[INFO] fetching crate rsomics-methyl 0.1.0...
[INFO] testing rsomics-methyl-0.1.0 against 1.99.0-beta.8+cargoflags=--release for beta-release-1.100-2
[INFO] extracting crate rsomics-methyl 0.1.0 into /workspace/builds/worker-1-tc1/source
[INFO] started tweaking crates.io crate rsomics-methyl 0.1.0
[INFO] removed 0 missing tests
[INFO] finished tweaking crates.io crate rsomics-methyl 0.1.0
[INFO] tweaked toml for crates.io crate rsomics-methyl 0.1.0 written to /workspace/builds/worker-1-tc1/source/Cargo.toml
[INFO] validating manifest of crates.io crate rsomics-methyl 0.1.0 on toolchain 1.99.0-beta.8
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+1.99.0-beta.8" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate crates.io crate rsomics-methyl 0.1.0 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" "+1.99.0-beta.8" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Updating crates.io index
[INFO] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded rsomics-bamio v0.8.1
[INFO] [stderr]   Downloaded thiserror v2.0.19
[INFO] [stderr]   Downloaded thiserror-impl v2.0.19
[INFO] [stderr]   Downloaded rustc_version v0.1.7
[INFO] [stderr]   Downloaded rsomics-pileup v0.8.0
[INFO] [stderr]   Downloaded fs-utils v1.1.4
[INFO] [stderr]   Downloaded semver v0.1.20
[INFO] [stderr]   Downloaded derive-new v0.6.0
[INFO] [stderr]   Downloaded custom_derive v0.1.7
[INFO] [stderr]   Downloaded terminal_size v0.4.4
[INFO] [stderr]   Downloaded rsomics-help v0.4.0
[INFO] [stderr]   Downloaded derive-new v0.7.0
[INFO] [stderr]   Downloaded newtype_derive v0.1.6
[INFO] [stderr]   Downloaded noodles-core v0.20.0
[INFO] [stderr]   Downloaded rsomics-intervals v0.3.0
[INFO] [stderr]   Downloaded pkg-config v0.3.33
[INFO] [stderr]   Downloaded ieee754 v0.2.6
[INFO] [stderr]   Downloaded libdeflater v1.25.2
[INFO] [stderr]   Downloaded bio-types v1.0.4
[INFO] [stderr]   Downloaded strum_macros v0.26.4
[INFO] [stderr]   Downloaded noodles-util v0.79.0
[INFO] [stderr]   Downloaded bit-vec v0.9.1
[INFO] [stderr]   Downloaded lexical-core v1.0.6
[INFO] [stderr]   Downloaded noodles v0.110.0
[INFO] [stderr]   Downloaded either v1.17.0
[INFO] [stderr]   Downloaded linear-map v1.2.0
[INFO] [stderr]   Downloaded clap_derive v4.6.4
[INFO] [stderr]   Downloaded noodles-bgzf v0.47.0
[INFO] [stderr]   Downloaded noodles-fasta v0.61.0
[INFO] [stderr]   Downloaded bzip2 v0.6.1
[INFO] [stderr]   Downloaded noodles-csi v0.56.0
[INFO] [stderr]   Downloaded lexical-parse-integer v1.0.6
[INFO] [stderr]   Downloaded libbz2-rs-sys v0.2.5
[INFO] [stderr]   Downloaded rsomics-common v0.12.1
[INFO] [stderr]   Downloaded clap v4.6.5
[INFO] [stderr]   Downloaded lexical-write-integer v1.0.6
[INFO] [stderr]   Downloaded noodles-bam v0.89.0
[INFO] [stderr]   Downloaded cc v1.4.0
[INFO] [stderr]   Downloaded lexical-write-float v1.0.6
[INFO] [stderr]   Downloaded noodles-sam v0.85.0
[INFO] [stderr]   Downloaded lexical-util v1.0.7
[INFO] [stderr]   Downloaded noodles-cram v0.93.0
[INFO] [stderr]   Downloaded rust-htslib v1.0.1
[INFO] [stderr]   Downloaded clap_builder v4.6.5
[INFO] [stderr]   Downloaded zlib-rs v0.6.6
[INFO] [stderr]   Downloaded lexical-parse-float v1.0.6
[INFO] [stderr]   Downloaded libdeflate-sys v1.25.2
[INFO] [stderr]   Downloaded syn v3.0.3
[INFO] [stderr]   Downloaded lzma-rust2 v0.16.5
[INFO] [stderr]   Downloaded bstr v1.13.0
[INFO] [stderr]   Downloaded regex-automata v0.4.16
[INFO] [stderr]   Downloaded bzip2-sys v0.1.13+1.0.8
[INFO] [stderr]   Downloaded libz-sys v1.1.29
[INFO] [stderr]   Downloaded hts-sys v2.2.1
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-tc1/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-tc1/target:/opt/rustwide/target:rw,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" "-m" "1610612736" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:77db811e55d90add9212f6832c23229e3de5f1c1f9905e8cb07319ea15df73ac" "sleep" "infinity", kill_on_drop: false }`
[INFO] [stdout] a6e974c499c65448c0bf99daf7e53dcc075be3c23c2cf1a902b770e56d0eaa9d
[INFO] running `Command { std: "docker" "start" "a6e974c499c65448c0bf99daf7e53dcc075be3c23c2cf1a902b770e56d0eaa9d", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "a6e974c499c65448c0bf99daf7e53dcc075be3c23c2cf1a902b770e56d0eaa9d", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "exec" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-w" "/opt/rustwide/workdir" "--user" "0:0" "a6e974c499c65448c0bf99daf7e53dcc075be3c23c2cf1a902b770e56d0eaa9d" "/opt/rustwide/cargo-home/bin/cargo" "+1.99.0-beta.8" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "a6e974c499c65448c0bf99daf7e53dcc075be3c23c2cf1a902b770e56d0eaa9d", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "exec" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-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" "-w" "/opt/rustwide/workdir" "--user" "0:0" "a6e974c499c65448c0bf99daf7e53dcc075be3c23c2cf1a902b770e56d0eaa9d" "/opt/rustwide/cargo-home/bin/cargo" "+1.99.0-beta.8" "build" "--frozen" "--message-format=json" "--release", kill_on_drop: false }`
[INFO] [stderr]    Compiling libc v0.2.189
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[INFO] [stderr]    Compiling bindgen v0.72.1
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[INFO] [stderr]    Compiling rustc-hash v2.1.3
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[INFO] [stderr]    Compiling aho-corasick v1.1.4
[INFO] [stderr]    Compiling getrandom v0.4.3
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[INFO] [stderr]    Compiling percent-encoding v2.3.2
[INFO] [stderr]    Compiling jobserver v0.1.35
[INFO] [stderr]    Compiling block-buffer v0.12.1
[INFO] [stderr]    Compiling crypto-common v0.2.2
[INFO] [stderr]    Compiling serde_json v1.0.151
[INFO] [stderr]    Compiling form_urlencoded v1.2.2
[INFO] [stderr]    Compiling cc v1.4.0
[INFO] [stderr]    Compiling regex-automata v0.4.16
[INFO] [stderr]    Compiling lazy_static v1.5.0
[INFO] [stderr]    Compiling bzip2 v0.6.1
[INFO] [stderr]    Compiling fastrand v2.5.0
[INFO] [stderr]    Compiling byteorder v1.5.0
[INFO] [stderr]    Compiling custom_derive v0.1.7
[INFO] [stderr]    Compiling ieee754 v0.2.6
[INFO] [stderr]    Compiling linear-map v1.2.0
[INFO] [stderr]    Compiling digest v0.11.3
[INFO] [stderr]    Compiling sha2 v0.11.0
[INFO] [stderr]    Compiling md-5 v0.11.0
[INFO] [stderr]    Compiling cmake v0.1.58
[INFO] [stderr]    Compiling cexpr v0.6.0
[INFO] [stderr]    Compiling terminal_size v0.4.4
[INFO] [stderr]    Compiling clap_builder v4.6.5
[INFO] [stderr]    Compiling flate2 v1.1.9
[INFO] [stderr]    Compiling tempfile v3.27.0
[INFO] [stderr]    Compiling libdeflate-sys v1.25.2
[INFO] [stderr]    Compiling regex v1.13.1
[INFO] [stderr]    Compiling lzma-sys v0.1.20
[INFO] [stderr]    Compiling bzip2-sys v0.1.13+1.0.8
[INFO] [stderr]    Compiling libz-sys v1.1.29
[INFO] [stderr]    Compiling displaydoc v0.2.7
[INFO] [stderr]    Compiling thiserror-impl v2.0.19
[INFO] [stderr]    Compiling clap_derive v4.6.4
[INFO] [stderr]    Compiling lzma-rust2 v0.16.5
[INFO] [stderr]    Compiling synstructure v0.13.2
[INFO] [stderr]    Compiling serde_derive v1.0.229
[INFO] [stderr]    Compiling rsomics-intervals v0.3.0
[INFO] [stderr]    Compiling zerofrom-derive v0.1.7
[INFO] [stderr]    Compiling yoke-derive v0.8.2
[INFO] [stderr]    Compiling zerovec-derive v0.11.3
[INFO] [stderr]    Compiling thiserror-impl v1.0.69
[INFO] [stderr]    Compiling zerofrom v0.1.8
[INFO] [stderr]    Compiling derive-new v0.6.0
[INFO] [stderr]    Compiling strum_macros v0.26.4
[INFO] [stderr]    Compiling yoke v0.8.3
[INFO] [stderr]    Compiling clap v4.6.5
[INFO] [stderr]    Compiling derive-new v0.7.0
[INFO] [stderr]    Compiling rsomics-help v0.4.0
[INFO] [stderr]    Compiling thiserror v1.0.69
[INFO] [stderr]    Compiling zerovec v0.11.6
[INFO] [stderr]    Compiling zerotrie v0.2.4
[INFO] [stderr]    Compiling tinystr v0.8.3
[INFO] [stderr]    Compiling potential_utf v0.1.5
[INFO] [stderr]    Compiling icu_locale_core v2.2.0
[INFO] [stderr]    Compiling icu_collections v2.2.0
[INFO] [stderr]    Compiling serde v1.0.229
[INFO] [stderr]    Compiling rsomics-common v0.12.1
[INFO] [stderr]    Compiling bio-types v1.0.4
[INFO] [stderr]    Compiling icu_provider v2.2.0
[INFO] [stderr]    Compiling icu_normalizer v2.2.0
[INFO] [stderr]    Compiling icu_properties v2.2.0
[INFO] [stderr]    Compiling hts-sys v2.2.1
[INFO] [stderr]    Compiling idna_adapter v1.2.2
[INFO] [stderr]    Compiling idna v1.1.0
[INFO] [stderr]    Compiling url v2.5.8
[INFO] [stderr]    Compiling libdeflater v1.25.2
[INFO] [stderr]    Compiling noodles-bgzf v0.47.0
[INFO] [stderr]    Compiling noodles-csi v0.56.0
[INFO] [stderr]    Compiling noodles-fasta v0.61.0
[INFO] [stderr]    Compiling noodles-sam v0.85.0
[INFO] [stderr]    Compiling noodles-bam v0.89.0
[INFO] [stderr]    Compiling noodles-cram v0.93.0
[INFO] [stderr]    Compiling noodles-util v0.79.0
[INFO] [stderr]    Compiling noodles v0.110.0
[INFO] [stderr]    Compiling rust-htslib v1.0.1
[INFO] [stderr]    Compiling rsomics-bamio v0.8.1
[INFO] [stderr]    Compiling rsomics-pileup v0.8.0
[INFO] [stderr]    Compiling rsomics-methyl v0.1.0 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished `release` profile [optimized] target(s) in 2m 16s
[INFO] running `Command { std: "docker" "inspect" "a6e974c499c65448c0bf99daf7e53dcc075be3c23c2cf1a902b770e56d0eaa9d", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "exec" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-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" "-w" "/opt/rustwide/workdir" "--user" "0:0" "a6e974c499c65448c0bf99daf7e53dcc075be3c23c2cf1a902b770e56d0eaa9d" "/opt/rustwide/cargo-home/bin/cargo" "+1.99.0-beta.8" "test" "--frozen" "--no-run" "--message-format=json" "--release", kill_on_drop: false }`
[INFO] [stderr]    Compiling rsomics-methyl v0.1.0 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished `release` profile [optimized] target(s) in 10.68s
[INFO] running `Command { std: "docker" "inspect" "a6e974c499c65448c0bf99daf7e53dcc075be3c23c2cf1a902b770e56d0eaa9d", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "exec" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-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" "-w" "/opt/rustwide/workdir" "--user" "0:0" "a6e974c499c65448c0bf99daf7e53dcc075be3c23c2cf1a902b770e56d0eaa9d" "/opt/rustwide/cargo-home/bin/cargo" "+1.99.0-beta.8" "test" "--frozen" "--release", kill_on_drop: false }`
[INFO] [stderr]     Finished `release` profile [optimized] target(s) in 0.15s
[INFO] [stderr]      Running unittests src/lib.rs (/opt/rustwide/target/release/deps/rsomics_methyl-a0ed461545f4ae4a)
[INFO] [stdout] 
[INFO] [stdout] running 30 tests
[INFO] [stdout] test extract::tests::exhaustive_scan_crosses_reference_boundaries ... ok
[INFO] [stdout] test bed::tests::rejects_malformed_and_outside_intervals ... ok
[INFO] [stdout] test conversion::tests::follows_the_full_cigar_and_ignores_low_quality_bases ... ok
[INFO] [stdout] test context::tests::classifies_both_strands_and_boundaries ... ok
[INFO] [stdout] test extract::tests::quality_boost_is_checked ... ok
[INFO] [stdout] test bed::tests::empty_bed_matches_nothing ... ok
[INFO] [stdout] test merge_context::tests::rejects_unknown_reference_and_invalid_rows ... ok
[INFO] [stdout] test mbias::tests::suggestions_find_biased_read_ends ... ok
[INFO] [stdout] test mbias::tests::metrics_match_the_live_methyldackel_golden ... ok
[INFO] [stdout] test extract::tests::rejects_invalid_variant_fractions ... ok
[INFO] [stdout] test extract::tests::overlap_adjustment_matches_across_depth_paths ... ok
[INFO] [stdout] test bed::tests::merges_intervals_and_applies_bed_strands ... ok
[INFO] [stdout] test trimming::tests::fixed_bounds_remove_counts_from_each_end ... ok
[INFO] [stdout] test trimming::tests::inclusion_positions_are_one_based_and_inclusive ... ok
[INFO] [stdout] test trimming::tests::invalid_inclusion_order_is_rejected ... ok
[INFO] [stdout] test trimming::tests::parses_zero_bounds_without_hidden_process_state ... ok
[INFO] [stdout] test calling::tests::reports_nondirectional_read_two_strands ... ok
[INFO] [stdout] test merge_context::tests::merges_cpg_and_chg_without_reordering_intervening_rows ... ok
[INFO] [stdout] test mbias::tests::region_limits_mapped_columns_without_rebasing_read_positions ... ok
[INFO] [stdout] test per_read::tests::low_quality_bases_do_not_advance_the_alignment_twice ... ok
[INFO] [stdout] test merge_context::tests::rejects_unsorted_and_reappearing_chromosomes ... ok
[INFO] [stdout] test per_read::tests::consumes_the_shared_long_cigar_contract ... ok
[INFO] [stdout] test selection::tests::clips_region_end_to_the_reference ... ok
[INFO] [stdout] test conversion::tests::rejects_invalid_thresholds ... ok
[INFO] [stdout] test bed::tests::reads_gzip_by_magic_and_clips_the_reference_end ... ok
[INFO] [stdout] test selection::tests::rejects_unknown_and_outside_regions ... ok
[INFO] [stdout] test per_read::tests::reads_cpgs_beyond_the_upstream_ten_kilobase_window ... ok
[INFO] [stdout] test reference::tests::rejects_duplicate_fasta_index_names ... ok
[INFO] [stdout] test trimming::tests::bounds_select_the_matching_strand_and_read ... ok
[INFO] [stdout] test reference::tests::advances_the_reference_cache_across_chunk_boundaries ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 30 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.06s
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]      Running unittests src/main.rs (/opt/rustwide/target/release/deps/rsomics_methyl-2f73604e3bb5001e)
[INFO] [stdout] running 2 tests
[INFO] [stdout] test extract_output::tests::later_commit_failure_restores_an_earlier_output ... ok
[INFO] [stdout] test cli::tests::integer_percentage_matches_six_decimal_float_output ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 2 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.16s
[INFO] [stdout] 
[INFO] [stderr]      Running tests/cli.rs (/opt/rustwide/target/release/deps/cli-cad48d5339a0a720)
[INFO] [stdout] 
[INFO] [stdout] running 29 tests
[INFO] [stdout] test failed_merge_preserves_existing_output ... ok
[INFO] [stdout] test exhaustive_report_obeys_bed_selection ... ok
[INFO] [stdout] test cytosine_report_rejects_context_merging ... ok
[INFO] [stdout] test invalid_bed_preserves_per_read_output ... ok
[INFO] [stdout] test failed_extract_preserves_every_existing_context_output ... ok
[INFO] [stdout] test failed_per_read_preserves_existing_output ... ok
[INFO] [stdout] test failed_cytosine_report_preserves_existing_output ... ok
[INFO] [stdout] test extract_region_bounds_the_reported_sites ... ok
[INFO] [stdout] test cytosine_report_region_is_exhaustive_only_inside_the_interval ... ok
[INFO] [stdout] test extract_cli_matches_methyldackel_golden ... ok
[INFO] [stdout] test failed_mbias_preserves_every_existing_output ... ok
[INFO] [stdout] test inclusion_bounds_are_one_based_inclusive_and_accept_zero_sentinels ... ok
[INFO] [stdout] test methylkit_rejects_context_merging ... ok
[INFO] [stdout] test cytosine_report_covers_all_contexts_and_reference_boundaries ... ok
[INFO] [stdout] test merge_context_cli_matches_golden ... ok
[INFO] [stdout] test mbias_cli_matches_metrics_and_suggestions_from_methyldackel ... ok
[INFO] [stdout] test cytosine_reports_match_live_methyldackel_including_zero_coverage ... ok
[INFO] [stdout] test per_read_region_requires_the_alignment_start_inside_the_interval ... ok
[INFO] [stdout] test variant_filter_matches_all_context_goldens ... ok
[INFO] [stdout] test fixed_end_trimming_matches_live_methyldackel_goldens ... ok
[INFO] [stdout] test opposite_strand_variant_filter_matches_live_goldens ... ok
[INFO] [stdout] test per_read_bed_selection_uses_alignment_spans_and_bisulfite_strands ... ok
[INFO] [stdout] test region_rejects_unknown_and_outside_references ... ok
[INFO] [stdout] test merged_extract_formats_match_methyldackel_after_combined_depth_filtering ... ok
[INFO] [stdout] test alternative_extract_formats_match_methyldackel_goldens ... ok
[INFO] [stdout] test variant_filter_applies_documented_boundaries_and_merged_exclusion ... ok
[INFO] [stdout] test per_read_matches_the_documented_methyldackel_contract ... ok
[INFO] [stdout] test conversion_filter_matches_live_extract_and_mbias_goldens ... ok
[INFO] [stderr]      Running tests/extract.rs (/opt/rustwide/target/release/deps/extract-378ae7cf0a085d27)
[INFO] [stdout] test bed_selection_matches_live_extract_and_mbias_goldens ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 29 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.22s
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] running 3 tests
[INFO] [stdout] test default_cpg_calls_match_methyldackel_golden ... ok
[INFO] [stdout] test stricter_mapq_filters_all_records ... ok
[INFO] [stdout] test variant_events_report_the_usable_opposite_strand_evidence ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 3 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s
[INFO] [stdout] 
[INFO] running `Command { std: "docker" "inspect" "a6e974c499c65448c0bf99daf7e53dcc075be3c23c2cf1a902b770e56d0eaa9d", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "a6e974c499c65448c0bf99daf7e53dcc075be3c23c2cf1a902b770e56d0eaa9d", kill_on_drop: false }`
[INFO] [stdout] a6e974c499c65448c0bf99daf7e53dcc075be3c23c2cf1a902b770e56d0eaa9d