker" "inspect" "992a80c9330688a3d1883d6d580e479780eb3745fbccd34d338543a88ef9cb94", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "992a80c9330688a3d1883d6d580e479780eb3745fbccd34d338543a88ef9cb94", kill_on_drop: false }`
[INFO] [stdout] 992a80c9330688a3d1883d6d580e479780eb3745fbccd34d338543a88ef9cb94