Dec 06 08:54:37.171 INFO testing TuBieJun/consensus against try#6eb0fd3ac58f9b16bddb9924a17c3b6c156aa468 for pr-56514
Dec 06 08:54:37.171 INFO running `"docker" "create" "-v" "/mnt/big/crater/work/local/target-dirs/pr-56514/worker-2/try#6eb0fd3ac58f9b16bddb9924a17c3b6c156aa468:/target:rw,Z" "-v" "/mnt/big/crater/work/local/test-source/worker-2/pr-56514/try#6eb0fd3ac58f9b16bddb9924a17c3b6c156aa468:/source:ro,Z" "-v" "/mnt/big/crater/work/local/cargo-home:/cargo-home:ro,Z" "-v" "/mnt/big/crater/work/local/rustup-home:/rustup-home:ro,Z" "-e" "USER_ID=1000" "-e" "SOURCE_DIR=/source" "-e" "USER_ID=1000" "-e" "CMD=cargo +6eb0fd3ac58f9b16bddb9924a17c3b6c156aa468-alt build --frozen" "-e" "CARGO_TARGET_DIR=/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/cargo-home" "-e" "RUSTUP_HOME=/rustup-home" "-m" "1536M" "--network" "none" "crater"`
Dec 06 08:54:37.675 INFO [stdout] f2c738c9c0ffffe541b1e88166bd34c8bf88b7595492c9201048637adfd14225
Dec 06 08:54:37.678 INFO running `"docker" "start" "-a" "f2c738c9c0ffffe541b1e88166bd34c8bf88b7595492c9201048637adfd14225"`
Dec 06 08:54:40.068 INFO [stderr] usermod: no changes
Dec 06 08:54:40.240 INFO [stderr]    Compiling fs-utils v1.0.0
Dec 06 08:54:40.240 INFO [stderr]    Compiling itertools v0.6.5
Dec 06 08:54:41.641 INFO [stderr]    Compiling rust-htslib v0.15.0
Dec 06 08:55:13.718 INFO [stderr]    Compiling consensus v0.1.0 (/source)
Dec 06 08:55:15.188 INFO [stderr] warning: unused import: `std::env`
Dec 06 08:55:15.189 INFO [stderr]   --> src/main.rs:12:5
Dec 06 08:55:15.189 INFO [stderr]    |
Dec 06 08:55:15.189 INFO [stderr] 12 | use std::env;
Dec 06 08:55:15.189 INFO [stderr]    |     ^^^^^^^^
Dec 06 08:55:15.190 INFO [stderr]    |
Dec 06 08:55:15.190 INFO [stderr]    = note: #[warn(unused_imports)] on by default
Dec 06 08:55:15.190 INFO [stderr] 
Dec 06 08:55:15.190 INFO [stderr] warning: unused import: `rust_htslib::prelude::*`
Dec 06 08:55:15.191 INFO [stderr]   --> src/main.rs:16:5
Dec 06 08:55:15.191 INFO [stderr]    |
Dec 06 08:55:15.191 INFO [stderr] 16 | use rust_htslib::prelude::*;
Dec 06 08:55:15.191 INFO [stderr]    |     ^^^^^^^^^^^^^^^^^^^^^^^
Dec 06 08:55:15.191 INFO [stderr] 
Dec 06 08:55:15.192 INFO [stderr] warning: unused import: `std::io`
Dec 06 08:55:15.192 INFO [stderr]   --> src/main.rs:21:5
Dec 06 08:55:15.192 INFO [stderr]    |
Dec 06 08:55:15.192 INFO [stderr] 21 | use std::io;
Dec 06 08:55:15.193 INFO [stderr]    |     ^^^^^^^
Dec 06 08:55:15.193 INFO [stderr] 
Dec 06 08:55:15.193 INFO [stderr] warning: unused import: `PathBuf`
Dec 06 08:55:15.193 INFO [stderr]   --> src/main.rs:25:23
Dec 06 08:55:15.194 INFO [stderr]    |
Dec 06 08:55:15.194 INFO [stderr] 25 | use std::path::{Path, PathBuf};
Dec 06 08:55:15.194 INFO [stderr]    |                       ^^^^^^^
Dec 06 08:55:15.195 INFO [stderr] 
Dec 06 08:55:15.195 INFO [stderr] warning: unused import: `SubCommand`
Dec 06 08:55:15.195 INFO [stderr]   --> src/main.rs:26:22
Dec 06 08:55:15.195 INFO [stderr]    |
Dec 06 08:55:15.196 INFO [stderr] 26 | use clap::{Arg, App, SubCommand};
Dec 06 08:55:15.196 INFO [stderr]    |                      ^^^^^^^^^^
Dec 06 08:55:15.196 INFO [stderr] 
Dec 06 08:55:15.196 INFO [stderr] warning: unnecessary parentheses around `if` condition
Dec 06 08:55:15.197 INFO [stderr]    --> src/main.rs:218:20
Dec 06 08:55:15.197 INFO [stderr]     |
Dec 06 08:55:15.197 INFO [stderr] 218 |                 if (num_position[&(i as usize)] == num_position[&(0 as usize)]) {
Dec 06 08:55:15.198 INFO [stderr]     |                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses
Dec 06 08:55:15.198 INFO [stderr]     |
Dec 06 08:55:15.198 INFO [stderr]     = note: #[warn(unused_parens)] on by default
Dec 06 08:55:15.198 INFO [stderr] 
Dec 06 08:55:15.199 INFO [stderr] warning: unnecessary parentheses around `if` condition
Dec 06 08:55:15.199 INFO [stderr]    --> src/main.rs:239:16
Dec 06 08:55:15.199 INFO [stderr]     |
Dec 06 08:55:15.199 INFO [stderr] 239 |             if (baseEach_percent_record.len() > 0) {
Dec 06 08:55:15.200 INFO [stderr]     |                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses
Dec 06 08:55:15.200 INFO [stderr] 
Dec 06 08:55:15.376 INFO [stderr] warning: unused import: `std::io::prelude`
Dec 06 08:55:15.377 INFO [stderr]   --> src/main.rs:22:5
Dec 06 08:55:15.377 INFO [stderr]    |
Dec 06 08:55:15.377 INFO [stderr] 22 | use std::io::prelude::*;
Dec 06 08:55:15.378 INFO [stderr]    |     ^^^^^^^^^^^^^^^^
Dec 06 08:55:15.378 INFO [stderr] 
Dec 06 08:55:15.388 INFO [stderr] warning: unused variable: `consensus_base`
Dec 06 08:55:15.389 INFO [stderr]    --> src/main.rs:139:9
Dec 06 08:55:15.389 INFO [stderr]     |
Dec 06 08:55:15.389 INFO [stderr] 139 |     let consensus_base:Vec<u8> = Vec::new();
Dec 06 08:55:15.390 INFO [stderr]     |         ^^^^^^^^^^^^^^ help: consider using `_consensus_base` instead
Dec 06 08:55:15.390 INFO [stderr]     |
Dec 06 08:55:15.390 INFO [stderr]     = note: #[warn(unused_variables)] on by default
Dec 06 08:55:15.390 INFO [stderr] 
Dec 06 08:55:15.391 INFO [stderr] warning: unused variable: `consensus_source_reads`
Dec 06 08:55:15.391 INFO [stderr]    --> src/main.rs:144:13
Dec 06 08:55:15.391 INFO [stderr]     |
Dec 06 08:55:15.392 INFO [stderr] 144 |     let mut consensus_source_reads = String::new();
Dec 06 08:55:15.392 INFO [stderr]     |             ^^^^^^^^^^^^^^^^^^^^^^ help: consider using `_consensus_source_reads` instead
Dec 06 08:55:15.392 INFO [stderr] 
Dec 06 08:55:15.392 INFO [stderr] warning: unused variable: `chrom`
Dec 06 08:55:15.393 INFO [stderr]    --> src/main.rs:283:121
Dec 06 08:55:15.393 INFO [stderr]     |
Dec 06 08:55:15.393 INFO [stderr] 283 | fn  block_consensus(pd:& mut HashMap<String, HashMap<String, Vec<(Vec<u8>, Vec<u8>, Vec<u8>, CigarStringView, bool)>>>, chrom: i32, use_check:bool, min_t_s: &u32, min_t_p: &f32, o_r1: & mut File, o_r2: & mut File, need_trim:bool) {
Dec 06 08:55:15.393 INFO [stderr]     |                                                                                                                         ^^^^^ help: consider using `_chrom` instead
Dec 06 08:55:15.394 INFO [stderr] 
Dec 06 08:55:15.394 INFO [stderr] warning: value assigned to `new_seq_b` is never read
Dec 06 08:55:15.394 INFO [stderr]    --> src/main.rs:370:21
Dec 06 08:55:15.394 INFO [stderr]     |
Dec 06 08:55:15.395 INFO [stderr] 370 |             let mut new_seq_b:Vec<u8> = Vec::new();
Dec 06 08:55:15.395 INFO [stderr]     |                     ^^^^^^^^^
Dec 06 08:55:15.395 INFO [stderr]     |
Dec 06 08:55:15.396 INFO [stderr]     = note: #[warn(unused_assignments)] on by default
Dec 06 08:55:15.396 INFO [stderr] 
Dec 06 08:55:15.396 INFO [stderr] warning: variable does not need to be mutable
Dec 06 08:55:15.396 INFO [stderr]   --> src/main.rs:74:9
Dec 06 08:55:15.397 INFO [stderr]    |
Dec 06 08:55:15.397 INFO [stderr] 74 |     let mut pair;
Dec 06 08:55:15.397 INFO [stderr]    |         ----^^^^
Dec 06 08:55:15.398 INFO [stderr]    |         |
Dec 06 08:55:15.398 INFO [stderr]    |         help: remove this `mut`
Dec 06 08:55:15.398 INFO [stderr]    |
Dec 06 08:55:15.398 INFO [stderr]    = note: #[warn(unused_mut)] on by default
Dec 06 08:55:15.399 INFO [stderr] 
Dec 06 08:55:15.399 INFO [stderr] warning: variable does not need to be mutable
Dec 06 08:55:15.399 INFO [stderr]   --> src/main.rs:75:9
Dec 06 08:55:15.400 INFO [stderr]    |
Dec 06 08:55:15.400 INFO [stderr] 75 |     let mut strand;
Dec 06 08:55:15.400 INFO [stderr]    |         ----^^^^^^
Dec 06 08:55:15.401 INFO [stderr]    |         |
Dec 06 08:55:15.401 INFO [stderr]    |         help: remove this `mut`
Dec 06 08:55:15.401 INFO [stderr] 
Dec 06 08:55:15.401 INFO [stderr] warning: variable does not need to be mutable
Dec 06 08:55:15.402 INFO [stderr]   --> src/main.rs:76:9
Dec 06 08:55:15.402 INFO [stderr]    |
Dec 06 08:55:15.402 INFO [stderr] 76 |     let mut aln_pos;
Dec 06 08:55:15.403 INFO [stderr]    |         ----^^^^^^^
Dec 06 08:55:15.403 INFO [stderr]    |         |
Dec 06 08:55:15.403 INFO [stderr]    |         help: remove this `mut`
Dec 06 08:55:15.403 INFO [stderr] 
Dec 06 08:55:15.420 INFO [stderr] warning: variable does not need to be mutable
Dec 06 08:55:15.420 INFO [stderr]    --> src/main.rs:144:9
Dec 06 08:55:15.420 INFO [stderr]     |
Dec 06 08:55:15.421 INFO [stderr] 144 |     let mut consensus_source_reads = String::new();
Dec 06 08:55:15.421 INFO [stderr]     |         ----^^^^^^^^^^^^^^^^^^^^^^
Dec 06 08:55:15.421 INFO [stderr]     |         |
Dec 06 08:55:15.421 INFO [stderr]     |         help: remove this `mut`
Dec 06 08:55:15.422 INFO [stderr] 
Dec 06 08:55:15.422 INFO [stderr] warning: variable does not need to be mutable
Dec 06 08:55:15.422 INFO [stderr]    --> src/main.rs:151:9
Dec 06 08:55:15.423 INFO [stderr]     |
Dec 06 08:55:15.423 INFO [stderr] 151 |     let mut top_cigar:&CigarStringView;
Dec 06 08:55:15.423 INFO [stderr]     |         ----^^^^^^^^^
Dec 06 08:55:15.423 INFO [stderr]     |         |
Dec 06 08:55:15.424 INFO [stderr]     |         help: remove this `mut`
Dec 06 08:55:15.424 INFO [stderr] 
Dec 06 08:55:15.432 INFO [stderr] warning: variable does not need to be mutable
Dec 06 08:55:15.433 INFO [stderr]    --> src/main.rs:338:9
Dec 06 08:55:15.433 INFO [stderr]     |
Dec 06 08:55:15.433 INFO [stderr] 338 |     let mut need_trim:bool;
Dec 06 08:55:15.433 INFO [stderr]     |         ----^^^^^^^^^
Dec 06 08:55:15.434 INFO [stderr]     |         |
Dec 06 08:55:15.434 INFO [stderr]     |         help: remove this `mut`
Dec 06 08:55:15.434 INFO [stderr] 
Dec 06 08:55:15.434 INFO [stderr] warning: variable does not need to be mutable
Dec 06 08:55:15.434 INFO [stderr]    --> src/main.rs:355:9
Dec 06 08:55:15.435 INFO [stderr]     |
Dec 06 08:55:15.435 INFO [stderr] 355 |     let mut chrom = 0;
Dec 06 08:55:15.435 INFO [stderr]     |         ----^^^^^
Dec 06 08:55:15.435 INFO [stderr]     |         |
Dec 06 08:55:15.436 INFO [stderr]     |         help: remove this `mut`
Dec 06 08:55:15.436 INFO [stderr] 
Dec 06 08:55:15.444 INFO [stderr] warning: function `bamLineParse` should have a snake case name such as `bam_line_parse`
Dec 06 08:55:15.444 INFO [stderr]   --> src/main.rs:68:1
Dec 06 08:55:15.444 INFO [stderr]    |
Dec 06 08:55:15.444 INFO [stderr] 68 | / fn bamLineParse(record:&Record) -> (String, String, String, i32, i32){
Dec 06 08:55:15.445 INFO [stderr] 69 | |
Dec 06 08:55:15.445 INFO [stderr] 70 | |     let qname_str = String::from_utf8_lossy(record.qname()).to_string();
Dec 06 08:55:15.445 INFO [stderr] 71 | |     let temp_v:Vec<&str> = qname_str.split('#').collect();
Dec 06 08:55:15.445 INFO [stderr] ...  |
Dec 06 08:55:15.446 INFO [stderr] 97 | |     (index, pair.to_string(), strand.to_string(), insert_size.abs(), aln_pos)
Dec 06 08:55:15.446 INFO [stderr] 98 | | }
Dec 06 08:55:15.446 INFO [stderr]    | |_^
Dec 06 08:55:15.446 INFO [stderr]    |
Dec 06 08:55:15.446 INFO [stderr]    = note: #[warn(non_snake_case)] on by default
Dec 06 08:55:15.446 INFO [stderr] 
Dec 06 08:55:15.447 INFO [stderr] warning: variable `baseEach_num_record` should have a snake case name such as `base_each_num_record`
Dec 06 08:55:15.447 INFO [stderr]    --> src/main.rs:147:9
Dec 06 08:55:15.447 INFO [stderr]     |
Dec 06 08:55:15.447 INFO [stderr] 147 |     let mut baseEach_num_record = String::new();
Dec 06 08:55:15.448 INFO [stderr]     |         ^^^^^^^^^^^^^^^^^^^^^^^
Dec 06 08:55:15.448 INFO [stderr] 
Dec 06 08:55:15.448 INFO [stderr] warning: variable `baseEach_percent_record` should have a snake case name such as `base_each_percent_record`
Dec 06 08:55:15.448 INFO [stderr]    --> src/main.rs:148:9
Dec 06 08:55:15.448 INFO [stderr]     |
Dec 06 08:55:15.448 INFO [stderr] 148 |     let mut baseEach_percent_record = String::new();
Dec 06 08:55:15.449 INFO [stderr]     |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^
Dec 06 08:55:15.449 INFO [stderr] 
Dec 06 08:55:15.449 INFO [stderr] warning: unused `std::result::Result` that must be used
Dec 06 08:55:15.449 INFO [stderr]    --> src/main.rs:267:9
Dec 06 08:55:15.449 INFO [stderr]     |
Dec 06 08:55:15.449 INFO [stderr] 267 |         o_buff.write(&member_record.2);
Dec 06 08:55:15.449 INFO [stderr]     |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Dec 06 08:55:15.449 INFO [stderr]     |
Dec 06 08:55:15.449 INFO [stderr]     = note: #[warn(unused_must_use)] on by default
Dec 06 08:55:15.449 INFO [stderr]     = note: this `Result` may be an `Err` variant, which should be handled
Dec 06 08:55:15.449 INFO [stderr] 
Dec 06 08:55:15.449 INFO [stderr] warning: unused `std::result::Result` that must be used
Dec 06 08:55:15.449 INFO [stderr]    --> src/main.rs:269:9
Dec 06 08:55:15.450 INFO [stderr]     |
Dec 06 08:55:15.450 INFO [stderr] 269 |         o_buff.write(&member_record.0);
Dec 06 08:55:15.450 INFO [stderr]     |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Dec 06 08:55:15.450 INFO [stderr]     |
Dec 06 08:55:15.450 INFO [stderr]     = note: this `Result` may be an `Err` variant, which should be handled
Dec 06 08:55:15.450 INFO [stderr] 
Dec 06 08:55:15.450 INFO [stderr] warning: unused `std::result::Result` that must be used
Dec 06 08:55:15.450 INFO [stderr]    --> src/main.rs:272:9
Dec 06 08:55:15.450 INFO [stderr]     |
Dec 06 08:55:15.450 INFO [stderr] 272 |         o_buff.write(&real_qual_temp);
Dec 06 08:55:15.450 INFO [stderr]     |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Dec 06 08:55:15.450 INFO [stderr]     |
Dec 06 08:55:15.450 INFO [stderr]     = note: this `Result` may be an `Err` variant, which should be handled
Dec 06 08:55:15.450 INFO [stderr] 
Dec 06 08:55:15.450 INFO [stderr] warning: unused `std::result::Result` that must be used
Dec 06 08:55:15.450 INFO [stderr]    --> src/main.rs:274:5
Dec 06 08:55:15.450 INFO [stderr]     |
Dec 06 08:55:15.450 INFO [stderr] 274 |     o_buff.write(b"\n");
Dec 06 08:55:15.450 INFO [stderr]     |     ^^^^^^^^^^^^^^^^^^^^
Dec 06 08:55:15.450 INFO [stderr]     |
Dec 06 08:55:15.450 INFO [stderr]     = note: this `Result` may be an `Err` variant, which should be handled
Dec 06 08:55:15.450 INFO [stderr] 
Dec 06 08:55:15.450 INFO [stderr] warning: unused `std::result::Result` that must be used
Dec 06 08:55:15.450 INFO [stderr]    --> src/main.rs:277:5
Dec 06 08:55:15.450 INFO [stderr]     |
Dec 06 08:55:15.450 INFO [stderr] 277 |     o_buff.write(b"\n");
Dec 06 08:55:15.450 INFO [stderr]     |     ^^^^^^^^^^^^^^^^^^^^
Dec 06 08:55:15.450 INFO [stderr]     |
Dec 06 08:55:15.450 INFO [stderr]     = note: this `Result` may be an `Err` variant, which should be handled
Dec 06 08:55:15.450 INFO [stderr] 
Dec 06 08:55:15.450 INFO [stderr] warning: unused `std::result::Result` that must be used
Dec 06 08:55:15.450 INFO [stderr]    --> src/main.rs:280:5
Dec 06 08:55:15.450 INFO [stderr]     |
Dec 06 08:55:15.450 INFO [stderr] 280 |     o_buff.write(b"\n");
Dec 06 08:55:15.450 INFO [stderr]     |     ^^^^^^^^^^^^^^^^^^^^
Dec 06 08:55:15.450 INFO [stderr]     |
Dec 06 08:55:15.450 INFO [stderr]     = note: this `Result` may be an `Err` variant, which should be handled
Dec 06 08:55:15.450 INFO [stderr] 
Dec 06 08:55:15.451 INFO [stderr] warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group`
Dec 06 08:55:15.451 INFO [stderr]    --> src/main.rs:286:10
Dec 06 08:55:15.451 INFO [stderr]     |
Dec 06 08:55:15.451 INFO [stderr] 286 |     for (key_dupGroup, pair_dup) in pd.iter() {
Dec 06 08:55:15.451 INFO [stderr]     |          ^^^^^^^^^^^^
Dec 06 08:55:15.451 INFO [stderr] 
Dec 06 08:55:15.451 INFO [stderr] warning: variable `position_dupGroup` should have a snake case name such as `position_dup_group`
Dec 06 08:55:15.451 INFO [stderr]    --> src/main.rs:357:9
Dec 06 08:55:15.451 INFO [stderr]     |
Dec 06 08:55:15.451 INFO [stderr] 357 |     let mut position_dupGroup: HashMap<String, HashMap<String, Vec<(Vec<u8>, Vec<u8>, Vec<u8>, CigarStringView, bool)>>> = HashMap::new();
Dec 06 08:55:15.451 INFO [stderr]     |         ^^^^^^^^^^^^^^^^^^^^^
Dec 06 08:55:15.451 INFO [stderr] 
Dec 06 08:55:15.451 INFO [stderr] warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group`
Dec 06 08:55:15.451 INFO [stderr]    --> src/main.rs:387:17
Dec 06 08:55:15.451 INFO [stderr]     |
Dec 06 08:55:15.451 INFO [stderr] 387 |             let key_dupGroup = format!("{}_{}_{}_{}{}", index, chrom, aln_pos, strand, insert_size);
Dec 06 08:55:15.451 INFO [stderr]     |                 ^^^^^^^^^^^^
Dec 06 08:55:15.451 INFO [stderr] 
Dec 06 08:55:18.952 INFO [stderr]     Finished dev [unoptimized + debuginfo] target(s) in 38.84s
Dec 06 08:55:18.961 INFO [stderr] su: No module specific data is present
Dec 06 08:55:20.928 INFO running `"docker" "inspect" "f2c738c9c0ffffe541b1e88166bd34c8bf88b7595492c9201048637adfd14225"`
Dec 06 08:55:21.280 INFO running `"docker" "rm" "-f" "f2c738c9c0ffffe541b1e88166bd34c8bf88b7595492c9201048637adfd14225"`
Dec 06 08:55:21.640 INFO [stdout] f2c738c9c0ffffe541b1e88166bd34c8bf88b7595492c9201048637adfd14225
Dec 06 08:55:21.642 INFO running `"docker" "create" "-v" "/mnt/big/crater/work/local/target-dirs/pr-56514/worker-2/try#6eb0fd3ac58f9b16bddb9924a17c3b6c156aa468:/target:rw,Z" "-v" "/mnt/big/crater/work/local/test-source/worker-2/pr-56514/try#6eb0fd3ac58f9b16bddb9924a17c3b6c156aa468:/source:ro,Z" "-v" "/mnt/big/crater/work/local/cargo-home:/cargo-home:ro,Z" "-v" "/mnt/big/crater/work/local/rustup-home:/rustup-home:ro,Z" "-e" "USER_ID=1000" "-e" "SOURCE_DIR=/source" "-e" "USER_ID=1000" "-e" "CMD=cargo +6eb0fd3ac58f9b16bddb9924a17c3b6c156aa468-alt test --frozen --no-run" "-e" "CARGO_TARGET_DIR=/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/cargo-home" "-e" "RUSTUP_HOME=/rustup-home" "-m" "1536M" "--network" "none" "crater"`
Dec 06 08:55:22.119 INFO [stdout] e2a3e2945f149d793cc6aa87ff5c6fba8ef4b0c7d120a059c784a69b1f0c6882
Dec 06 08:55:22.122 INFO running `"docker" "start" "-a" "e2a3e2945f149d793cc6aa87ff5c6fba8ef4b0c7d120a059c784a69b1f0c6882"`
Dec 06 08:55:24.600 INFO [stderr] usermod: no changes
Dec 06 08:55:24.740 INFO [stderr]    Compiling consensus v0.1.0 (/source)
Dec 06 08:55:26.235 INFO [stderr] warning: unused import: `std::env`
Dec 06 08:55:26.235 INFO [stderr]   --> src/main.rs:12:5
Dec 06 08:55:26.235 INFO [stderr]    |
Dec 06 08:55:26.235 INFO [stderr] 12 | use std::env;
Dec 06 08:55:26.235 INFO [stderr]    |     ^^^^^^^^
Dec 06 08:55:26.236 INFO [stderr]    |
Dec 06 08:55:26.236 INFO [stderr]    = note: #[warn(unused_imports)] on by default
Dec 06 08:55:26.236 INFO [stderr] 
Dec 06 08:55:26.236 INFO [stderr] warning: unused import: `rust_htslib::prelude::*`
Dec 06 08:55:26.236 INFO [stderr]   --> src/main.rs:16:5
Dec 06 08:55:26.236 INFO [stderr]    |
Dec 06 08:55:26.236 INFO [stderr] 16 | use rust_htslib::prelude::*;
Dec 06 08:55:26.237 INFO [stderr]    |     ^^^^^^^^^^^^^^^^^^^^^^^
Dec 06 08:55:26.237 INFO [stderr] 
Dec 06 08:55:26.237 INFO [stderr] warning: unused import: `std::io`
Dec 06 08:55:26.237 INFO [stderr]   --> src/main.rs:21:5
Dec 06 08:55:26.237 INFO [stderr]    |
Dec 06 08:55:26.237 INFO [stderr] 21 | use std::io;
Dec 06 08:55:26.238 INFO [stderr]    |     ^^^^^^^
Dec 06 08:55:26.238 INFO [stderr] 
Dec 06 08:55:26.238 INFO [stderr] warning: unused import: `PathBuf`
Dec 06 08:55:26.238 INFO [stderr]   --> src/main.rs:25:23
Dec 06 08:55:26.238 INFO [stderr]    |
Dec 06 08:55:26.238 INFO [stderr] 25 | use std::path::{Path, PathBuf};
Dec 06 08:55:26.239 INFO [stderr]    |                       ^^^^^^^
Dec 06 08:55:26.239 INFO [stderr] 
Dec 06 08:55:26.239 INFO [stderr] warning: unused import: `SubCommand`
Dec 06 08:55:26.239 INFO [stderr]   --> src/main.rs:26:22
Dec 06 08:55:26.239 INFO [stderr]    |
Dec 06 08:55:26.239 INFO [stderr] 26 | use clap::{Arg, App, SubCommand};
Dec 06 08:55:26.240 INFO [stderr]    |                      ^^^^^^^^^^
Dec 06 08:55:26.240 INFO [stderr] 
Dec 06 08:55:26.240 INFO [stderr] warning: unnecessary parentheses around `if` condition
Dec 06 08:55:26.240 INFO [stderr]    --> src/main.rs:218:20
Dec 06 08:55:26.240 INFO [stderr]     |
Dec 06 08:55:26.240 INFO [stderr] 218 |                 if (num_position[&(i as usize)] == num_position[&(0 as usize)]) {
Dec 06 08:55:26.241 INFO [stderr]     |                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses
Dec 06 08:55:26.241 INFO [stderr]     |
Dec 06 08:55:26.241 INFO [stderr]     = note: #[warn(unused_parens)] on by default
Dec 06 08:55:26.241 INFO [stderr] 
Dec 06 08:55:26.241 INFO [stderr] warning: unnecessary parentheses around `if` condition
Dec 06 08:55:26.241 INFO [stderr]    --> src/main.rs:239:16
Dec 06 08:55:26.242 INFO [stderr]     |
Dec 06 08:55:26.242 INFO [stderr] 239 |             if (baseEach_percent_record.len() > 0) {
Dec 06 08:55:26.242 INFO [stderr]     |                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses
Dec 06 08:55:26.242 INFO [stderr] 
Dec 06 08:55:26.351 INFO [stderr] warning: unused import: `std::io::prelude`
Dec 06 08:55:26.351 INFO [stderr]   --> src/main.rs:22:5
Dec 06 08:55:26.352 INFO [stderr]    |
Dec 06 08:55:26.352 INFO [stderr] 22 | use std::io::prelude::*;
Dec 06 08:55:26.352 INFO [stderr]    |     ^^^^^^^^^^^^^^^^
Dec 06 08:55:26.352 INFO [stderr] 
Dec 06 08:55:26.360 INFO [stderr] warning: unused variable: `consensus_base`
Dec 06 08:55:26.361 INFO [stderr]    --> src/main.rs:139:9
Dec 06 08:55:26.361 INFO [stderr]     |
Dec 06 08:55:26.361 INFO [stderr] 139 |     let consensus_base:Vec<u8> = Vec::new();
Dec 06 08:55:26.361 INFO [stderr]     |         ^^^^^^^^^^^^^^ help: consider using `_consensus_base` instead
Dec 06 08:55:26.361 INFO [stderr]     |
Dec 06 08:55:26.362 INFO [stderr]     = note: #[warn(unused_variables)] on by default
Dec 06 08:55:26.362 INFO [stderr] 
Dec 06 08:55:26.362 INFO [stderr] warning: unused variable: `consensus_source_reads`
Dec 06 08:55:26.362 INFO [stderr]    --> src/main.rs:144:13
Dec 06 08:55:26.362 INFO [stderr]     |
Dec 06 08:55:26.362 INFO [stderr] 144 |     let mut consensus_source_reads = String::new();
Dec 06 08:55:26.362 INFO [stderr]     |             ^^^^^^^^^^^^^^^^^^^^^^ help: consider using `_consensus_source_reads` instead
Dec 06 08:55:26.363 INFO [stderr] 
Dec 06 08:55:26.363 INFO [stderr] warning: unused variable: `chrom`
Dec 06 08:55:26.363 INFO [stderr]    --> src/main.rs:283:121
Dec 06 08:55:26.363 INFO [stderr]     |
Dec 06 08:55:26.363 INFO [stderr] 283 | fn  block_consensus(pd:& mut HashMap<String, HashMap<String, Vec<(Vec<u8>, Vec<u8>, Vec<u8>, CigarStringView, bool)>>>, chrom: i32, use_check:bool, min_t_s: &u32, min_t_p: &f32, o_r1: & mut File, o_r2: & mut File, need_trim:bool) {
Dec 06 08:55:26.363 INFO [stderr]     |                                                                                                                         ^^^^^ help: consider using `_chrom` instead
Dec 06 08:55:26.364 INFO [stderr] 
Dec 06 08:55:26.364 INFO [stderr] warning: value assigned to `new_seq_b` is never read
Dec 06 08:55:26.364 INFO [stderr]    --> src/main.rs:370:21
Dec 06 08:55:26.364 INFO [stderr]     |
Dec 06 08:55:26.364 INFO [stderr] 370 |             let mut new_seq_b:Vec<u8> = Vec::new();
Dec 06 08:55:26.364 INFO [stderr]     |                     ^^^^^^^^^
Dec 06 08:55:26.365 INFO [stderr]     |
Dec 06 08:55:26.365 INFO [stderr]     = note: #[warn(unused_assignments)] on by default
Dec 06 08:55:26.365 INFO [stderr] 
Dec 06 08:55:26.369 INFO [stderr] warning: variable does not need to be mutable
Dec 06 08:55:26.369 INFO [stderr]   --> src/main.rs:74:9
Dec 06 08:55:26.369 INFO [stderr]    |
Dec 06 08:55:26.370 INFO [stderr] 74 |     let mut pair;
Dec 06 08:55:26.370 INFO [stderr]    |         ----^^^^
Dec 06 08:55:26.370 INFO [stderr]    |         |
Dec 06 08:55:26.370 INFO [stderr]    |         help: remove this `mut`
Dec 06 08:55:26.370 INFO [stderr]    |
Dec 06 08:55:26.370 INFO [stderr]    = note: #[warn(unused_mut)] on by default
Dec 06 08:55:26.370 INFO [stderr] 
Dec 06 08:55:26.370 INFO [stderr] warning: variable does not need to be mutable
Dec 06 08:55:26.370 INFO [stderr]   --> src/main.rs:75:9
Dec 06 08:55:26.370 INFO [stderr]    |
Dec 06 08:55:26.370 INFO [stderr] 75 |     let mut strand;
Dec 06 08:55:26.370 INFO [stderr]    |         ----^^^^^^
Dec 06 08:55:26.370 INFO [stderr]    |         |
Dec 06 08:55:26.370 INFO [stderr]    |         help: remove this `mut`
Dec 06 08:55:26.370 INFO [stderr] 
Dec 06 08:55:26.370 INFO [stderr] warning: variable does not need to be mutable
Dec 06 08:55:26.370 INFO [stderr]   --> src/main.rs:76:9
Dec 06 08:55:26.370 INFO [stderr]    |
Dec 06 08:55:26.370 INFO [stderr] 76 |     let mut aln_pos;
Dec 06 08:55:26.370 INFO [stderr]    |         ----^^^^^^^
Dec 06 08:55:26.370 INFO [stderr]    |         |
Dec 06 08:55:26.370 INFO [stderr]    |         help: remove this `mut`
Dec 06 08:55:26.370 INFO [stderr] 
Dec 06 08:55:26.397 INFO [stderr] warning: variable does not need to be mutable
Dec 06 08:55:26.397 INFO [stderr]    --> src/main.rs:144:9
Dec 06 08:55:26.397 INFO [stderr]     |
Dec 06 08:55:26.397 INFO [stderr] 144 |     let mut consensus_source_reads = String::new();
Dec 06 08:55:26.397 INFO [stderr]     |         ----^^^^^^^^^^^^^^^^^^^^^^
Dec 06 08:55:26.397 INFO [stderr]     |         |
Dec 06 08:55:26.398 INFO [stderr]     |         help: remove this `mut`
Dec 06 08:55:26.398 INFO [stderr] 
Dec 06 08:55:26.398 INFO [stderr] warning: variable does not need to be mutable
Dec 06 08:55:26.398 INFO [stderr]    --> src/main.rs:151:9
Dec 06 08:55:26.398 INFO [stderr]     |
Dec 06 08:55:26.398 INFO [stderr] 151 |     let mut top_cigar:&CigarStringView;
Dec 06 08:55:26.398 INFO [stderr]     |         ----^^^^^^^^^
Dec 06 08:55:26.398 INFO [stderr]     |         |
Dec 06 08:55:26.398 INFO [stderr]     |         help: remove this `mut`
Dec 06 08:55:26.398 INFO [stderr] 
Dec 06 08:55:26.411 INFO [stderr] warning: variable does not need to be mutable
Dec 06 08:55:26.411 INFO [stderr]    --> src/main.rs:338:9
Dec 06 08:55:26.411 INFO [stderr]     |
Dec 06 08:55:26.411 INFO [stderr] 338 |     let mut need_trim:bool;
Dec 06 08:55:26.411 INFO [stderr]     |         ----^^^^^^^^^
Dec 06 08:55:26.411 INFO [stderr]     |         |
Dec 06 08:55:26.412 INFO [stderr]     |         help: remove this `mut`
Dec 06 08:55:26.412 INFO [stderr] 
Dec 06 08:55:26.412 INFO [stderr] warning: variable does not need to be mutable
Dec 06 08:55:26.412 INFO [stderr]    --> src/main.rs:355:9
Dec 06 08:55:26.412 INFO [stderr]     |
Dec 06 08:55:26.412 INFO [stderr] 355 |     let mut chrom = 0;
Dec 06 08:55:26.412 INFO [stderr]     |         ----^^^^^
Dec 06 08:55:26.412 INFO [stderr]     |         |
Dec 06 08:55:26.412 INFO [stderr]     |         help: remove this `mut`
Dec 06 08:55:26.412 INFO [stderr] 
Dec 06 08:55:26.423 INFO [stderr] warning: function `bamLineParse` should have a snake case name such as `bam_line_parse`
Dec 06 08:55:26.423 INFO [stderr]   --> src/main.rs:68:1
Dec 06 08:55:26.423 INFO [stderr]    |
Dec 06 08:55:26.423 INFO [stderr] 68 | / fn bamLineParse(record:&Record) -> (String, String, String, i32, i32){
Dec 06 08:55:26.423 INFO [stderr] 69 | |
Dec 06 08:55:26.423 INFO [stderr] 70 | |     let qname_str = String::from_utf8_lossy(record.qname()).to_string();
Dec 06 08:55:26.423 INFO [stderr] 71 | |     let temp_v:Vec<&str> = qname_str.split('#').collect();
Dec 06 08:55:26.423 INFO [stderr] ...  |
Dec 06 08:55:26.424 INFO [stderr] 97 | |     (index, pair.to_string(), strand.to_string(), insert_size.abs(), aln_pos)
Dec 06 08:55:26.424 INFO [stderr] 98 | | }
Dec 06 08:55:26.424 INFO [stderr]    | |_^
Dec 06 08:55:26.424 INFO [stderr]    |
Dec 06 08:55:26.424 INFO [stderr]    = note: #[warn(non_snake_case)] on by default
Dec 06 08:55:26.424 INFO [stderr] 
Dec 06 08:55:26.424 INFO [stderr] warning: variable `baseEach_num_record` should have a snake case name such as `base_each_num_record`
Dec 06 08:55:26.424 INFO [stderr]    --> src/main.rs:147:9
Dec 06 08:55:26.424 INFO [stderr]     |
Dec 06 08:55:26.424 INFO [stderr] 147 |     let mut baseEach_num_record = String::new();
Dec 06 08:55:26.424 INFO [stderr]     |         ^^^^^^^^^^^^^^^^^^^^^^^
Dec 06 08:55:26.424 INFO [stderr] 
Dec 06 08:55:26.424 INFO [stderr] warning: variable `baseEach_percent_record` should have a snake case name such as `base_each_percent_record`
Dec 06 08:55:26.424 INFO [stderr]    --> src/main.rs:148:9
Dec 06 08:55:26.424 INFO [stderr]     |
Dec 06 08:55:26.424 INFO [stderr] 148 |     let mut baseEach_percent_record = String::new();
Dec 06 08:55:26.424 INFO [stderr]     |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^
Dec 06 08:55:26.424 INFO [stderr] 
Dec 06 08:55:26.424 INFO [stderr] warning: unused `std::result::Result` that must be used
Dec 06 08:55:26.424 INFO [stderr]    --> src/main.rs:267:9
Dec 06 08:55:26.424 INFO [stderr]     |
Dec 06 08:55:26.424 INFO [stderr] 267 |         o_buff.write(&member_record.2);
Dec 06 08:55:26.424 INFO [stderr]     |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Dec 06 08:55:26.424 INFO [stderr]     |
Dec 06 08:55:26.424 INFO [stderr]     = note: #[warn(unused_must_use)] on by default
Dec 06 08:55:26.424 INFO [stderr]     = note: this `Result` may be an `Err` variant, which should be handled
Dec 06 08:55:26.424 INFO [stderr] 
Dec 06 08:55:26.425 INFO [stderr] warning: unused `std::result::Result` that must be used
Dec 06 08:55:26.425 INFO [stderr]    --> src/main.rs:269:9
Dec 06 08:55:26.425 INFO [stderr]     |
Dec 06 08:55:26.425 INFO [stderr] 269 |         o_buff.write(&member_record.0);
Dec 06 08:55:26.425 INFO [stderr]     |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Dec 06 08:55:26.425 INFO [stderr]     |
Dec 06 08:55:26.425 INFO [stderr]     = note: this `Result` may be an `Err` variant, which should be handled
Dec 06 08:55:26.425 INFO [stderr] 
Dec 06 08:55:26.425 INFO [stderr] warning: unused `std::result::Result` that must be used
Dec 06 08:55:26.426 INFO [stderr]    --> src/main.rs:272:9
Dec 06 08:55:26.426 INFO [stderr]     |
Dec 06 08:55:26.426 INFO [stderr] 272 |         o_buff.write(&real_qual_temp);
Dec 06 08:55:26.426 INFO [stderr]     |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Dec 06 08:55:26.426 INFO [stderr]     |
Dec 06 08:55:26.426 INFO [stderr]     = note: this `Result` may be an `Err` variant, which should be handled
Dec 06 08:55:26.426 INFO [stderr] 
Dec 06 08:55:26.426 INFO [stderr] warning: unused `std::result::Result` that must be used
Dec 06 08:55:26.426 INFO [stderr]    --> src/main.rs:274:5
Dec 06 08:55:26.426 INFO [stderr]     |
Dec 06 08:55:26.426 INFO [stderr] 274 |     o_buff.write(b"\n");
Dec 06 08:55:26.426 INFO [stderr]     |     ^^^^^^^^^^^^^^^^^^^^
Dec 06 08:55:26.426 INFO [stderr]     |
Dec 06 08:55:26.426 INFO [stderr]     = note: this `Result` may be an `Err` variant, which should be handled
Dec 06 08:55:26.426 INFO [stderr] 
Dec 06 08:55:26.427 INFO [stderr] warning: unused `std::result::Result` that must be used
Dec 06 08:55:26.427 INFO [stderr]    --> src/main.rs:277:5
Dec 06 08:55:26.427 INFO [stderr]     |
Dec 06 08:55:26.427 INFO [stderr] 277 |     o_buff.write(b"\n");
Dec 06 08:55:26.427 INFO [stderr]     |     ^^^^^^^^^^^^^^^^^^^^
Dec 06 08:55:26.427 INFO [stderr]     |
Dec 06 08:55:26.427 INFO [stderr]     = note: this `Result` may be an `Err` variant, which should be handled
Dec 06 08:55:26.427 INFO [stderr] 
Dec 06 08:55:26.427 INFO [stderr] warning: unused `std::result::Result` that must be used
Dec 06 08:55:26.427 INFO [stderr]    --> src/main.rs:280:5
Dec 06 08:55:26.427 INFO [stderr]     |
Dec 06 08:55:26.427 INFO [stderr] 280 |     o_buff.write(b"\n");
Dec 06 08:55:26.427 INFO [stderr]     |     ^^^^^^^^^^^^^^^^^^^^
Dec 06 08:55:26.427 INFO [stderr]     |
Dec 06 08:55:26.427 INFO [stderr]     = note: this `Result` may be an `Err` variant, which should be handled
Dec 06 08:55:26.427 INFO [stderr] 
Dec 06 08:55:26.427 INFO [stderr] warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group`
Dec 06 08:55:26.427 INFO [stderr]    --> src/main.rs:286:10
Dec 06 08:55:26.427 INFO [stderr]     |
Dec 06 08:55:26.427 INFO [stderr] 286 |     for (key_dupGroup, pair_dup) in pd.iter() {
Dec 06 08:55:26.427 INFO [stderr]     |          ^^^^^^^^^^^^
Dec 06 08:55:26.427 INFO [stderr] 
Dec 06 08:55:26.428 INFO [stderr] warning: variable `position_dupGroup` should have a snake case name such as `position_dup_group`
Dec 06 08:55:26.428 INFO [stderr]    --> src/main.rs:357:9
Dec 06 08:55:26.428 INFO [stderr]     |
Dec 06 08:55:26.428 INFO [stderr] 357 |     let mut position_dupGroup: HashMap<String, HashMap<String, Vec<(Vec<u8>, Vec<u8>, Vec<u8>, CigarStringView, bool)>>> = HashMap::new();
Dec 06 08:55:26.428 INFO [stderr]     |         ^^^^^^^^^^^^^^^^^^^^^
Dec 06 08:55:26.428 INFO [stderr] 
Dec 06 08:55:26.428 INFO [stderr] warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group`
Dec 06 08:55:26.428 INFO [stderr]    --> src/main.rs:387:17
Dec 06 08:55:26.428 INFO [stderr]     |
Dec 06 08:55:26.428 INFO [stderr] 387 |             let key_dupGroup = format!("{}_{}_{}_{}{}", index, chrom, aln_pos, strand, insert_size);
Dec 06 08:55:26.428 INFO [stderr]     |                 ^^^^^^^^^^^^
Dec 06 08:55:26.428 INFO [stderr] 
Dec 06 08:55:26.841 INFO [stderr]     Finished dev [unoptimized + debuginfo] target(s) in 2.22s
Dec 06 08:55:26.846 INFO [stderr] su: No module specific data is present
Dec 06 08:55:28.443 INFO running `"docker" "inspect" "e2a3e2945f149d793cc6aa87ff5c6fba8ef4b0c7d120a059c784a69b1f0c6882"`
Dec 06 08:55:28.838 INFO running `"docker" "rm" "-f" "e2a3e2945f149d793cc6aa87ff5c6fba8ef4b0c7d120a059c784a69b1f0c6882"`
Dec 06 08:55:29.204 INFO [stdout] e2a3e2945f149d793cc6aa87ff5c6fba8ef4b0c7d120a059c784a69b1f0c6882
Dec 06 08:55:29.206 INFO running `"docker" "create" "-v" "/mnt/big/crater/work/local/target-dirs/pr-56514/worker-2/try#6eb0fd3ac58f9b16bddb9924a17c3b6c156aa468:/target:rw,Z" "-v" "/mnt/big/crater/work/local/test-source/worker-2/pr-56514/try#6eb0fd3ac58f9b16bddb9924a17c3b6c156aa468:/source:ro,Z" "-v" "/mnt/big/crater/work/local/cargo-home:/cargo-home:ro,Z" "-v" "/mnt/big/crater/work/local/rustup-home:/rustup-home:ro,Z" "-e" "USER_ID=1000" "-e" "SOURCE_DIR=/source" "-e" "USER_ID=1000" "-e" "CMD=cargo +6eb0fd3ac58f9b16bddb9924a17c3b6c156aa468-alt test --frozen" "-e" "CARGO_TARGET_DIR=/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/cargo-home" "-e" "RUSTUP_HOME=/rustup-home" "-m" "1536M" "--network" "none" "crater"`
Dec 06 08:55:29.740 INFO [stdout] b2d3a89b0c0405ac9eff1bda126b07fad0e30a333659dbf37dc56ec9d724835a
Dec 06 08:55:29.743 INFO running `"docker" "start" "-a" "b2d3a89b0c0405ac9eff1bda126b07fad0e30a333659dbf37dc56ec9d724835a"`
Dec 06 08:55:31.688 INFO [stderr] usermod: no changes
Dec 06 08:55:31.893 INFO [stderr]     Finished dev [unoptimized + debuginfo] target(s) in 0.17s
Dec 06 08:55:31.902 INFO [stderr]      Running /target/debug/deps/consensus-1853a237827635a3
Dec 06 08:55:31.921 INFO [stdout] 
Dec 06 08:55:31.921 INFO [stdout] running 0 tests
Dec 06 08:55:31.921 INFO [stdout] 
Dec 06 08:55:31.921 INFO [stdout] test result: ok. 0 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out
Dec 06 08:55:31.921 INFO [stdout] 
Dec 06 08:55:31.923 INFO [stderr] su: No module specific data is present
Dec 06 08:55:33.286 INFO running `"docker" "inspect" "b2d3a89b0c0405ac9eff1bda126b07fad0e30a333659dbf37dc56ec9d724835a"`
Dec 06 08:55:33.620 INFO running `"docker" "rm" "-f" "b2d3a89b0c0405ac9eff1bda126b07fad0e30a333659dbf37dc56ec9d724835a"`
Dec 06 08:55:34.000 INFO [stdout] b2d3a89b0c0405ac9eff1bda126b07fad0e30a333659dbf37dc56ec9d724835a