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[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/xiexm1/kmertk" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fxiexm1%2Fkmertk", kill_on_drop: false }`
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[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] 4cb1394d7cb2ae73a2ba6b639a6cac12ede4ac34
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[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fxiexm1%2Fkmertk" "/workspace/builds/worker-7-tc2/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-7-tc2/source'...
[INFO] [stderr] done.
[INFO] started tweaking git repo https://github.com/xiexm1/kmertk
[INFO] finished tweaking git repo https://github.com/xiexm1/kmertk
[INFO] tweaked toml for git repo https://github.com/xiexm1/kmertk written to /workspace/builds/worker-7-tc2/source/Cargo.toml
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[INFO] [stdout] warning: unused import: `rand::seq::SliceRandom`
[INFO] [stdout]  --> src/modules/distance.rs:5:5
[INFO] [stdout]   |
[INFO] [stdout] 5 | use rand::seq::SliceRandom;
[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: `crate::utils::read_kmers`
[INFO] [stdout]   --> src/modules/miniset.rs:11:5
[INFO] [stdout]    |
[INFO] [stdout] 11 | use crate::utils::read_kmers;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `parse_fasta`
[INFO] [stdout]  --> src/modules/collection.rs:9:32
[INFO] [stdout]   |
[INFO] [stdout] 9 | use crate::utils::{read_kmers, parse_fasta, fasta_to_map};
[INFO] [stdout]   |                                ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `rand::seq::SliceRandom`
[INFO] [stdout]  --> src/modules/distance.rs:5:5
[INFO] [stdout]   |
[INFO] [stdout] 5 | use rand::seq::SliceRandom;
[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: `crate::utils::read_kmers`
[INFO] [stdout]   --> src/modules/miniset.rs:11:5
[INFO] [stdout]    |
[INFO] [stdout] 11 | use crate::utils::read_kmers;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `parse_fasta`
[INFO] [stdout]  --> src/modules/collection.rs:9:32
[INFO] [stdout]   |
[INFO] [stdout] 9 | use crate::utils::{read_kmers, parse_fasta, fasta_to_map};
[INFO] [stdout]   |                                ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `text`
[INFO] [stdout]    --> src/modules/collection.rs:157:22
[INFO] [stdout]     |
[INFO] [stdout] 157 | fn find_crispr_match(text: &[u8], pattern: &[u8]) -> bool {
[INFO] [stdout]     |                      ^^^^ help: if this is intentional, prefix it with an underscore: `_text`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `count_sequences` is never used
[INFO] [stdout]   --> src/utils/fasta.rs:55:8
[INFO] [stdout]    |
[INFO] [stdout] 55 | pub fn count_sequences<P: AsRef<Path>>(file_path: P) -> io::Result<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: field `gene_hits` is never read
[INFO] [stdout]   --> src/modules/miniset.rs:41:5
[INFO] [stdout]    |
[INFO] [stdout] 37 | struct Data {
[INFO] [stdout]    |        ---- field in this struct
[INFO] [stdout] ...
[INFO] [stdout] 41 |     gene_hits: Vec<usize>,        // 记录每个基因被多少k-mer覆盖
[INFO] [stdout]    |     ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: fields `flag`, `position`, `cigar`, and `sequence` are never read
[INFO] [stdout]   --> src/modules/collection.rs:81:5
[INFO] [stdout]    |
[INFO] [stdout] 79 | struct SamAlignment {
[INFO] [stdout]    |        ------------ fields in this struct
[INFO] [stdout] 80 |     query_id: String,
[INFO] [stdout] 81 |     flag: u16,
[INFO] [stdout]    |     ^^^^
[INFO] [stdout] 82 |     ref_id: String,
[INFO] [stdout] 83 |     position: usize,
[INFO] [stdout]    |     ^^^^^^^^
[INFO] [stdout] 84 |     cigar: String,
[INFO] [stdout]    |     ^^^^^
[INFO] [stdout] 85 |     sequence: String,
[INFO] [stdout]    |     ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: method `count_indels` is never used
[INFO] [stdout]   --> src/modules/collection.rs:91:8
[INFO] [stdout]    |
[INFO] [stdout] 89 | impl SamAlignment {
[INFO] [stdout]    | ----------------- method in this implementation
[INFO] [stdout] 90 |     // 计算插入删除数量
[INFO] [stdout] 91 |     fn count_indels(&self) -> usize {
[INFO] [stdout]    |        ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: fields `strand`, `position`, `sequence`, and `mismatches` are never read
[INFO] [stdout]    --> src/modules/collection.rs:121:5
[INFO] [stdout]     |
[INFO] [stdout] 119 | struct BowtieAlignment {
[INFO] [stdout]     |        --------------- fields in this struct
[INFO] [stdout] 120 |     query_id: String,
[INFO] [stdout] 121 |     strand: char,
[INFO] [stdout]     |     ^^^^^^
[INFO] [stdout] 122 |     ref_id: String,
[INFO] [stdout] 123 |     position: usize,
[INFO] [stdout]     |     ^^^^^^^^
[INFO] [stdout] 124 |     sequence: String,
[INFO] [stdout]     |     ^^^^^^^^
[INFO] [stdout] 125 |     mismatches: Vec<(usize, char, char)>, // 位置，参考碱基，查询碱基
[INFO] [stdout]     |     ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `text`
[INFO] [stdout]    --> src/modules/collection.rs:157:22
[INFO] [stdout]     |
[INFO] [stdout] 157 | fn find_crispr_match(text: &[u8], pattern: &[u8]) -> bool {
[INFO] [stdout]     |                      ^^^^ help: if this is intentional, prefix it with an underscore: `_text`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `count_sequences` is never used
[INFO] [stdout]   --> src/utils/fasta.rs:55:8
[INFO] [stdout]    |
[INFO] [stdout] 55 | pub fn count_sequences<P: AsRef<Path>>(file_path: P) -> io::Result<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: field `gene_hits` is never read
[INFO] [stdout]   --> src/modules/miniset.rs:41:5
[INFO] [stdout]    |
[INFO] [stdout] 37 | struct Data {
[INFO] [stdout]    |        ---- field in this struct
[INFO] [stdout] ...
[INFO] [stdout] 41 |     gene_hits: Vec<usize>,        // 记录每个基因被多少k-mer覆盖
[INFO] [stdout]    |     ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: fields `flag`, `position`, `cigar`, and `sequence` are never read
[INFO] [stdout]   --> src/modules/collection.rs:81:5
[INFO] [stdout]    |
[INFO] [stdout] 79 | struct SamAlignment {
[INFO] [stdout]    |        ------------ fields in this struct
[INFO] [stdout] 80 |     query_id: String,
[INFO] [stdout] 81 |     flag: u16,
[INFO] [stdout]    |     ^^^^
[INFO] [stdout] 82 |     ref_id: String,
[INFO] [stdout] 83 |     position: usize,
[INFO] [stdout]    |     ^^^^^^^^
[INFO] [stdout] 84 |     cigar: String,
[INFO] [stdout]    |     ^^^^^
[INFO] [stdout] 85 |     sequence: String,
[INFO] [stdout]    |     ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: method `count_indels` is never used
[INFO] [stdout]   --> src/modules/collection.rs:91:8
[INFO] [stdout]    |
[INFO] [stdout] 89 | impl SamAlignment {
[INFO] [stdout]    | ----------------- method in this implementation
[INFO] [stdout] 90 |     // 计算插入删除数量
[INFO] [stdout] 91 |     fn count_indels(&self) -> usize {
[INFO] [stdout]    |        ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: fields `strand`, `position`, `sequence`, and `mismatches` are never read
[INFO] [stdout]    --> src/modules/collection.rs:121:5
[INFO] [stdout]     |
[INFO] [stdout] 119 | struct BowtieAlignment {
[INFO] [stdout]     |        --------------- fields in this struct
[INFO] [stdout] 120 |     query_id: String,
[INFO] [stdout] 121 |     strand: char,
[INFO] [stdout]     |     ^^^^^^
[INFO] [stdout] 122 |     ref_id: String,
[INFO] [stdout] 123 |     position: usize,
[INFO] [stdout]     |     ^^^^^^^^
[INFO] [stdout] 124 |     sequence: String,
[INFO] [stdout]     |     ^^^^^^^^
[INFO] [stdout] 125 |     mismatches: Vec<(usize, char, char)>, // 位置，参考碱基，查询碱基
[INFO] [stdout]     |     ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 49.58s
[INFO] running `Command { std: "docker" "inspect" "254f31df97a01ad2dca6c22e745c47659433068d4898932d5f70ccb7c5b23429", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "254f31df97a01ad2dca6c22e745c47659433068d4898932d5f70ccb7c5b23429", kill_on_drop: false }`
[INFO] [stdout] 254f31df97a01ad2dca6c22e745c47659433068d4898932d5f70ccb7c5b23429
