[INFO] fetching crate ngs 0.4.0...
[INFO] testing ngs-0.4.0 against 1.91.0 for beta-1.92-2
[INFO] extracting crate ngs 0.4.0 into /workspace/builds/worker-7-tc1/source
[INFO] removed /workspace/builds/worker-7-tc1/source/.cargo/config
[INFO] started tweaking crates.io crate ngs 0.4.0
[INFO] finished tweaking crates.io crate ngs 0.4.0
[INFO] tweaked toml for crates.io crate ngs 0.4.0 written to /workspace/builds/worker-7-tc1/source/Cargo.toml
[INFO] validating manifest of crates.io crate ngs 0.4.0 on toolchain 1.91.0
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+1.91.0" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate crates.io crate ngs 0.4.0 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" "+1.91.0" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Updating crates.io index
[INFO] [stderr]  Downloading crates ...
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[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc1/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@sha256:4848fb76d95f26979359cc7e45710b1dbc8f3acb7aeedee7c460d7702230f228" "/opt/rustwide/cargo-home/bin/cargo" "+1.91.0" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] 308a96dffcaae411cae20b60dcb9f292e3f8530dc3e879165693fe8c2efc8104
[INFO] running `Command { std: "docker" "start" "-a" "308a96dffcaae411cae20b60dcb9f292e3f8530dc3e879165693fe8c2efc8104", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "308a96dffcaae411cae20b60dcb9f292e3f8530dc3e879165693fe8c2efc8104", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "308a96dffcaae411cae20b60dcb9f292e3f8530dc3e879165693fe8c2efc8104", kill_on_drop: false }`
[INFO] [stdout] 308a96dffcaae411cae20b60dcb9f292e3f8530dc3e879165693fe8c2efc8104
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc1/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=warn" "-e" "RUSTDOCFLAGS=--cap-lints=warn" "-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@sha256:4848fb76d95f26979359cc7e45710b1dbc8f3acb7aeedee7c460d7702230f228" "/opt/rustwide/cargo-home/bin/cargo" "+1.91.0" "build" "--frozen" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 6f14c151cbab8f91f02feb1057c4b7b7a272c880191ce171b4763217d6bbc79d
[INFO] running `Command { std: "docker" "start" "-a" "6f14c151cbab8f91f02feb1057c4b7b7a272c880191ce171b4763217d6bbc79d", kill_on_drop: false }`
[INFO] [stderr]    Compiling proc-macro2 v1.0.46
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[INFO] [stderr]    Compiling memchr v2.5.0
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[INFO] [stderr]    Compiling pin-project-lite v0.2.9
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[INFO] [stderr]    Compiling num_cpus v1.13.1
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[INFO] [stderr]    Compiling tracing v0.1.36
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[INFO] [stderr]    Compiling csv v1.1.6
[INFO] [stderr]    Compiling noodles-bam v0.28.0
[INFO] [stderr]    Compiling prettytable-rs v0.9.0
[INFO] [stderr]    Compiling askama_shared v0.12.2
[INFO] [stderr]    Compiling noodles-cram v0.25.0
[INFO] [stderr]    Compiling noodles v0.34.0
[INFO] [stderr]    Compiling askama_derive v0.11.2
[INFO] [stderr]    Compiling askama v0.11.1
[INFO] [stderr]    Compiling plotly v0.8.1
[INFO] [stderr]    Compiling ngs v0.4.0 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 1m 09s
[INFO] running `Command { std: "docker" "inspect" "6f14c151cbab8f91f02feb1057c4b7b7a272c880191ce171b4763217d6bbc79d", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "6f14c151cbab8f91f02feb1057c4b7b7a272c880191ce171b4763217d6bbc79d", kill_on_drop: false }`
[INFO] [stdout] 6f14c151cbab8f91f02feb1057c4b7b7a272c880191ce171b4763217d6bbc79d
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc1/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=warn" "-e" "RUSTDOCFLAGS=--cap-lints=warn" "-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@sha256:4848fb76d95f26979359cc7e45710b1dbc8f3acb7aeedee7c460d7702230f228" "/opt/rustwide/cargo-home/bin/cargo" "+1.91.0" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] efbc6c51c27902dc106a0b80fb4e6b9d760f2aeccbc29e9e154ef435619a827d
[INFO] running `Command { std: "docker" "start" "-a" "efbc6c51c27902dc106a0b80fb4e6b9d760f2aeccbc29e9e154ef435619a827d", kill_on_drop: false }`
[INFO] [stderr]    Compiling ngs v0.4.0 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished `test` profile [unoptimized + debuginfo] target(s) in 8.23s
[INFO] running `Command { std: "docker" "inspect" "efbc6c51c27902dc106a0b80fb4e6b9d760f2aeccbc29e9e154ef435619a827d", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "efbc6c51c27902dc106a0b80fb4e6b9d760f2aeccbc29e9e154ef435619a827d", kill_on_drop: false }`
[INFO] [stdout] efbc6c51c27902dc106a0b80fb4e6b9d760f2aeccbc29e9e154ef435619a827d
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc1/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=warn" "-e" "RUSTDOCFLAGS=--cap-lints=warn" "-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@sha256:4848fb76d95f26979359cc7e45710b1dbc8f3acb7aeedee7c460d7702230f228" "/opt/rustwide/cargo-home/bin/cargo" "+1.91.0" "test" "--frozen", kill_on_drop: false }`
[INFO] [stdout] 23b8a2da7fe44100f54771a3737a24d92fe0ea68494a41debb43c774affad094
[INFO] running `Command { std: "docker" "start" "-a" "23b8a2da7fe44100f54771a3737a24d92fe0ea68494a41debb43c774affad094", kill_on_drop: false }`
[INFO] [stderr]     Finished `test` profile [unoptimized + debuginfo] target(s) in 0.23s
[INFO] [stderr]      Running unittests src/lib.rs (/opt/rustwide/target/debug/deps/ngs-03e7e46aa77e3b55)
[INFO] [stdout] 
[INFO] [stdout] running 70 tests
[INFO] [stdout] test derive::instrument::reads::tests::test_parse_failure ... ok
[INFO] [stdout] test derive::instrument::reads::tests::test_parse_illumina_1_4_fmt ... ok
[INFO] [stdout] test generate::providers::reference_provider::tests::test_invalid_str_bad_error_frequency ... ok
[INFO] [stdout] test generate::providers::reference_provider::tests::test_invalid_str_bad_mean ... ok
[INFO] [stdout] test derive::instrument::reads::tests::test_parse_illumina_1_8_fmt ... ok
[INFO] [stdout] test generate::providers::reference_provider::tests::test_invalid_str_bad_read_length ... ok
[INFO] [stdout] test derive::instrument::compute::tests::test_derive_instrument_low_flowcell_evidence ... ok
[INFO] [stdout] test derive::instrument::compute::tests::test_derive_instrument_from_valid_flowcell_name ... ok
[INFO] [stdout] test derive::instrument::compute::tests::test_derive_instrument_medium_flowcell_evidence ... ok
[INFO] [stdout] test derive::instrument::compute::tests::test_derive_instrument_from_invalid_flowcell_name ... ok
[INFO] [stdout] test generate::providers::reference_provider::tests::test_invalid_str_bad_weight ... ok
[INFO] [stdout] test generate::providers::reference_provider::tests::test_invalid_str_malformed ... ok
[INFO] [stdout] test generate::utils::tests::test_compliment_valid ... ok
[INFO] [stdout] test qc::tests::it_returns_the_correct_number_of_facets_when_only_is_specified ... ok
[INFO] [stdout] test generate::providers::reference_provider::tests::test_invalid_str_bad_std_dev ... ok
[INFO] [stdout] test utils::alignment::tests::it_correctly_handles_softclips ... ok
[INFO] [stdout] test qc::record_based::gc_content::tests::it_defaults_with_zero_based_100_capacity_histogram ... ok
[INFO] [stdout] test utils::alignment::tests::it_correctly_returns_one_edit_when_sequences_have_one_edit ... ok
[INFO] [stdout] test generate::utils::tests::test_compliment_invalid ... ok
[INFO] [stdout] test qc::tests::it_returns_the_correct_number_of_facets_by_default ... ok
[INFO] [stdout] test utils::alignment::tests::it_catches_a_malformed_record_with_too_few_record_bases ... ok
[INFO] [stdout] test utils::formats::fasta::phred::tests::it_correctly_converts_to_chars ... ok
[INFO] [stdout] test utils::formats::fasta::phred::tests::it_is_not_valid_from_a_score_thats_too_high ... ok
[INFO] [stdout] test utils::formats::fasta::phred::tests::it_is_valid_from_a_lowest_score ... ok
[INFO] [stdout] test utils::alignment::tests::it_catches_a_malformed_record_with_too_few_reference_bases ... ok
[INFO] [stdout] test utils::formats::sam::tests::test_illumina_lowercase_fix ... ok
[INFO] [stdout] test utils::formats::tests::it_correctly_identifies_bam_files ... ok
[INFO] [stdout] test generate::providers::reference_provider::tests::test_valid_str ... ok
[INFO] [stdout] test utils::formats::tests::it_correctly_identifies_bcf_files ... ok
[INFO] [stdout] test utils::alignment::tests::it_correctly_returns_zero_edits_when_sequences_are_identical ... ok
[INFO] [stdout] test utils::formats::fasta::phred::tests::it_correctly_converts_from_chars ... ok
[INFO] [stdout] test utils::formats::tests::it_correctly_identifies_bed_files ... ok
[INFO] [stdout] test utils::formats::tests::it_correctly_identifies_cram_files ... ok
[INFO] [stdout] test utils::formats::tests::it_correctly_identifies_fasta_files ... ok
[INFO] [stdout] test utils::formats::tests::it_correctly_identifies_gff_files ... ok
[INFO] [stdout] test utils::formats::tests::it_correctly_identifies_ubam_files ... ok
[INFO] [stdout] test utils::genome::ncbi::grch38_no_alt::tests::it_contains_the_mitochodrion_chromosome ... ok
[INFO] [stdout] test utils::genome::ncbi::grch38_no_alt::tests::it_contains_the_epstein_barr_virus ... ok
[INFO] [stdout] test utils::formats::fasta::phred::tests::it_correctly_computes_probabilities ... ok
[INFO] [stdout] test utils::genome::ncbi::grch38_no_alt::tests::it_does_not_contain_any_other_sequences ... ok
[INFO] [stdout] test utils::genome::ncbi::grch38_no_alt::tests::it_has_the_correct_number_of_decoy_sequences ... ok
[INFO] [stdout] test utils::genome::ncbi::grch38_no_alt::tests::it_has_the_correct_number_of_autosomes ... ok
[INFO] [stdout] test utils::genome::ncbi::grch38_no_alt::tests::it_has_the_correct_number_of_sex_chromosomes ... ok
[INFO] [stdout] test utils::formats::tests::it_correctly_identifies_fastq_files ... ok
[INFO] [stdout] test utils::formats::tests::it_correctly_identifies_vcf_files ... ok
[INFO] [stdout] test utils::formats::tests::it_correctly_identifies_sam_files ... ok
[INFO] [stdout] test utils::formats::tests::it_correctly_identifies_gtf_files ... ok
[INFO] [stdout] test utils::genome::ncbi::grch38_no_alt::tests::it_has_the_correct_number_of_sequence_in_the_primary_assembly ... ok
[INFO] [stdout] test utils::genome::ncbi::grch38_no_alt::tests::it_does_not_contain_any_alternative_contigs ... ok
[INFO] [stdout] test utils::histogram::tests::test_initialization ... ok
[INFO] [stdout] test utils::histogram::tests::test_default_is_one_hundred_zero_based ... ok
[INFO] [stdout] test utils::histogram::tests::test_median_extensively ... ok
[INFO] [stdout] test utils::histogram::tests::test_valid_incremements_and_mean_median ... ok
[INFO] [stdout] test utils::histogram::tests::test_median_on_empty_histogram ... ok
[INFO] [stdout] test utils::histogram::tests::test_values_normalized ... ok
[INFO] [stdout] test utils::histogram::tests::test_values ... ok
[INFO] [stdout] test utils::histogram::tests::test_count_values_from_bottom ... ok
[INFO] [stdout] test utils::histogram::tests::test_invalid_increments ... ok
[INFO] [stdout] test utils::histogram::tests::test_count_values_from_top ... ok
[INFO] [stdout] test utils::genome::ncbi::grch38_no_alt::tests::it_has_the_correct_number_of_unlocalized_sequences ... ok
[INFO] [stdout] test utils::genome::ncbi::grch38_no_alt::tests::it_has_the_correct_number_of_unplaced_sequences ... ok
[INFO] [stdout] test derive::instrument::compute::tests::test_derive_instrument_low_instrument_evidence ... ok
[INFO] [stdout] test derive::instrument::compute::tests::test_derive_instrument_conflicting_flowcell_and_instrument_evidence ... ok
[INFO] [stdout] test derive::instrument::compute::tests::test_derive_instrument_novaseq_succesfully ... ok
[INFO] [stdout] test derive::instrument::compute::tests::test_derive_instrument_medium_instrument_evidence ... ok
[INFO] [stdout] test derive::instrument::compute::tests::test_derive_instrument_from_valid_instrument_name ... ok
[INFO] [stdout] test derive::instrument::compute::tests::test_derive_instrument_no_matches ... ok
[INFO] [stdout] test derive::instrument::compute::tests::test_derive_instrument_from_invalid_instrument_name ... ok
[INFO] [stdout] test derive::instrument::compute::tests::test_derive_instrument_conflicting_flowcell_ids ... ok
[INFO] [stdout] test derive::instrument::compute::tests::test_derive_instrument_conflicting_instrument_ids ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 70 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.20s
[INFO] [stdout] 
[INFO] [stderr]      Running unittests src/main.rs (/opt/rustwide/target/debug/deps/ngs-449129b2db9700c6)
[INFO] [stdout] 
[INFO] [stdout] running 1 test
[INFO] [stdout] test tests::verify_cli ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 1 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.01s
[INFO] [stdout] 
[INFO] [stderr]    Doc-tests ngs
[INFO] [stdout] 
[INFO] [stdout] running 10 tests
[INFO] [stdout] test src/generate/utils.rs - generate::utils::compliment (line 90) ... ok
[INFO] [stdout] test src/utils/histogram.rs - utils::histogram (line 41) ... ok
[INFO] [stdout] test src/utils/pathbuf.rs - utils::pathbuf::AppendExtension::append_extension (line 45) ... ok
[INFO] [stdout] test src/utils/histogram.rs - utils::histogram::Histogram::in_range (line 241) ... ok
[INFO] [stdout] test src/utils/genome.rs - utils::genome::ReferenceGenome::triplet_id (line 277) ... ok
[INFO] [stdout] test src/utils/histogram.rs - utils::histogram (line 72) ... ok
[INFO] [stdout] test src/utils/histogram.rs - utils::histogram (line 98) ... ok
[INFO] [stdout] test src/utils/histogram.rs - utils::histogram (line 60) ... ok
[INFO] [stdout] test src/utils/histogram.rs - utils::histogram (line 85) ... ok
[INFO] [stdout] test src/utils/pathbuf.rs - utils::pathbuf (line 20) ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 10 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 2.72s
[INFO] [stdout] 
[INFO] running `Command { std: "docker" "inspect" "23b8a2da7fe44100f54771a3737a24d92fe0ea68494a41debb43c774affad094", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "23b8a2da7fe44100f54771a3737a24d92fe0ea68494a41debb43c774affad094", kill_on_drop: false }`
[INFO] [stdout] 23b8a2da7fe44100f54771a3737a24d92fe0ea68494a41debb43c774affad094
