[Debian-med-packaging] Bug#1103009: genomicsdb: FTBFS in testing/arm64: tests failed
Lucas Nussbaum
lucas at debian.org
Sun Apr 13 17:34:59 BST 2025
Source: genomicsdb
Version: 1.5.4-5
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-20250413 ftbfs-trixie
Hi,
During a rebuild of all packages in testing (trixie), your package failed
to build on arm64.
Relevant part (hopefully):
> make[2]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu'
> Running tests...
> /usr/bin/ctest --force-new-ctest-process --verbose -j4
> UpdateCTestConfiguration from :/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/DartConfiguration.tcl
> UpdateCTestConfiguration from :/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/DartConfiguration.tcl
> Test project /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu
> Constructing a list of tests
> Done constructing a list of tests
> Updating test list for fixtures
> Added 0 tests to meet fixture requirements
> Checking test dependency graph...
> Checking test dependency graph end
> Connected to MAKE jobserver
> test 1
> Start 1: test_array_schema
>
> 1: Test command: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/test_array_schema
> 1: Working Directory: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test
> 1: Test timeout computed to be: 10000000
> test 2
> Start 2: test_print_array_schema
>
> 2: Test command: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/test_print_array_schema
> 2: Working Directory: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test
> 2: Test timeout computed to be: 10000000
> test 3
> Start 3: test_print_book_keeping
>
> 3: Test command: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/test_print_book_keeping
> 3: Working Directory: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test
> 3: Test timeout computed to be: 10000000
> test 4
> Start 4: test_sparse_array_benchmark
>
> 4: Test command: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/test_sparse_array_benchmark
> 4: Working Directory: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test
> 4: Test timeout computed to be: 10000000
> 1: Randomness seeded to: 2001397775
> 1: [TileDB::ArraySchema] Error: Cannot set attributes; No attributes given.
> 1: [TileDB::ArraySchema] Error: Cannot set attributes; The number of attributes must be positive.
> 1: [TileDB::ArraySchema] Error: Cannot set attributes; Duplicate attribute names.
> 1: [TileDB::ArraySchema] Error: Cannot set cell order; Invalid cell order.
> 1: [TileDB::ArraySchema] Error: Unsupported. For a given VAR attribute, both compression and offsets_compression have to either have compression or not
> 1: .
> 1: [TileDB::ArraySchema] Error: Cannot set dimensions; No dimensions given.
> 1: [TileDB::ArraySchema] Error: Cannot set dimensions; The number of dimensions must be positive.
> 1: [TileDB::ArraySchema] Error: Cannot set dimensions; Duplicate dimension names.
> 1: [TileDB::ArraySchema] Error: Cannot set dimensions; Attribute name same as dimension name.
> 1: [TileDB::ArraySchema] Error: Cannot set types; Types not provided.
> 1: [TileDB::ArraySchema] Error: Cannot set types; Invalid type.
> 1: [TileDB::ArraySchema] Error: Cannot set domain; Domain not provided.
> 1: [TileDB::ArraySchema] Error: Cannot set tile order; Invalid tile order.
> 1: Array Schema Version:
> 1: 2
> 1: Array workspace:
> 1: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test
> 1: Array name:
> 1:
> 1: Dimension names:
> 1: dim1
> 1: dim2
> 1: Attribute names:
> 1: test_attr
> 1: test_attr1
> 1: Domain:
> 1: dim1: [0,99]
> 1: dim2: [0,99]
> 1: Types:
> 1: test_attr: int32[1]
> 1: test_attr1: int32[var]
> 1: Coordinates: int32
> 1: Cell sizes (in bytes):
> 1: test_attr: 4
> 1: test_attr1: var
> 1: Coordinates: 8
> 1: Dense:
> 1: false
> 1: Tile types:
> 1: irregular
> 1: Tile order:
> 1: -
> 1: Cell order:
> 1: column-major
> 1: Capacity:
> 1: 10000
> 1: Tile extents:
> 1: -
> 1: Compression for test_attr
> 1: Type = GZIP
> 1: Level= -1
> 1: Compression for test_attr1
> 1: Type = GZIP
> 1: Level= -1
> 1: Compression for offsets of test_attr1
> 1: Type = GZIP + DELTA_ENCODE
> 1: Level= -1
> 1: Compression for Coordinates:
> 1: Type = GZIP
> 1: Array Schema Version:
> 1: 2
> 1: Array name:
> 1: this_array
> 1: Dimension names:
> 1: one_dim
> 1: Attribute names:
> 1: this_attribute
> 1: Domain:
> 1: one_dim: [1,100]
> 1: Types:
> 1: this_attribute: int32[1]
> 1: Coordinates: int32
> 1: Cell sizes (in bytes):
> 1: this_attribute: 4
> 1: Coordinates: 4
> 1: Dense:
> 1: false
> 1: Tile types:
> 1: regular
> 1: Tile order:
> 1: row-major
> 1: Cell order:
> 1: row-major
> 1: Capacity:
> 1: -
> 1: Tile extents:
> 1: one_dim: 25
> 1: Compression for this_attribute
> 1: Type = NONE
> 1: Level= -1
> 1: Compression for Coordinates:
> 1: Type = NONE
> 1: Array Schema Version:
> 1: 2
> 1: Array name:
> 1: this_array
> 1: Dimension names:
> 1: one_dim
> 1: Attribute names:
> 1: this_attribute
> 1: Domain:
> 1: one_dim: [1,100]
> 1: Types:
> 1: this_attribute: int32[1]
> 1: Coordinates: int32
> 1: Cell sizes (in bytes):
> 1: this_attribute: 4
> 1: Coordinates: 4
> 1: Dense:
> 1: false
> 1: Tile types:
> 1: regular
> 1: Tile order:
> 1: row-major
> 1: Cell order:
> 1: row-major
> 1: Capacity:
> 1: -
> 1: Tile extents:
> 1: one_dim: 25
> 1: Compression for this_attribute
> 1: Type = NONE
> 1: Level= -1
> 1: Compression for Coordinates:
> 1: Type = NONE
> 1: Array Schema Version:
> 1: 2
> 1: Array name:
> 1: this_array_64
> 1: Dimension names:
> 1: one_dim_64
> 1: Attribute names:
> 1: this_attribute
> 1: Domain:
> 1: one_dim_64: [1,1]
> 1: Types:
> 1: this_attribute: int64[1]
> 1: Coordinates: int64
> 1: Cell sizes (in bytes):
> 1: this_attribute: 8
> 1: Coordinates: 8
> 1: Dense:
> 1: false
> 1: Tile types:
> 1: regular
> 1: Tile order:
> 1: row-major
> 1: Cell order:
> 1: row-major
> 1: Capacity:
> 1: -
> 1: Tile extents:
> 1: one_dim_64: 25
> 1: Compression for this_attribute
> 1: Type = NONE
> 1: Level= -1
> 1: Compression for Coordinates:
> 1: Type = NONE
> 1: ===============================================================================
> 1: All tests passed (43 assertions in 7 test cases)
> 1:
> 2: No arguments specified
> 2: Usage: test_print_array_schema /path/to/TileDBArray
> 1/22 Test #1: test_array_schema ................ Passed 0.01 sec
> 2/22 Test #2: test_print_array_schema .......... Passed 0.00 sec
> test 5
> Start 5: test_array_iterator
>
> 5: Test command: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/test_array_iterator
> 5: Working Directory: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test
> 5: Test timeout computed to be: 10000000
> test 6
> Start 6: test_array_schema_api
>
> 6: Test command: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/test_array_schema_api
> 6: Working Directory: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test
> 6: Test timeout computed to be: 10000000
> 3: No arguments specified
> 3: Usage: test_print_book_keeping /path/to/TileDBArray/<fragment>
> 3/22 Test #3: test_print_book_keeping .......... Passed 0.01 sec
> test 7
> Start 7: test_dense_array_api
>
> 7: Test command: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/test_dense_array_api
> 7: Working Directory: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test
> 7: Test timeout computed to be: 10000000
> 4: Randomness seeded to: 1376267798
> 4: ===============================================================================
> 4: test cases: 1 | 1 passed
> 4: assertions: - none -
> 4:
> 4/22 Test #4: test_sparse_array_benchmark ...... Passed 0.01 sec
> test 8
> Start 8: test_sparse_array_api
>
> 8: Test command: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/test_sparse_array_api
> 8: Working Directory: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test
> 8: Test timeout computed to be: 10000000
> 5: Randomness seeded to: 2251606868
> 5: [TileDB::utils] Error: (gzip_handle_error) Cannot compress with GZIP: deflateInit error: Z_STREAM_ERROR
> 5:
> 5: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 5: test_array_iterator is a Catch2 v3.7.1 host application.
> 5: Run with -? for options
> 5:
> 5: -------------------------------------------------------------------------------
> 5: Test sparse array iterator
> 5: -------------------------------------------------------------------------------
> 5: ./genomicsdb-tiledb/test/src/c_api/test_array_iterator.cc:194
> 5: ...............................................................................
> 5:
> 5: ./genomicsdb-tiledb/test/src/c_api/test_array_iterator.cc:194: FAILED:
> 5: {Unknown expression after the reported line}
> 5: due to a fatal error condition:
> 5: SIGSEGV - Segmentation violation signal
> 5:
> 5: ===============================================================================
> 5: test cases: 1 | 1 failed
> 5: assertions: 7 | 6 passed | 1 failed
> 5:
> 5/22 Test #5: test_array_iterator ..............***Exception: SegFault 0.01 sec
> Randomness seeded to: 2251606868
> [TileDB::utils] Error: (gzip_handle_error) Cannot compress with GZIP: deflateInit error: Z_STREAM_ERROR
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> test_array_iterator is a Catch2 v3.7.1 host application.
> Run with -? for options
>
> -------------------------------------------------------------------------------
> Test sparse array iterator
> -------------------------------------------------------------------------------
> ./genomicsdb-tiledb/test/src/c_api/test_array_iterator.cc:194
> ...............................................................................
>
> ./genomicsdb-tiledb/test/src/c_api/test_array_iterator.cc:194: FAILED:
> {Unknown expression after the reported line}
> due to a fatal error condition:
> SIGSEGV - Segmentation violation signal
>
> ===============================================================================
> test cases: 1 | 1 failed
> assertions: 7 | 6 passed | 1 failed
>
>
> test 9
> Start 9: test_tiledb_utils
>
> 9: Test command: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/test_tiledb_utils
> 9: Working Directory: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test
> 9: Test timeout computed to be: 10000000
> 6: Randomness seeded to: 3189999997
> 6:
> 6: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 6: test_array_schema_api is a Catch2 v3.7.1 host application.
> 6: Run with -? for options
> 6:
> 6: -------------------------------------------------------------------------------
> 6: Test array schema backward compatibility 2
> 6: -------------------------------------------------------------------------------
> 6: ./genomicsdb-tiledb/test/src/c_api/test_array_schema_api.cc:349
> 6: ...............................................................................
> 6:
> 6: ./genomicsdb-tiledb/test/src/c_api/test_array_schema_api.cc:368: FAILED:
> 6: CHECK( array_schema.compression_level_[1] == -1 )
> 6: with expansion:
> 6: 255 == -1
> 6:
> 6: ===============================================================================
> 6: test cases: 13 | 12 passed | 1 failed
> 6: assertions: 335 | 334 passed | 1 failed
> 6:
> 6/22 Test #6: test_array_schema_api ............***Failed 0.01 sec
> Randomness seeded to: 3189999997
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> test_array_schema_api is a Catch2 v3.7.1 host application.
> Run with -? for options
>
> -------------------------------------------------------------------------------
> Test array schema backward compatibility 2
> -------------------------------------------------------------------------------
> ./genomicsdb-tiledb/test/src/c_api/test_array_schema_api.cc:349
> ...............................................................................
>
> ./genomicsdb-tiledb/test/src/c_api/test_array_schema_api.cc:368: FAILED:
> CHECK( array_schema.compression_level_[1] == -1 )
> with expansion:
> 255 == -1
>
> ===============================================================================
> test cases: 13 | 12 passed | 1 failed
> assertions: 335 | 334 passed | 1 failed
>
>
> test 10
> Start 10: test_codec
>
> 10: Test command: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/test_codec
> 10: Working Directory: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test
> 10: Test timeout computed to be: 10000000
> 9: Randomness seeded to: 1015850288
> 9: [TileDB::utils] Error: (set_working_dir) Failed to set_working_dir as /tmp/TileDBTestlesjua/WORKSPACE.nonexistent does not exist
> 9: [TileDB::FileSystem] Error: (get_dirs) Cannot open directory path=/tmp/TileDBTests02csJ/WORKSPACE errno=2(No such file or directory)
> 9: [TileDB::FileSystem] Error: (get_files) Cannot open directory path=/tmp/TileDBTests02csJ/WORKSPACE errno=2(No such file or directory)
> 9: [TileDB::FileSystem] Error: (get_dirs) Cannot open directory path=/tmp/TileDBTest9v2GW6/WORKSPACE errno=2(No such file or directory)
> 10: Randomness seeded to: 4283861272
> 10: [TileDB::utils] Error: (gzip_handle_error) Cannot decompress with GZIP: inflate error: Z_BUF_ERROR
> 10: [TileDB::Codec] Error: Could not decompress with GZIP.
> 10: [TileDB::utils] Error: (gzip_handle_error) Cannot decompress with GZIP: inflate error: Z_BUF_ERROR
> 10: [TileDB::Codec] Error: Could not decompress with GZIP.
> 10: [TileDB::utils] Error: (gzip_handle_error) Cannot decompress with GZIP: inflate error: Z_DATA_ERROR
> 10: [TileDB::Codec] Error: Could not decompress with GZIP.
> 10: [TileDB::Codec] Error: Codec for compression type=15 has already been registered.
> 10: ===============================================================================
> 10: All tests passed (31 assertions in 5 test cases)
> 10:
> 7/22 Test #10: test_codec ....................... Passed 0.01 sec
> test 11
> Start 11: test_codec_filter
>
> 11: Test command: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/test_codec_filter
> 11: Working Directory: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test
> 11: Test timeout computed to be: 10000000
> 9: 7e820c3ee657b1a27a56a7be9d202a7a7e820c3ee657b1a27a56a7be9d202a7a[TileDB::FileSystem] Error: (read_from_file) EOF reached; File reading error path=/tmp/TileDBTestwBJ4ah/test_file
> 9: [TileDB::FileSystem] Error: (read_from_file) EOF reached; File reading error path=/tmp/TileDBTestwBJ4ah/test_file
> 11: Randomness seeded to: 1612411201
> 11: [TileDB::CodecFilter] Error: virtual method should be overridden.
> 11: [TileDB::CodecFilter] Error: virtual method should be overridden.
> 11: [TileDB::CodecFilter] Error: virtual method should be overridden.
> 11: [TileDB::CodecFilter] Error: virtual method should be overridden.
> 11: [TileDB::CodecFilter] Error: Tile size to pre-compression filter Delta Encoding should be a multiple of sizeof type.
> 11: [TileDB::CodecFilter] Error: Tile size to pre-compression filter Delta Encoding should be a multiple of sizeof type.
> 11: [TileDB::CodecFilter] Error: Tile size to pre-compression filter Delta Encoding should be a multiple of sizeof type.
> 11: [TileDB::CodecFilter] Error: Tile size to pre-compression filter Delta Encoding should be a multiple of sizeof type.
> 11: [TileDB::CodecFilter] Error: Tile size to pre-compression filter Delta Encoding should be a multiple of sizeof type.
> 11: [TileDB::CodecFilter] Error: Tile size to pre-compression filter Delta Encoding should be a multiple of sizeof type.
> 11: [TileDB::CodecFilter] Error: Tile size to pre-compression filter Delta Encoding should be a multiple of sizeof type.
> 11: [TileDB::CodecFilter] Error: Tile size to pre-compression filter Delta Encoding should be a multiple of sizeof type.
> 11: [TileDB::CodecFilter] Error: Tile size to pre-compression filter Delta Encoding should be a multiple of sizeof type.
> 11: [TileDB::CodecFilter] Error: Tile size to pre-compression filter Delta Encoding should be a multiple of sizeof type.
> 11: [TileDB::CodecFilter] Error: Tile size to pre-compression filter Delta Encoding should be a multiple of sizeof type.
> 11: [TileDB::CodecFilter] Error: Tile size to pre-compression filter Delta Encoding should be a multiple of sizeof type.
> 11: [TileDB::CodecFilter] Error: Tile size to pre-compression filter Delta Encoding should be a multiple of sizeof type.
> 11: [TileDB::CodecFilter] Error: Tile size to pre-compression filter Delta Encoding should be a multiple of sizeof type.
> 11: [TileDB::CodecFilter] Error: Tile size to pre-compression filter Bit Shuffle should be a multiple of sizeof type.
> 11: [TileDB::CodecFilter] Error: Tile size to pre-compression filter Bit Shuffle should be a multiple of sizeof type.
> 11: [TileDB::CodecFilter] Error: Tile size to pre-compression filter Bit Shuffle should be a multiple of sizeof type.
> 11: [TileDB::CodecFilter] Error: Tile size to pre-compression filter Bit Shuffle should be a multiple of sizeof type.
> 11: [TileDB::CodecFilter] Error: Tile size to pre-compression filter Bit Shuffle should be a multiple of sizeof type.
> 11: [TileDB::CodecFilter] Error: Tile size to pre-compression filter Bit Shuffle should be a multiple of sizeof type.
> 11: [TileDB::CodecFilter] Error: Tile size to pre-compression filter Bit Shuffle should be a multiple of sizeof type.
> 11: [TileDB::CodecFilter] Error: Tile size to pre-compression filter Bit Shuffle should be a multiple of sizeof type.
> 11: [TileDB::CodecFilter] Error: Tile size to pre-compression filter Bit Shuffle should be a multiple of sizeof type.
> 11: [TileDB::CodecFilter] Error: Tile size to pre-compression filter Bit Shuffle should be a multiple of sizeof type.
> 11: ===============================================================================
> 11: All tests passed (192 assertions in 2 test cases)
> 11:
> 8/22 Test #11: test_codec_filter ................ Passed 0.00 sec
> test 12
> Start 12: test_expressions
>
> 12: Test command: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/test_expressions
> 12: Working Directory: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test
> 12: Test timeout computed to be: 10000000
> 12: Randomness seeded to: 2406179012
> 12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression:
> 12: Index to variable "a1" is out of bounds.
> 12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression:
> 12: Index to variable "a1" is out of bounds.
> 12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression:
> 12: Index to variable "a1" is out of bounds.
> 12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression:
> 12: Index to variable "a1" is out of bounds.
> 12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression:
> 12: Index to variable "a1" is out of bounds.
> 12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression:
> 12: Index to variable "a1" is out of bounds.
> 12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression:
> 12: Index to variable "a1" is out of bounds.
> 12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression:
> 12: Index to variable "a1" is out of bounds.
> 12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression:
> 12: Index to variable "a1" is out of bounds.
> 12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression:
> 12: Index to variable "a1" is out of bounds.
> 12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression:
> 12: Index to variable "a1" is out of bounds.
> 12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression:
> 12: Index to variable "a1" is out of bounds.
> 12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression:
> 12: Index to variable "a1" is out of bounds.
> 12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression:
> 12: Index to variable "a1" is out of bounds.
> 12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression:
> 12: Index to variable "a1" is out of bounds.
> 12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression:
> 12: Index to variable "a1" is out of bounds.
> 12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression:
> 12: Index to variable "a1" is out of bounds.
> 12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression:
> 12: Index to variable "a1" is out of bounds.
> 12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression:
> 12: Index to variable "a1" is out of bounds.
> 12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression:
> 12: Index to variable "a1" is out of bounds.
> 12: [TileDB::Expression] Error: (init) Attribute a2 in expression filter not present in the array schema
> 12: [TileDB::Expression] Error: (init) Parser SetExpr error for expression 'a1 === 22': Unexpected operator "=" found at position 5.
> 12: [TileDB::Expression] Error: (evaluate) Initialization not completed
> 12: [TileDB::Expression] Error: (evaluate_cell) Initialization not completed
> 12: [TileDB::Expression] Error: (evaluate_cell) Only expressions evaluating to booleans is supported
> 12: [TileDB::Expression] Error: (init) Parser SetExpr error for expression 'resolve(a1) &= ""': Too few parameters passed to function "resolve".
> 12: [TileDB::Expression] Error: (init) Expression parsing for dense arrays not yet implemented
> 12: ===============================================================================
> 12: All tests passed (3334 assertions in 83 test cases)
> 12:
> 9/22 Test #12: test_expressions ................. Passed 0.02 sec
> test 13
> Start 13: test_filter_api
>
> 13: Test command: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/test_filter_api
> 13: Working Directory: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test
> 13: Test timeout computed to be: 10000000
> 13: Randomness seeded to: 75739269
> 13: ===============================================================================
> 13: All tests passed (288 assertions in 3 test cases)
> 13:
> 10/22 Test #13: test_filter_api .................. Passed 0.02 sec
> test 14
> Start 14: test_mem_utils
>
> 14: Test command: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/test_mem_utils
> 14: Working Directory: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test
> 14: Test timeout computed to be: 10000000
> 14: Randomness seeded to: 2944208117
> 14: Sun Apr 13 13:46:20 2025 Memory stats Tracking memory usage START size=6MB resident=1MB share=1MB text=604KB lib=0 data=540KB dt=0
> 9: ===============================================================================
> 9: All tests passed (10488234 assertions in 9 test cases)
> 9:
> 11/22 Test #9: test_tiledb_utils ................ Passed 0.58 sec
> test 15
> Start 15: test_uri
>
> 15: Test command: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/test_uri
> 15: Working Directory: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test
> 15: Test timeout computed to be: 10000000
> 15: Randomness seeded to: 4126063120
> 15: ===============================================================================
> 15: All tests passed (113 assertions in 1 test case)
> 15:
> 12/22 Test #15: test_uri ......................... Passed 0.01 sec
> test 16
> Start 16: test_utils
>
> 16: Test command: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/test_utils
> 16: Working Directory: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test
> 16: Test timeout computed to be: 10000000
> 16: Randomness seeded to: 3085543028
> 16: [TileDB::utils] Error: (RLE_compress) Failed compressing with RLE; invalid input buffer format
> 16: [TileDB::utils] Error: (RLE_compress) Failed compressing with RLE; output buffer overflow
> 16: [TileDB::utils] Error: (RLE_compress_coords_row) Failed compressing coordinates with RLE; invalid buffer format
> 16: [TileDB::utils] Error: (RLE_compress_coords_row) Filed compressing coordinates with RLE; output buffer overflow
> 16: [TileDB::utils] Error: (RLE_compress_coords_col) Failed compressing coordinates with RLE; invalid buffer format
> 16: [TileDB::utils] Error: (RLE_compress_coords_col) Failed compressing coordinates with RLE; output buffer overflow
> 16: [TileDB::FileSystem] Error: (create_dir) Cannot create directory path=/non-existent-dir/dir errno=2(No such file or directory)
> 16: [TileDB::FileSystem] Error: (create_file) Failed to create file path=/non-existent-dir/file errno=2(No such file or directory)
> 16: [TileDB::FileSystem] Error: (write_to_file) Cannot write to file; File opening error path=/non-existent-dir/file errno=2(No such file or directory)
> 16: [TileDB::FileSystem] Error: (read_from_file) Cannot read from file; File opening error path=/non-existent-dir/file errno=2(No such file or directory)
> 16: [TileDB::FileSystem] Error: (delete_file) Cannot remove file path=/non-existent-dir/file errno=2(No such file or directory)
> 16: [TileDB::FileSystem] Error: (delete_dir) Could not recursively delete directory path=/non-existent-dir/dir errno=2(No such file or directory)
> 16: [TileDB::FileSystem] Error: (move_path) Cannot rename path path=/non-existent-dir/old errno=2(No such file or directory)
> 16: ===============================================================================
> 16: All tests passed (86 assertions in 6 test cases)
> 16:
> 13/22 Test #16: test_utils ....................... Passed 0.02 sec
> test 17
> Start 17: test_posixfs
>
> 17: Test command: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/test_posixfs
> 17: Working Directory: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test
> 17: Test timeout computed to be: 10000000
> 17: Randomness seeded to: 3934059981
> 17: [TileDB::FileSystem] Error: (create_dir) Cannot create directory; Directory already exists path=/tmp/TileDBTestxuGWDJ/test_posixfs_dirdir
> 17: [TileDB::FileSystem] Error: (create_dir) Cannot create directory path=/non-existent-dir/foo errno=2(No such file or directory)
> 17: [TileDB::FileSystem] Error: (create_file) Failed to create file path=/tmp/TileDBTestxuGWDJ/test_posixfs_dirdir errno=21(Is a directory)
> 17: [TileDB::FileSystem] Error: (create_file) Failed to create file path=/tmp/TileDBTestxuGWDJ/test_posixfs_dirdir errno=21(Is a directory)
> 17: [TileDB::FileSystem] Error: (get_dirs) Cannot open directory path=non-existent-dir errno=2(No such file or directory)
> 17: [TileDB::FileSystem] Error: (move_path) Cannot rename path path=non-existent-dir errno=18(Invalid cross-device link)
> 17: [TileDB::FileSystem] Error: (delete_dir) Could not recursively delete directory path=non-existent-dir errno=2(No such file or directory)
> 17: [TileDB::FileSystem] Error: (get_files) Cannot open directory path=non-existent-dir errno=2(No such file or directory)
> 17: [TileDB::FileSystem] Error: (delete_file) Cannot remove file path=/tmp/TileDBTestRfp6d4/test_posixfs_dirfile/foo1 errno=2(No such file or directory)
> 17: [TileDB::FileSystem] Error: (read_from_file) EOF reached; File reading error path=/tmp/TileDBTestnowTrR/test_posixfs_dirread_write/foo
> 17: [TileDB::FileSystem] Error: (read_from_file) EOF reached; File reading error path=/tmp/TileDBTestnowTrR/test_posixfs_dirread_write/foo
> 17: [TileDB::FileSystem] Error: (read_from_file) EOF reached; File reading error path=/tmp/TileDBTestnowTrR/test_posixfs_dirread_write/foo
> 17: [TileDB::FileSystem] Error: (read_from_file) Cannot read from file; File opening error path=non-existent-dir/foo errno=2(No such file or directory)
> 17: [TileDB::FileSystem] Error: (write_to_file) Cannot write to file; File opening error path=non-existent-dir/foo errno=2(No such file or directory)
> 17: [TileDB::FileSystem] Error: (read_from_file) Cannot open simultaneously for reads/writes path=test_posixfs_dir_locking/foo
> 17: [TileDB::FileSystem] Error: (~PosixFS) File does not seem to be closed path=test_dir_locking1/foo_sync
> 17: [TileDB::FileSystem] Error: (~PosixFS) File does not seem to be closed path=test_dir_locking1/foo_no_close
> 17: ===============================================================================
> 17: All tests passed (258 assertions in 11 test cases)
> 17:
> 14/22 Test #17: test_posixfs ..................... Passed 0.41 sec
> test 18
> Start 18: test_storage_buffer
>
> 18: Test command: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/test_storage_buffer
> 18: Working Directory: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test
> 18: Test timeout computed to be: 10000000
> 18: Randomness seeded to: 2865397563
> 18: [TileDB::StorageBuffer] Error: (StorageBuffer) Cannot perform buffered reads or writes as there is no buffer chunk size set path=/tmp/TileDBTestuT4N1H/test-file
> 18: [TileDB::StorageBuffer] Error: (StorageBuffer) File does not seem to exist or is of zero length path=/tmp/TileDBTestuT4N1H/test-file-non-existent errno=2(No such file or directory)
> 18: [TileDB::StorageBuffer] Error: (StorageBuffer) Cannot perform buffered reads or writes as there is no buffer chunk size set path=/tmp/TileDBTestuT4N1H/test-file
> 18: [TileDB::StorageBuffer] Error: (read_buffer) Cannot read past the filesize from buffer path=/tmp/TileDBTestuT4N1H/test-file
> 18: [TileDB::FileSystem] Error: (write_to_file) Cannot write to file; File opening error path=/non-existent-file errno=13(Permission denied)
> 18: [TileDB::StorageBuffer] Error: (write_buffer) Cannot write bytes path=/non-existent-file errno=13(Permission denied)
> 18: [TileDB::StorageBuffer] Error: (finalize) Could not finalize buffer after compression path=/non-existent-file errno=13(Permission denied)
> 18: [TileDB::FileSystem] Error: (write_to_file) Cannot write to file; File opening error path=/non-existent-file errno=13(Permission denied)
> 18: [TileDB::StorageBuffer] Error: (gzip_write_buffer) Cannot write bytes path=/non-existent-file errno=13(Permission denied)
> 18: [TileDB::StorageBuffer] Error: (write_buffer) Cannot compress and/or write bytes path=/non-existent-file errno=13(Permission denied)
> 18: [TileDB::StorageBuffer] Error: (finalize) Could not finalize buffer after compression path=/non-existent-file errno=13(Permission denied)
> 18: [TileDB::StorageBuffer] Error: (StorageBuffer) File does not seem to exist or is of zero length path=/non-existent-file errno=2(No such file or directory)
> 18: [TileDB::StorageBuffer] Error: (StorageBuffer) File does not seem to exist or is of zero length path=/non-existent-file errno=2(No such file or directory)
> 18: [TileDB::StorageBuffer] Error: (StorageBuffer) File does not seem to exist or is of zero length path=/non-existent-file errno=2(No such file or directory)
> 18: [TileDB::StorageBuffer] Error: (StorageBuffer) File does not seem to exist or is of zero length path=/non-existent-file errno=2(No such file or directory)
> 18: [TileDB::StorageBuffer] Error: (write_buffer) Compression type=1000 not supported in StorageBuffer
> 18: [TileDB::StorageBuffer] Error: (finalize) Could not finalize buffer after compression path=/non-existent-file errno=2(No such file or directory)
> 18: [TileDB::StorageBuffer] Error: (read_buffer) Compression type=1000 for read_buffer not supported for CompressedStorageBuffer
> 18: [TileDB::StorageBuffer] Error: (read_buffer) Cannot read past the filesize from buffer path=/tmp/TileDBTestlKhC7n/compressed_foo
> 14: Sun Apr 13 13:46:21 2025 Memory stats Tracking memory usage END size=6MB resident=1MB share=1MB text=604KB lib=0 data=540KB dt=0
> 14: ===============================================================================
> 14: test cases: 1 | 1 passed
> 14: assertions: - none -
> 14:
> 15/22 Test #14: test_mem_utils ................... Passed 1.00 sec
> test 19
> Start 19: ci_tests
>
> 19: Test command: /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/run_examples.sh "&&" "echo" "Running diff with expected_results" "&&" "diff" "log" "/build/reproducible-path/genomicsdb-1.5.4/examples/expected_results"
> 19: Working Directory: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples
> 19: Test timeout computed to be: 10000000
> 19: Example 1: Running ./tiledb_workspace_group_create...
> 19: Example 1: Done running ./tiledb_workspace_group_create
> 19: Example 2: Running ./tiledb_ls_workspaces...
> 19: [TileDB::FileSystem] Error: (get_dirs) Cannot open directory path=&& errno=2(No such file or directory)
> 19: Example 2: Done running ./tiledb_ls_workspaces
> 19: Example 3: Running ./tiledb_array_create_dense...
> 19: Example 3: Done running ./tiledb_array_create_dense
> 19: Example 4: Running ./tiledb_array_create_sparse...
> 19: Example 4: Done running ./tiledb_array_create_sparse
> 19: Example 5: Running ./tiledb_array_primitive...
> 19: Array name: my_workspace/dense_arrays/my_array_A
> 19: Attributes: a1 a2 a3
> 19: The array is dense
> 19: Array name: my_workspace/sparse_arrays/my_array_B
> 19: Attributes: a1 a2 a3
> 19: The array is sparse
> 19: Example 5: Done running ./tiledb_array_primitive
> 19: Example 6: Running ./tiledb_array_write_dense_1...
> 19: [TileDB::utils] Error: (gzip_handle_error) Cannot compress with GZIP: deflateInit error: Z_STREAM_ERROR
> 19: [TileDB::Codec] Error: Could not compress with GZIP.
> 19: [TileDB::WriteState] Error: Cannot compress tile for /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/my_workspace/dense_arrays/my_array_A/.__6156c619-b534-43da-a5c2-776530a9ee3f281473534844960_1744551981809/a1.tdb.
> 19: [TileDB::WriteState] Error: Cannot compress tile for /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/my_workspace/dense_arrays/my_array_A/.__6156c619-b534-43da-a5c2-776530a9ee3f281473534844960_1744551981809/a1.tdb[Examples::./genomicsdb-tiledb/examples/src/tiledb_array_write_dense_1.cc] Runtime Error.
> 19:
> 19: Exit Status=255. Quitting execution of run_examples.sh
> 16/22 Test #19: ci_tests .........................***Failed 0.06 sec
> Example 1: Running ./tiledb_workspace_group_create...
> Example 1: Done running ./tiledb_workspace_group_create
> Example 2: Running ./tiledb_ls_workspaces...
> [TileDB::FileSystem] Error: (get_dirs) Cannot open directory path=&& errno=2(No such file or directory)
> Example 2: Done running ./tiledb_ls_workspaces
> Example 3: Running ./tiledb_array_create_dense...
> Example 3: Done running ./tiledb_array_create_dense
> Example 4: Running ./tiledb_array_create_sparse...
> Example 4: Done running ./tiledb_array_create_sparse
> Example 5: Running ./tiledb_array_primitive...
> Array name: my_workspace/dense_arrays/my_array_A
> Attributes: a1 a2 a3
> The array is dense
> Array name: my_workspace/sparse_arrays/my_array_B
> Attributes: a1 a2 a3
> The array is sparse
> Example 5: Done running ./tiledb_array_primitive
> Example 6: Running ./tiledb_array_write_dense_1...
> [TileDB::utils] Error: (gzip_handle_error) Cannot compress with GZIP: deflateInit error: Z_STREAM_ERROR
> [TileDB::Codec] Error: Could not compress with GZIP.
> [TileDB::WriteState] Error: Cannot compress tile for /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/my_workspace/dense_arrays/my_array_A/.__6156c619-b534-43da-a5c2-776530a9ee3f281473534844960_1744551981809/a1.tdb.
> [TileDB::WriteState] Error: Cannot compress tile for /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/my_workspace/dense_arrays/my_array_A/.__6156c619-b534-43da-a5c2-776530a9ee3f281473534844960_1744551981809/a1.tdb[Examples::./genomicsdb-tiledb/examples/src/tiledb_array_write_dense_1.cc] Runtime Error.
>
> Exit Status=255. Quitting execution of run_examples.sh
>
> test 20
> Start 20: ctests
>
> 20: Test command: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests "-d" "yes"
> 20: Working Directory: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp
> 20: Test timeout computed to be: 10000000
> 20: 13:46:21.870 DEBUG NativeGenomicsDB - pid=7313 tid=7313 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 20: 13:46:21.871 WARN NativeGenomicsDB - pid=7313 tid=7313 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 20: 13:46:21.871 DEBUG NativeGenomicsDB - pid=7313 tid=7313 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 20: Randomness seeded to: 3428592844
> 20: 0.002 s: Check loader configuration with json file
> 20: 13:46:21.871 DEBUG NativeGenomicsDB - pid=7313 tid=7313 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 20: 13:46:21.871 WARN NativeGenomicsDB - pid=7313 tid=7313 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 20: 13:46:21.872 DEBUG NativeGenomicsDB - pid=7313 tid=7313 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 20: 0.001 s: Check configuration with json file
> 20: 13:46:21.872 DEBUG NativeGenomicsDB - pid=7313 tid=7313 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 20: 13:46:21.872 WARN NativeGenomicsDB - pid=7313 tid=7313 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 20: 13:46:21.873 DEBUG NativeGenomicsDB - pid=7313 tid=7313 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 20: 0.001 s: Check configuration with json file and shared posifs optim
> 20: 13:46:21.873 DEBUG NativeGenomicsDB - pid=7313 tid=7313 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 20: 13:46:21.873 WARN NativeGenomicsDB - pid=7313 tid=7313 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 20: 13:46:21.873 DEBUG NativeGenomicsDB - pid=7313 tid=7313 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 20: 0.001 s: Compare configuration with json file and string
> 20: 0.000 s: genotype_ordering haploid_5_alleles
> 20: 0.000 s: genotype_ordering diploid_2_alleles
> 20: 0.000 s: genotype_ordering diploid_3_alleles
> 20: 0.000 s: genotype_ordering diploid_4_alleles
> 20: 0.000 s: genotype_ordering triploid_2_alleles
> 20: 0.000 s: genotype_ordering triploid_3_alleles
> 20: 0.000 s: genotype_ordering triploid_4_alleles
> 20: 0.000 s: genotype_ordering triploid_4_alleles_reordered_alleles
> 20: 0.000 s: genotype_ordering triploid_4_alleles_reordered_alleles_without_NON_REF
> 20: 0.000 s: multid_vector 2D_test
> 20: 0.000 s: multid_vector 3D_test
> 20: 0.000 s: multid_vector 2D_test_with_missing_values
> 20: 0.000 s: multid_vector 2D_float_test
> 20: 0.000 s: multid_vector 2D_tuple_test
> 20: 0.000 s: pb_query_config_test
> 20: 0.001 s: pb_vid_mapping_test
> 20: 13:46:21.876 INFO NativeGenomicsDB - pid=7313 tid=7313 Contig/chromosome 2 begins at TileDB column 249250601 and intersects with contig/chromosome 1 that spans columns [0, 249250620]
> 20: 0.000 s: pb_overlapping_vid_mapping_test
> 20: 13:46:21.876 INFO NativeGenomicsDB - pid=7313 tid=7313 This is a test
> 20: 13:46:21.876 WARN NativeGenomicsDB - pid=7313 tid=7313 This is a test
> 20: 13:46:21.876 ERROR NativeGenomicsDB - pid=7313 tid=7313 This is a test
> 20: 13:46:21.876 DEBUG NativeGenomicsDB - pid=7313 tid=7313 This is a test
> 20: This is a test
> 20: This is a test
> 20: This is a test
> 20: This is a test
> 20: This is a once_only test
> 20: Trying format Hello1 Hello2
> 20: 0.000 s: test logger
> 20: 13:46:21.876 INFO NativeGenomicsDB - pid=7313 tid=7313 i=1 str=This is a test
> 20: 13:46:21.876 WARN NativeGenomicsDB - pid=7313 tid=7313 i=2 str=This is a test
> 20: 13:46:21.876 ERROR NativeGenomicsDB - pid=7313 tid=7313 i=3 str=This is a test
> 20: 13:46:21.876 DEBUG NativeGenomicsDB - pid=7313 tid=7313 i=4 str=This is a test
> 20: 13:46:21.876 INFO NativeGenomicsDB - pid=7313 tid=7313 i=6 str=This is a once_only test
> 20: 13:46:21.876 WARN NativeGenomicsDB - pid=7313 tid=7313 i=7 str=This is a once_only test
> 20: 0.000 s: test logger format
> 20: 13:46:21.876 ERROR NativeGenomicsDB - pid=7313 tid=7313 i=1 str=This is a test
> 20: 13:46:21.877 ERROR NativeGenomicsDB - pid=7313 tid=7313 Test Exception
> 20: 13:46:21.877 ERROR NativeGenomicsDB - pid=7313 tid=7313 Test Exception
> 20: 13:46:21.877 ERROR NativeGenomicsDB - pid=7313 tid=7313 Test Exception
> 20: 13:46:21.877 ERROR NativeGenomicsDB - pid=7313 tid=7313 Native Stack Trace:
> 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x7b768) [0xaaaacfe0b768]
> 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x6a5a0) [0xaaaacfdfa5a0]
> 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x2277cc) [0xaaaacffb77cc]
> 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x228180) [0xaaaacffb8180]
> 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x2285b4) [0xaaaacffb85b4]
> 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x1fe1d8) [0xaaaacff8e1d8]
> 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x1fe724) [0xaaaacff8e724]
> 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x40250) [0xaaaacfdd0250]
> 20: /lib/aarch64-linux-gnu/libc.so.6(+0x2229c) [0xffff8317229c]
> 20: 13:46:21.877 ERROR NativeGenomicsDB - pid=7313 tid=7313 Test Exception
> 20: 13:46:21.877 ERROR NativeGenomicsDB - pid=7313 tid=7313 Native Stack Trace:
> 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x7b768) [0xaaaacfe0b768]
> 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x6a5cc) [0xaaaacfdfa5cc]
> 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x2277cc) [0xaaaacffb77cc]
> 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x228180) [0xaaaacffb8180]
> 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x2285b4) [0xaaaacffb85b4]
> 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x1fe1d8) [0xaaaacff8e1d8]
> 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x1fe724) [0xaaaacff8e724]
> 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x40250) [0xaaaacfdd0250]
> 20: /lib/aarch64-linux-gnu/libc.so.6(+0x2229c) [0xffff8317229c]
> 20: 0.001 s: test logger exceptions
> 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x7b768) [0xaaaacfe0b768]
> 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x6cea4) [0xaaaacfdfcea4]
> 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x2277cc) [0xaaaacffb77cc]
> 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x228180) [0xaaaacffb8180]
> 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x2285b4) [0xaaaacffb85b4]
> 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x1fe1d8) [0xaaaacff8e1d8]
> 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x1fe724) [0xaaaacff8e724]
> 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x40250) [0xaaaacfdd0250]
> 20: /lib/aarch64-linux-gnu/libc.so.6(+0x2229c) [0xffff8317229c]
> 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x7b768) [0xaaaacfe0b768]
> 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x6ce80) [0xaaaacfdfce80]
> 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x2277cc) [0xaaaacffb77cc]
> 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x228180) [0xaaaacffb8180]
> 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x2285b4) [0xaaaacffb85b4]
> 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x1fe1d8) [0xaaaacff8e1d8]
> 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x1fe724) [0xaaaacff8e724]
> 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x40250) [0xaaaacfdd0250]
> 20: /lib/aarch64-linux-gnu/libc.so.6(+0x2229c) [0xffff8317229c]
> 20: This is a test
> 20: 0.001 s: test explicit logger
> 20: 13:46:21.878 DEBUG NativeGenomicsDB - pid=7313 tid=7313 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 20: 13:46:21.878 WARN NativeGenomicsDB - pid=7313 tid=7313 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 20: 13:46:21.878 DEBUG NativeGenomicsDB - pid=7313 tid=7313 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 20: 0.011 s: gvcf iterator
> 20: 13:46:21.889 DEBUG NativeGenomicsDB - pid=7313 tid=7313 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 20: 13:46:21.889 WARN NativeGenomicsDB - pid=7313 tid=7313 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 20: 13:46:21.889 DEBUG NativeGenomicsDB - pid=7313 tid=7313 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 20: 0.007 s: columnar_gvcf_iterator_test
> 20: 13:46:21.896 ERROR NativeGenomicsDB - pid=7313 tid=7313 hts_plugin could not find /tmp/GenomicsDBbp4agh
> 20: [TileDB] Error: No TileDB support for URL=dfdfd://ddd.
> 20: 13:46:21.896 ERROR NativeGenomicsDB - pid=7313 tid=7313 htslib_plugin could not open dfdfd://ddd
> 20: No TileDB support for URL=dfdfd://ddd
> 20: 13:46:21.896 ERROR NativeGenomicsDB - pid=7313 tid=7313 hts_plugin could not find /tmp/GenomicsDBbp4agh/foo
> 20: 13:46:21.896 ERROR NativeGenomicsDB - pid=7313 tid=7313 hts_plugin could not find /tmp/GenomicsDBbp4agh/foo
> 20: [TileDB::FileSystem] Error: (write_to_file) Cannot write to file; File opening error path=/dfdfd/dfdfd/non-existent-file errno=2(No such file or directory)
> 20: 13:46:21.896 ERROR NativeGenomicsDB - pid=7313 tid=7313 hts_plugin write /dfdfd/dfdfd/non-existent-file error [TileDB::FileSystem] Error: (write_to_file) Cannot write to file; File opening error path=/dfdfd/dfdfd/non-existent-file errno=2(No such file or directory)
> 20: [TileDB::FileSystem] Error: (read_from_file) Cannot read from file; File opening error path=non-existent-file errno=2(No such file or directory)
> 20: 13:46:21.896 ERROR NativeGenomicsDB - pid=7313 tid=7313 hts_plugin read non-existent-file error [TileDB::FileSystem] Error: (read_from_file) Cannot read from file; File opening error path=non-existent-file errno=2(No such file or directory)
> 20: 0.001 s: test htslib plugin
> 20: 0.000 s: alleles_combiner
> 20: 0.000 s: gt_remapper
> 20:
> 20: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 20: ctests is a Catch2 v3.7.1 host application.
> 20: Run with -? for options
> 20:
> 20: -------------------------------------------------------------------------------
> 20: test bgen
> 20: -------------------------------------------------------------------------------
> 20: ./src/test/cpp/src/test_bgen.cc:11
> 20: ...............................................................................
> 20:
> 20: ./src/test/cpp/src/test_bgen.cc:11: FAILED:
> 20: due to unexpected exception with message:
> 20: Direct - first BGEN test output did not match reference output
> 20:
> 20: 0.000 s: test bgen
> 20: 13:46:21.970 ERROR NativeGenomicsDB - pid=7313 tid=7313 VariantStorageManagerException exception : Could not open workspace
> 20: 13:46:21.970 ERROR NativeGenomicsDB - pid=7313 tid=7313 Could not open array non_existent_array in workspace /tmp/GenomicsDB02nJMW/ws
> 20: 13:46:21.970 ERROR NativeGenomicsDB - pid=7313 tid=7313 VariantQueryProcessorException : Could not open array non_existent_array at workspace /tmp/GenomicsDB02nJMW/ws
> 20: 0.001 s: constructor
> 20: 13:46:21.971 DEBUG NativeGenomicsDB - pid=7313 tid=7313 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 20: 13:46:21.971 WARN NativeGenomicsDB - pid=7313 tid=7313 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 20: 13:46:21.971 DEBUG NativeGenomicsDB - pid=7313 tid=7313 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 20: 13:46:21.975 ERROR NativeGenomicsDB - pid=7313 tid=7313 Invalid query attribute : non_existent_attribute
> 20: 0.005 s: test basic queries
> 20: 13:46:21.975 INFO NativeGenomicsDB - pid=7313 tid=7313 Mem usage Check basic memory usage rss=46M
> 20: 0.000 s: check basic memory usage
> 20: ===============================================================================
> 20: test cases: 34 | 33 passed | 1 failed
> 20: assertions: 1440 | 1439 passed | 1 failed
> 20:
> 20: 13:46:21.975 DEBUG NativeGenomicsDB - pid=7313 tid=7313 Deleting htslib_fs_adapter tiledb_ctx_map
> 17/22 Test #20: ctests ...........................***Failed 0.17 sec
> 13:46:21.870 DEBUG NativeGenomicsDB - pid=7313 tid=7313 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:21.871 WARN NativeGenomicsDB - pid=7313 tid=7313 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:21.871 DEBUG NativeGenomicsDB - pid=7313 tid=7313 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> Randomness seeded to: 3428592844
> 0.002 s: Check loader configuration with json file
> 13:46:21.871 DEBUG NativeGenomicsDB - pid=7313 tid=7313 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:21.871 WARN NativeGenomicsDB - pid=7313 tid=7313 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:21.872 DEBUG NativeGenomicsDB - pid=7313 tid=7313 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 0.001 s: Check configuration with json file
> 13:46:21.872 DEBUG NativeGenomicsDB - pid=7313 tid=7313 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:21.872 WARN NativeGenomicsDB - pid=7313 tid=7313 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:21.873 DEBUG NativeGenomicsDB - pid=7313 tid=7313 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 0.001 s: Check configuration with json file and shared posifs optim
> 13:46:21.873 DEBUG NativeGenomicsDB - pid=7313 tid=7313 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:21.873 WARN NativeGenomicsDB - pid=7313 tid=7313 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:21.873 DEBUG NativeGenomicsDB - pid=7313 tid=7313 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 0.001 s: Compare configuration with json file and string
> 0.000 s: genotype_ordering haploid_5_alleles
> 0.000 s: genotype_ordering diploid_2_alleles
> 0.000 s: genotype_ordering diploid_3_alleles
> 0.000 s: genotype_ordering diploid_4_alleles
> 0.000 s: genotype_ordering triploid_2_alleles
> 0.000 s: genotype_ordering triploid_3_alleles
> 0.000 s: genotype_ordering triploid_4_alleles
> 0.000 s: genotype_ordering triploid_4_alleles_reordered_alleles
> 0.000 s: genotype_ordering triploid_4_alleles_reordered_alleles_without_NON_REF
> 0.000 s: multid_vector 2D_test
> 0.000 s: multid_vector 3D_test
> 0.000 s: multid_vector 2D_test_with_missing_values
> 0.000 s: multid_vector 2D_float_test
> 0.000 s: multid_vector 2D_tuple_test
> 0.000 s: pb_query_config_test
> 0.001 s: pb_vid_mapping_test
> 13:46:21.876 INFO NativeGenomicsDB - pid=7313 tid=7313 Contig/chromosome 2 begins at TileDB column 249250601 and intersects with contig/chromosome 1 that spans columns [0, 249250620]
> 0.000 s: pb_overlapping_vid_mapping_test
> 13:46:21.876 INFO NativeGenomicsDB - pid=7313 tid=7313 This is a test
> 13:46:21.876 WARN NativeGenomicsDB - pid=7313 tid=7313 This is a test
> 13:46:21.876 ERROR NativeGenomicsDB - pid=7313 tid=7313 This is a test
> 13:46:21.876 DEBUG NativeGenomicsDB - pid=7313 tid=7313 This is a test
> This is a test
> This is a test
> This is a test
> This is a test
> This is a once_only test
> Trying format Hello1 Hello2
> 0.000 s: test logger
> 13:46:21.876 INFO NativeGenomicsDB - pid=7313 tid=7313 i=1 str=This is a test
> 13:46:21.876 WARN NativeGenomicsDB - pid=7313 tid=7313 i=2 str=This is a test
> 13:46:21.876 ERROR NativeGenomicsDB - pid=7313 tid=7313 i=3 str=This is a test
> 13:46:21.876 DEBUG NativeGenomicsDB - pid=7313 tid=7313 i=4 str=This is a test
> 13:46:21.876 INFO NativeGenomicsDB - pid=7313 tid=7313 i=6 str=This is a once_only test
> 13:46:21.876 WARN NativeGenomicsDB - pid=7313 tid=7313 i=7 str=This is a once_only test
> 0.000 s: test logger format
> 13:46:21.876 ERROR NativeGenomicsDB - pid=7313 tid=7313 i=1 str=This is a test
> 13:46:21.877 ERROR NativeGenomicsDB - pid=7313 tid=7313 Test Exception
> 13:46:21.877 ERROR NativeGenomicsDB - pid=7313 tid=7313 Test Exception
> 13:46:21.877 ERROR NativeGenomicsDB - pid=7313 tid=7313 Test Exception
> 13:46:21.877 ERROR NativeGenomicsDB - pid=7313 tid=7313 Native Stack Trace:
> /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x7b768) [0xaaaacfe0b768]
> /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x6a5a0) [0xaaaacfdfa5a0]
> /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x2277cc) [0xaaaacffb77cc]
> /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x228180) [0xaaaacffb8180]
> /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x2285b4) [0xaaaacffb85b4]
> /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x1fe1d8) [0xaaaacff8e1d8]
> /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x1fe724) [0xaaaacff8e724]
> /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x40250) [0xaaaacfdd0250]
> /lib/aarch64-linux-gnu/libc.so.6(+0x2229c) [0xffff8317229c]
> 13:46:21.877 ERROR NativeGenomicsDB - pid=7313 tid=7313 Test Exception
> 13:46:21.877 ERROR NativeGenomicsDB - pid=7313 tid=7313 Native Stack Trace:
> /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x7b768) [0xaaaacfe0b768]
> /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x6a5cc) [0xaaaacfdfa5cc]
> /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x2277cc) [0xaaaacffb77cc]
> /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x228180) [0xaaaacffb8180]
> /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x2285b4) [0xaaaacffb85b4]
> /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x1fe1d8) [0xaaaacff8e1d8]
> /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x1fe724) [0xaaaacff8e724]
> /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x40250) [0xaaaacfdd0250]
> /lib/aarch64-linux-gnu/libc.so.6(+0x2229c) [0xffff8317229c]
> 0.001 s: test logger exceptions
> /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x7b768) [0xaaaacfe0b768]
> /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x6cea4) [0xaaaacfdfcea4]
> /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x2277cc) [0xaaaacffb77cc]
> /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x228180) [0xaaaacffb8180]
> /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x2285b4) [0xaaaacffb85b4]
> /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x1fe1d8) [0xaaaacff8e1d8]
> /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x1fe724) [0xaaaacff8e724]
> /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x40250) [0xaaaacfdd0250]
> /lib/aarch64-linux-gnu/libc.so.6(+0x2229c) [0xffff8317229c]
> /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x7b768) [0xaaaacfe0b768]
> /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x6ce80) [0xaaaacfdfce80]
> /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x2277cc) [0xaaaacffb77cc]
> /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x228180) [0xaaaacffb8180]
> /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x2285b4) [0xaaaacffb85b4]
> /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x1fe1d8) [0xaaaacff8e1d8]
> /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x1fe724) [0xaaaacff8e724]
> /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x40250) [0xaaaacfdd0250]
> /lib/aarch64-linux-gnu/libc.so.6(+0x2229c) [0xffff8317229c]
> This is a test
> 0.001 s: test explicit logger
> 13:46:21.878 DEBUG NativeGenomicsDB - pid=7313 tid=7313 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:21.878 WARN NativeGenomicsDB - pid=7313 tid=7313 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:21.878 DEBUG NativeGenomicsDB - pid=7313 tid=7313 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 0.011 s: gvcf iterator
> 13:46:21.889 DEBUG NativeGenomicsDB - pid=7313 tid=7313 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:21.889 WARN NativeGenomicsDB - pid=7313 tid=7313 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:21.889 DEBUG NativeGenomicsDB - pid=7313 tid=7313 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 0.007 s: columnar_gvcf_iterator_test
> 13:46:21.896 ERROR NativeGenomicsDB - pid=7313 tid=7313 hts_plugin could not find /tmp/GenomicsDBbp4agh
> [TileDB] Error: No TileDB support for URL=dfdfd://ddd.
> 13:46:21.896 ERROR NativeGenomicsDB - pid=7313 tid=7313 htslib_plugin could not open dfdfd://ddd
> No TileDB support for URL=dfdfd://ddd
> 13:46:21.896 ERROR NativeGenomicsDB - pid=7313 tid=7313 hts_plugin could not find /tmp/GenomicsDBbp4agh/foo
> 13:46:21.896 ERROR NativeGenomicsDB - pid=7313 tid=7313 hts_plugin could not find /tmp/GenomicsDBbp4agh/foo
> [TileDB::FileSystem] Error: (write_to_file) Cannot write to file; File opening error path=/dfdfd/dfdfd/non-existent-file errno=2(No such file or directory)
> 13:46:21.896 ERROR NativeGenomicsDB - pid=7313 tid=7313 hts_plugin write /dfdfd/dfdfd/non-existent-file error [TileDB::FileSystem] Error: (write_to_file) Cannot write to file; File opening error path=/dfdfd/dfdfd/non-existent-file errno=2(No such file or directory)
> [TileDB::FileSystem] Error: (read_from_file) Cannot read from file; File opening error path=non-existent-file errno=2(No such file or directory)
> 13:46:21.896 ERROR NativeGenomicsDB - pid=7313 tid=7313 hts_plugin read non-existent-file error [TileDB::FileSystem] Error: (read_from_file) Cannot read from file; File opening error path=non-existent-file errno=2(No such file or directory)
> 0.001 s: test htslib plugin
> 0.000 s: alleles_combiner
> 0.000 s: gt_remapper
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> ctests is a Catch2 v3.7.1 host application.
> Run with -? for options
>
> -------------------------------------------------------------------------------
> test bgen
> -------------------------------------------------------------------------------
> ./src/test/cpp/src/test_bgen.cc:11
> ...............................................................................
>
> ./src/test/cpp/src/test_bgen.cc:11: FAILED:
> due to unexpected exception with message:
> Direct - first BGEN test output did not match reference output
>
> 0.000 s: test bgen
> 13:46:21.970 ERROR NativeGenomicsDB - pid=7313 tid=7313 VariantStorageManagerException exception : Could not open workspace
> 13:46:21.970 ERROR NativeGenomicsDB - pid=7313 tid=7313 Could not open array non_existent_array in workspace /tmp/GenomicsDB02nJMW/ws
> 13:46:21.970 ERROR NativeGenomicsDB - pid=7313 tid=7313 VariantQueryProcessorException : Could not open array non_existent_array at workspace /tmp/GenomicsDB02nJMW/ws
> 0.001 s: constructor
> 13:46:21.971 DEBUG NativeGenomicsDB - pid=7313 tid=7313 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:21.971 WARN NativeGenomicsDB - pid=7313 tid=7313 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:21.971 DEBUG NativeGenomicsDB - pid=7313 tid=7313 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:21.975 ERROR NativeGenomicsDB - pid=7313 tid=7313 Invalid query attribute : non_existent_attribute
> 0.005 s: test basic queries
> 13:46:21.975 INFO NativeGenomicsDB - pid=7313 tid=7313 Mem usage Check basic memory usage rss=46M
> 0.000 s: check basic memory usage
> ===============================================================================
> test cases: 34 | 33 passed | 1 failed
> assertions: 1440 | 1439 passed | 1 failed
>
> 13:46:21.975 DEBUG NativeGenomicsDB - pid=7313 tid=7313 Deleting htslib_fs_adapter tiledb_ctx_map
>
> test 21
> Start 21: api_tests
>
> 21: Test command: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/api_tests "-d" "yes"
> 21: Working Directory: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp
> 21: Test timeout computed to be: 10000000
> 21: Randomness seeded to: 2475962137
> 21: 0.000 s: utils
> 21: 0.000 s: api empty_args
> 21: 0.017 s: api query_variants direct DP
> 21: 0.007 s: api query_variants direct DP with huge row range
> 21: 0.007 s: api query_variants direct DP with huge disjoint row ranges
> 21: 0.010 s: api query_variants direct DP with range composed of multiple points
> 21: 0.010 s: api query_variants direct DP with range composed of overlapping ranges
> 21: 13:46:22.055 ERROR NativeGenomicsDB - pid=7318 tid=7318 Query interval 0:-100-1 is out of bounds
> 21: 0.005 s: api query_variants direct DP with invalid row range
> 21: 0.014 s: api query_variants direct DP and GT
> 21: 0.014 s: api query_variants direct DP and GT with PP
> 21: 13:46:22.085 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 21: 13:46:22.086 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.086 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.093 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 21: 13:46:22.093 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.093 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.101 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 21: 13:46:22.101 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.101 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 0.017 s: api query_variants with json
> 21: 13:46:22.101 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 21: 13:46:22.101 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.102 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/ws/t0_1_2/.__consolidation_lock
> 21: 13:46:22.109 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 21: 13:46:22.109 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.109 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.116 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 21: 13:46:22.116 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.117 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 0.016 s: api query variants with json string
> 21: 13:46:22.139 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 21: 13:46:22.139 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.140 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 0.029 s: api query variants with enabled shared posixfs optimizations
> 21: ----------------
> 21: Interval:[0,9223372036854775806]
> 21:
> 21: sample=HG00141
> 21: row=0 position=12140
> 21: genomic_interval=1:12141,12295
> 21: genomic_fields
> 21: REF:C ALT:[<NON_REF>]
> 21: sample=HG01958
> 21: row=1 position=12144
> 21: genomic_interval=1:12145,12277
> 21: genomic_fields
> 21: REF:C ALT:[<NON_REF>]
> 21: sample=HG00141
> 21: row=0 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[A, <NON_REF>]
> 21: sample=HG01958
> 21: row=1 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[T, <NON_REF>] DP:120
> 21: sample=HG01530
> 21: row=2 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[A, <NON_REF>] DP:76
> 21: ----------------
> 21: Interval:[0,1000000000]
> 21:
> 21: sample=HG00141
> 21: row=0 position=12140
> 21: genomic_interval=1:12141,12295
> 21: genomic_fields
> 21: REF:C ALT:[<NON_REF>]
> 21: sample=HG01958
> 21: row=1 position=12144
> 21: genomic_interval=1:12145,12277
> 21: genomic_fields
> 21: REF:C ALT:[<NON_REF>]
> 21: sample=HG00141
> 21: row=0 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[A, <NON_REF>]
> 21: sample=HG01958
> 21: row=1 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[T, <NON_REF>] DP:120
> 21: sample=HG01530
> 21: row=2 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[A, <NON_REF>] DP:76
> 21: 0.017 s: api query_variant_calls direct
> 21: ----------------
> 21: Interval:[0,1000000000]
> 21:
> 21: sample=HG00141
> 21: row=0 position=12140
> 21: genomic_interval=1:12141,12295
> 21: genomic_fields
> 21: REF:C ALT:[<NON_REF>] GT:0/0
> 21: sample=HG01958
> 21: row=1 position=12144
> 21: genomic_interval=1:12145,12277
> 21: genomic_fields
> 21: REF:C ALT:[<NON_REF>] GT:0/0
> 21: sample=HG00141
> 21: row=0 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[A, <NON_REF>] GT:0/1
> 21: sample=HG01958
> 21: row=1 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
> 21: sample=HG01530
> 21: row=2 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
> 21: 0.017 s: api query_variant_calls direct DP and GT
> 21: ----------------
> 21: Interval:[0,1000000000]
> 21:
> 21: sample=HG00141
> 21: row=0 position=12140
> 21: genomic_interval=1:12141,12295
> 21: genomic_fields
> 21: REF:C ALT:[<NON_REF>] GT:0/0
> 21: sample=HG01958
> 21: row=1 position=12144
> 21: genomic_interval=1:12145,12277
> 21: genomic_fields
> 21: REF:C ALT:[<NON_REF>] GT:0|0
> 21: sample=HG00141
> 21: row=0 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[A, <NON_REF>] GT:0/1
> 21: sample=HG01958
> 21: row=1 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
> 21: sample=HG01530
> 21: row=2 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
> 21: 0.017 s: api query_variant_calls direct DP and GT with PP
> 21: 13:46:22.197 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 21: 13:46:22.197 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.198 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: ----------------
> 21: Interval:[0,1000000000]
> 21:
> 21: sample=HG00141
> 21: row=0 position=12140
> 21: genomic_interval=1:12141,12295
> 21: genomic_fields
> 21: REF:C ALT:[<NON_REF>]
> 21: sample=HG01958
> 21: row=1 position=12144
> 21: genomic_interval=1:12145,12277
> 21: genomic_fields
> 21: REF:C ALT:[<NON_REF>]
> 21: sample=HG00141
> 21: row=0 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[A, <NON_REF>]
> 21: sample=HG01958
> 21: row=1 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[T, <NON_REF>] DP:120
> 21: sample=HG01530
> 21: row=2 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[A, <NON_REF>] DP:76
> 21: 13:46:22.205 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 21: 13:46:22.205 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.205 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.211 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 21: 13:46:22.211 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.211 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 0.014 s: api query_variant_calls with json
> 21: 13:46:22.211 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 21: 13:46:22.211 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.212 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.212 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.212 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.212 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 21: 13:46:22.212 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> 21: ----------------
> 21: Interval:[0,1000000000]
> 21:
> 21: sample=HG00141
> 21: row=0 position=12140
> 21: genomic_interval=1:12141,12295
> 21: genomic_fields
> 21: REF:C ALT:[<NON_REF>] GT:0/0
> 21: sample=HG01958
> 21: row=1 position=12144
> 21: genomic_interval=1:12145,12277
> 21: genomic_fields
> 21: REF:C ALT:[<NON_REF>] GT:0/0
> 21: sample=HG00141
> 21: row=0 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[A, <NON_REF>] GT:0/1
> 21: sample=HG01958
> 21: row=1 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
> 21: sample=HG01530
> 21: row=2 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
> 21: 13:46:22.219 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 21: 13:46:22.219 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.220 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.220 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.220 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.220 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 21: 13:46:22.220 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> 21: ----------------
> 21: Interval:[0,1000000000]
> 21:
> 21: sample=HG00141
> 21: row=0 position=12140
> 21: genomic_interval=1:12141,12295
> 21: genomic_fields
> 21: REF:C ALT:[<NON_REF>] GT:0/0
> 21: sample=HG01958
> 21: row=1 position=12144
> 21: genomic_interval=1:12145,12277
> 21: genomic_fields
> 21: REF:C ALT:[<NON_REF>] GT:0/0
> 21: sample=HG00141
> 21: row=0 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[A, <NON_REF>] GT:0/1
> 21: sample=HG01958
> 21: row=1 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
> 21: sample=HG01530
> 21: row=2 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
> 21: 13:46:22.228 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 21: 13:46:22.228 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.228 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.228 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.228 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.229 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 21: 13:46:22.229 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 0.007 s: Try query with contig intervals instead of tiledb column intervals
> 21: 0.023 s: api query_variant_calls with protobuf
> 21: 13:46:22.234 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 21: 13:46:22.234 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.235 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.235 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.235 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.235 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 21: 13:46:22.235 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> 21: ----------------
> 21: Interval:[0,1000000000]
> 21:
> 21: sample=HG00141
> 21: row=0 position=12140
> 21: genomic_interval=1:12141,12295
> 21: genomic_fields
> 21: REF:C ALT:[<NON_REF>] GT:0/0
> 21: sample=HG01958
> 21: row=1 position=12144
> 21: genomic_interval=1:12145,12277
> 21: genomic_fields
> 21: REF:C ALT:[<NON_REF>] GT:0/0
> 21: sample=HG00141
> 21: row=0 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[A, <NON_REF>] GT:0/1
> 21: sample=HG01958
> 21: row=1 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
> 21: sample=HG01530
> 21: row=2 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
> 21: 13:46:22.243 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 21: 13:46:22.243 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.243 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.244 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.244 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.244 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 21: 13:46:22.244 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> 21: ----------------
> 21: Interval:[0,1000000000]
> 21:
> 21: sample=HG00141
> 21: row=0 position=12140
> 21: genomic_interval=1:12141,12295
> 21: genomic_fields
> 21: REF:C ALT:[<NON_REF>] GT:0/0
> 21: sample=HG01958
> 21: row=1 position=12144
> 21: genomic_interval=1:12145,12277
> 21: genomic_fields
> 21: REF:C ALT:[<NON_REF>] GT:0/0
> 21: sample=HG00141
> 21: row=0 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[A, <NON_REF>] GT:0/1
> 21: sample=HG01958
> 21: row=1 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
> 21: sample=HG01530
> 21: row=2 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
> 21: 13:46:22.251 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 21: 13:46:22.251 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.251 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.252 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.252 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.252 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 21: 13:46:22.252 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 0.007 s: Try query with a filter
> 21: 0.024 s: api query_variant_calls with protobuf
> 21: 13:46:22.258 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 21: 13:46:22.258 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.258 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.259 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.259 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.259 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 21: 13:46:22.259 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> 21: ----------------
> 21: Interval:[0,1000000000]
> 21:
> 21: sample=HG00141
> 21: row=0 position=12140
> 21: genomic_interval=1:12141,12295
> 21: genomic_fields
> 21: REF:C ALT:[<NON_REF>] GT:0/0
> 21: sample=HG01958
> 21: row=1 position=12144
> 21: genomic_interval=1:12145,12277
> 21: genomic_fields
> 21: REF:C ALT:[<NON_REF>] GT:0/0
> 21: sample=HG00141
> 21: row=0 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[A, <NON_REF>] GT:0/1
> 21: sample=HG01958
> 21: row=1 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
> 21: sample=HG01530
> 21: row=2 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
> 21: 13:46:22.267 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 21: 13:46:22.267 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.267 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.268 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.268 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.268 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 21: 13:46:22.268 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> 21: ----------------
> 21: Interval:[0,1000000000]
> 21:
> 21: sample=HG00141
> 21: row=0 position=12140
> 21: genomic_interval=1:12141,12295
> 21: genomic_fields
> 21: REF:C ALT:[<NON_REF>] GT:0/0
> 21: sample=HG01958
> 21: row=1 position=12144
> 21: genomic_interval=1:12145,12277
> 21: genomic_fields
> 21: REF:C ALT:[<NON_REF>] GT:0/0
> 21: sample=HG00141
> 21: row=0 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[A, <NON_REF>] GT:0/1
> 21: sample=HG01958
> 21: row=1 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
> 21: sample=HG01530
> 21: row=2 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
> 21: 13:46:22.275 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 21: 13:46:22.275 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.276 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.276 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.276 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.276 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 21: 13:46:22.276 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 0.007 s: Try query with a filter and workspace with GT ploidy
> 21: 0.024 s: api query_variant_calls with protobuf
> 21: 13:46:22.282 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 21: 13:46:22.282 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.282 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.283 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.283 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.283 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 21: 13:46:22.283 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> 21: ----------------
> 21: Interval:[0,1000000000]
> 21:
> 21: sample=HG00141
> 21: row=0 position=12140
> 21: genomic_interval=1:12141,12295
> 21: genomic_fields
> 21: REF:C ALT:[<NON_REF>] GT:0/0
> 21: sample=HG01958
> 21: row=1 position=12144
> 21: genomic_interval=1:12145,12277
> 21: genomic_fields
> 21: REF:C ALT:[<NON_REF>] GT:0/0
> 21: sample=HG00141
> 21: row=0 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[A, <NON_REF>] GT:0/1
> 21: sample=HG01958
> 21: row=1 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
> 21: sample=HG01530
> 21: row=2 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
> 7: Randomness seeded to: 384332532
> 21: 13:46:22.290 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 21: 13:46:22.290 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.291 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.291 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.291 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.292 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 21: 13:46:22.292 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> 21: ----------------
> 21: Interval:[0,1000000000]
> 21:
> 21: sample=HG00141
> 21: row=0 position=12140
> 21: genomic_interval=1:12141,12295
> 21: genomic_fields
> 21: REF:C ALT:[<NON_REF>] GT:0/0
> 21: sample=HG01958
> 21: row=1 position=12144
> 21: genomic_interval=1:12145,12277
> 21: genomic_fields
> 21: REF:C ALT:[<NON_REF>] GT:0/0
> 21: sample=HG00141
> 21: row=0 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[A, <NON_REF>] GT:0/1
> 21: sample=HG01958
> 21: row=1 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
> 21: sample=HG01530
> 21: row=2 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
> 21: 13:46:22.299 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 21: 13:46:22.299 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.300 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.301 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.301 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.301 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 21: 13:46:22.301 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 0.008 s: Try query with a filter and a small segment size to force TileDB buffers overflow
> 21: 0.025 s: api query_variant_calls with protobuf
> 21: 13:46:22.307 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 21: 13:46:22.307 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.307 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.308 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.308 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.308 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 21: 13:46:22.308 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> 21: ----------------
> 21: Interval:[0,1000000000]
> 21:
> 21: sample=HG00141
> 21: row=0 position=12140
> 21: genomic_interval=1:12141,12295
> 21: genomic_fields
> 21: REF:C ALT:[<NON_REF>] GT:0/0
> 21: sample=HG01958
> 21: row=1 position=12144
> 21: genomic_interval=1:12145,12277
> 21: genomic_fields
> 21: REF:C ALT:[<NON_REF>] GT:0/0
> 21: sample=HG00141
> 21: row=0 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[A, <NON_REF>] GT:0/1
> 21: sample=HG01958
> 21: row=1 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
> 21: sample=HG01530
> 21: row=2 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
> 21: 13:46:22.316 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 21: 13:46:22.316 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.317 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.317 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.317 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.317 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 21: 13:46:22.317 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> 21: ----------------
> 21: Interval:[0,1000000000]
> 21:
> 21: sample=HG00141
> 21: row=0 position=12140
> 21: genomic_interval=1:12141,12295
> 21: genomic_fields
> 21: REF:C ALT:[<NON_REF>] GT:0/0
> 21: sample=HG01958
> 21: row=1 position=12144
> 21: genomic_interval=1:12145,12277
> 21: genomic_fields
> 21: REF:C ALT:[<NON_REF>] GT:0/0
> 21: sample=HG00141
> 21: row=0 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[A, <NON_REF>] GT:0/1
> 21: sample=HG01958
> 21: row=1 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
> 21: sample=HG01530
> 21: row=2 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
> 21: 13:46:22.325 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 21: 13:46:22.325 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.325 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.326 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.326 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.326 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 21: 13:46:22.326 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 0.007 s: Try query with POS and ROW with no match
> 21: 0.025 s: api query_variant_calls with protobuf
> 21: 13:46:22.332 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 21: 13:46:22.332 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.333 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.333 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.333 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.333 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 21: 13:46:22.333 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> 21: ----------------
> 21: Interval:[0,1000000000]
> 21:
> 21: sample=HG00141
> 21: row=0 position=12140
> 21: genomic_interval=1:12141,12295
> 21: genomic_fields
> 21: REF:C ALT:[<NON_REF>] GT:0/0
> 21: sample=HG01958
> 21: row=1 position=12144
> 21: genomic_interval=1:12145,12277
> 21: genomic_fields
> 21: REF:C ALT:[<NON_REF>] GT:0/0
> 21: sample=HG00141
> 21: row=0 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[A, <NON_REF>] GT:0/1
> 21: sample=HG01958
> 21: row=1 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
> 21: sample=HG01530
> 21: row=2 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
> 21: 13:46:22.340 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 21: 13:46:22.340 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.341 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.341 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.341 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.341 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 21: 13:46:22.341 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> 21: ----------------
> 21: Interval:[0,1000000000]
> 21:
> 21: sample=HG00141
> 21: row=0 position=12140
> 21: genomic_interval=1:12141,12295
> 21: genomic_fields
> 21: REF:C ALT:[<NON_REF>] GT:0/0
> 21: sample=HG01958
> 21: row=1 position=12144
> 21: genomic_interval=1:12145,12277
> 21: genomic_fields
> 21: REF:C ALT:[<NON_REF>] GT:0/0
> 21: sample=HG00141
> 21: row=0 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[A, <NON_REF>] GT:0/1
> 21: sample=HG01958
> 21: row=1 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
> 21: sample=HG01530
> 21: row=2 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
> 21: 13:46:22.349 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 21: 13:46:22.349 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.349 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.349 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.349 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.350 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 21: 13:46:22.350 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 0.007 s: Try query with POS and ROW
> 21: 0.023 s: api query_variant_calls with protobuf
> 21: 13:46:22.355 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 21: 13:46:22.355 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.356 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.356 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.356 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.356 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 21: 13:46:22.357 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> 21: ----------------
> 21: Interval:[0,1000000000]
> 21:
> 21: sample=HG00141
> 21: row=0 position=12140
> 21: genomic_interval=1:12141,12295
> 21: genomic_fields
> 21: REF:C ALT:[<NON_REF>] GT:0/0
> 21: sample=HG01958
> 21: row=1 position=12144
> 21: genomic_interval=1:12145,12277
> 21: genomic_fields
> 21: REF:C ALT:[<NON_REF>] GT:0/0
> 21: sample=HG00141
> 21: row=0 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[A, <NON_REF>] GT:0/1
> 21: sample=HG01958
> 21: row=1 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
> 21: sample=HG01530
> 21: row=2 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
> 21: 13:46:22.364 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 21: 13:46:22.364 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.364 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.365 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.365 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.365 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 21: 13:46:22.365 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> 21: ----------------
> 21: Interval:[0,1000000000]
> 21:
> 21: sample=HG00141
> 21: row=0 position=12140
> 21: genomic_interval=1:12141,12295
> 21: genomic_fields
> 21: REF:C ALT:[<NON_REF>] GT:0/0
> 21: sample=HG01958
> 21: row=1 position=12144
> 21: genomic_interval=1:12145,12277
> 21: genomic_fields
> 21: REF:C ALT:[<NON_REF>] GT:0/0
> 21: sample=HG00141
> 21: row=0 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[A, <NON_REF>] GT:0/1
> 21: sample=HG01958
> 21: row=1 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
> 21: sample=HG01530
> 21: row=2 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
> 21: 13:46:22.372 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 21: 13:46:22.372 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.372 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.373 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.373 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.373 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 21: 13:46:22.373 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 0.007 s: Try query with ISHOMREF
> 21: 0.023 s: api query_variant_calls with protobuf
> 21: 13:46:22.379 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 21: 13:46:22.379 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.379 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.379 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.380 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.380 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 21: 13:46:22.380 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> 21: ----------------
> 21: Interval:[0,1000000000]
> 21:
> 21: sample=HG00141
> 21: row=0 position=12140
> 21: genomic_interval=1:12141,12295
> 21: genomic_fields
> 21: REF:C ALT:[<NON_REF>] GT:0/0
> 21: sample=HG01958
> 21: row=1 position=12144
> 21: genomic_interval=1:12145,12277
> 21: genomic_fields
> 21: REF:C ALT:[<NON_REF>] GT:0/0
> 21: sample=HG00141
> 21: row=0 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[A, <NON_REF>] GT:0/1
> 21: sample=HG01958
> 21: row=1 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
> 21: sample=HG01530
> 21: row=2 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
> 21: 13:46:22.387 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 21: 13:46:22.387 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.387 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.388 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.388 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.388 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 21: 13:46:22.388 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> 21: ----------------
> 21: Interval:[0,1000000000]
> 21:
> 21: sample=HG00141
> 21: row=0 position=12140
> 21: genomic_interval=1:12141,12295
> 21: genomic_fields
> 21: REF:C ALT:[<NON_REF>] GT:0/0
> 21: sample=HG01958
> 21: row=1 position=12144
> 21: genomic_interval=1:12145,12277
> 21: genomic_fields
> 21: REF:C ALT:[<NON_REF>] GT:0/0
> 21: sample=HG00141
> 21: row=0 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[A, <NON_REF>] GT:0/1
> 21: sample=HG01958
> 21: row=1 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
> 21: sample=HG01530
> 21: row=2 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
> 21: 13:46:22.395 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 21: 13:46:22.395 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.395 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.396 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.396 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.396 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 21: 13:46:22.396 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 0.007 s: Try query with ISHOMREF
> 21: 0.023 s: api query_variant_calls with protobuf
> 21: 13:46:22.401 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 21: 13:46:22.401 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.402 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.402 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.402 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.402 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 21: 13:46:22.402 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> 21: ----------------
> 21: Interval:[0,1000000000]
> 21:
> 21: sample=HG00141
> 21: row=0 position=12140
> 21: genomic_interval=1:12141,12295
> 21: genomic_fields
> 21: REF:C ALT:[<NON_REF>] GT:0/0
> 21: sample=HG01958
> 21: row=1 position=12144
> 21: genomic_interval=1:12145,12277
> 21: genomic_fields
> 21: REF:C ALT:[<NON_REF>] GT:0/0
> 21: sample=HG00141
> 21: row=0 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[A, <NON_REF>] GT:0/1
> 21: sample=HG01958
> 21: row=1 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
> 21: sample=HG01530
> 21: row=2 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
> 21: 13:46:22.409 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 21: 13:46:22.409 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.410 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.410 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.410 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.410 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 21: 13:46:22.410 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> 21: ----------------
> 21: Interval:[0,1000000000]
> 21:
> 21: sample=HG00141
> 21: row=0 position=12140
> 21: genomic_interval=1:12141,12295
> 21: genomic_fields
> 21: REF:C ALT:[<NON_REF>] GT:0/0
> 21: sample=HG01958
> 21: row=1 position=12144
> 21: genomic_interval=1:12145,12277
> 21: genomic_fields
> 21: REF:C ALT:[<NON_REF>] GT:0/0
> 21: sample=HG00141
> 21: row=0 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[A, <NON_REF>] GT:0/1
> 21: sample=HG01958
> 21: row=1 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
> 21: sample=HG01530
> 21: row=2 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
> 21: 13:46:22.417 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 21: 13:46:22.418 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.418 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.418 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.418 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.419 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 21: 13:46:22.419 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 0.007 s: Try query with ISHOMREF
> 21: 0.023 s: api query_variant_calls with protobuf
> 21: 13:46:22.424 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 21: 13:46:22.424 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.425 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.425 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.425 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.425 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 21: 13:46:22.425 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> 21: ----------------
> 21: Interval:[0,1000000000]
> 21:
> 21: sample=HG00141
> 21: row=0 position=12140
> 21: genomic_interval=1:12141,12295
> 21: genomic_fields
> 21: REF:C ALT:[<NON_REF>] GT:0/0
> 21: sample=HG01958
> 21: row=1 position=12144
> 21: genomic_interval=1:12145,12277
> 21: genomic_fields
> 21: REF:C ALT:[<NON_REF>] GT:0/0
> 21: sample=HG00141
> 21: row=0 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[A, <NON_REF>] GT:0/1
> 21: sample=HG01958
> 21: row=1 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
> 21: sample=HG01530
> 21: row=2 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
> 21: 13:46:22.433 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 21: 13:46:22.433 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.433 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.434 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.434 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.434 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 21: 13:46:22.434 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> 21: ----------------
> 21: Interval:[0,1000000000]
> 21:
> 21: sample=HG00141
> 21: row=0 position=12140
> 21: genomic_interval=1:12141,12295
> 21: genomic_fields
> 21: REF:C ALT:[<NON_REF>] GT:0/0
> 21: sample=HG01958
> 21: row=1 position=12144
> 21: genomic_interval=1:12145,12277
> 21: genomic_fields
> 21: REF:C ALT:[<NON_REF>] GT:0/0
> 21: sample=HG00141
> 21: row=0 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[A, <NON_REF>] GT:0/1
> 21: sample=HG01958
> 21: row=1 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
> 21: sample=HG01530
> 21: row=2 position=17384
> 21: genomic_interval=1:17385,17385
> 21: genomic_fields
> 21: REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
> 21: 13:46:22.441 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 21: 13:46:22.441 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.442 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.442 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.442 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.442 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 21: 13:46:22.443 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 0.007 s: Try query with ISHOMREF
> 21: 0.024 s: api query_variant_calls with protobuf
> 21: 0.004 s: Base configuration
> 21: 0.006 s: api query_variant_calls with protobuf and config
> 21: 13:46:22.455 ERROR NativeGenomicsDB - pid=7318 tid=7318 Could not parse query_configuration. Only protobuf QueryConfiguration binary strings accepted as input argument
> 21: 0.000 s: Subset Array with pb string that is not Query or ExportConfiguration
> 21: 0.001 s: api query_variant_calls with protobuf and config
> 21: 0.004 s: Subset Array using QueryConfiguration
> 21: 0.006 s: api query_variant_calls with protobuf and config
> 21: 0.004 s: Subset Array using ExportConfiguration
> 21: 0.006 s: api query_variant_calls with protobuf and config
> 21: 0.004 s: Subset Array using QueryConfiguration - two intervals
> 21: 0.006 s: api query_variant_calls with protobuf and config
> 21: 0.006 s: Subset Array using QueryConfiguration - multiple queries
> 21: 0.007 s: api query_variant_calls with protobuf and config
> 21: 0.025 s: Test filter test for 0
> 21: 0.026 s: api query_variant_calls with protobuf new
> 21: 0.006 s: Test filter test for 1
> 21: 0.006 s: api query_variant_calls with protobuf new
> 21: 0.006 s: Test filter test for 2
> 21: 0.006 s: api query_variant_calls with protobuf new
> 21: 0.006 s: Test filter test for 3
> 21: 0.006 s: api query_variant_calls with protobuf new
> 21: 273 {"HG00141":{"CHR":["1","1"],"POS":[12141,17385],"DP":[null,null],"GT":["C/C","G/A"],"REF":["C","G"]},"HG01530":{"CHR":["1"],"POS":[17385],"DP":[76],"GT":["G/A"],"REF":["G"]},"HG01958":{"CHR":["1","1"],"POS":[12145,17385],"DP":[null,120],"GT":["C/C","T/T"],"REF":["C","G"]}}
> 21:
> 21: 207 {"FIELD":["CHR","POS","DP","GT","REF"],"HG00141":[["1",12141,null,"C/C","C"],["1",17385,null,"G/A","G"]],"HG01530":[["1",17385,76,"G/A","G"]],"HG01958":[["1",12145,null,"C/C","C"],["1",17385,120,"T/T","G"]]}
> 21:
> 21: 37 {"HG00141":2,"HG01530":1,"HG01958":2}
> 21:
> 21: 15 {"num_calls":5}
> 21:
> 21: 15 {"num_calls":5}
> 21:
> 21: 31 ["HG00141","HG01530","HG01958"]
> 21:
> 21:
> 21: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 21: api_tests is a Catch2 v3.7.1 host application.
> 21: Run with -? for options
> 21:
> 21: -------------------------------------------------------------------------------
> 21: api query_variant_calls with JSONVariantCallProcessor
> 21: -------------------------------------------------------------------------------
> 21: ./src/test/cpp/src/test_genomicsdb_api.cc:887
> 21: ...............................................................................
> 21:
> 21: ./src/test/cpp/src/test_genomicsdb_api.cc:997: FAILED:
> 21: CHECK( output.length() == 1805 )
> 21: with expansion:
> 21: 1807 (0x70f) == 1805 (0x70d)
> 21:
> 21: 1807 {"HG00141":{"CHR":["1","1"],"POS":[12141,17385],"AD":[null,58],"BaseQRankSum":[null,-2.0959999561309816],"ClippingRankSum":[null,-1.8589999675750733],"DP":[null,null],"DP_FORMAT":[2,80],"DS":["1","1"],"FILTER":[null,0],"GQ":[0,99],"GT":["C/C","G/A"],"HaplotypeScore":[null,null],"InbreedingCoeff":[null,null],"MIN_DP":[0,null],"MLEAC":[null,1],"MLEAF":[null,0.5],"MQ":[null,31.719999313354493],"MQ0":[null,8],"MQRankSum":[null,-0.32899999618530276],"PGT":[null,"0|1"],"PID":[null,"17385_G_A"],"PL":[0,504],"QUAL":[null,475.7699890136719],"RAW_MQ":[null,5.5],"REF":["C","G"],"ReadPosRankSum":[null,0.004999999888241291],"SB":[null,"[58, 0, 22, 0]"]},"HG01530":{"CHR":["1"],"POS":[17385],"AD":[40],"BaseQRankSum":[1.0460000038146973],"ClippingRankSum":[-2.242000102996826],"DP":[76],"DP_FORMAT":[76],"DS":["127"],"FILTER":[null],"GQ":[99],"GT":["G/A"],"HaplotypeScore":[null],"InbreedingCoeff":[null],"MIN_DP":[null],"MLEAC":[1],"MLEAF":[0.5],"MQ":[59.369998931884769],"MQ0":[0],"MQRankSum":[-0.4320000112056732],"PGT":[null],"PID":[null],"PL":[1018],"QUAL":[989.77001953125],"RAW_MQ":[null],"REF":["G"],"ReadPosRankSum":[2.055000066757202],"SB":["[9, 31, 13, 23]"]},"HG01958":{"CHR":["1","1"],"POS":[12145,17385],"AD":[null,0],"BaseQRankSum":[null,-2.0739998817443849],"ClippingRankSum":[null,0.5550000071525574],"DP":[null,120],"DP_FORMAT":[3,120],"DS":["1","127"],"FILTER":[null,0],"GQ":[0,99],"GT":["C/C","T/T"],"HaplotypeScore":[null,null],"InbreedingCoeff":[null,null],"MIN_DP":[0,null],"MLEAC":[null,2],"MLEAF":[null,1.0],"MQ":[null,29.81999969482422],"MQ0":[null,3],"MQRankSum":[null,-1.36899995803833],"PGT":[null,"0|1"],"PID":[null,"17385_G_T"],"PL":[0,3336],"QUAL":[null,3302.77001953125],"RAW_MQ":[null,2.5],"REF":["C","G"],"ReadPosRankSum":[null,-0.10100000351667404],"SB":[null,"[0, 0, 0, 0]"]}}
> 21:
> 21: 0.044 s: api query_variant_calls with JSONVariantCallProcessor
> 21: 0.000 s: Test genomicsdb demo test case
> 21: 0.039 s: api generate_vcf direct
> 21: 13:46:22.605 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 21: 13:46:22.605 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.605 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 0.009 s: api generate_vcf with json
> 21: 13:46:22.614 DEBUG NativeGenomicsDB - pid=7318 tid=7322 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 21: 13:46:22.614 WARN NativeGenomicsDB - pid=7318 tid=7322 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.615 DEBUG NativeGenomicsDB - pid=7318 tid=7325 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 21: 13:46:22.615 WARN NativeGenomicsDB - pid=7318 tid=7325 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.615 DEBUG NativeGenomicsDB - pid=7318 tid=7322 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.615 DEBUG NativeGenomicsDB - pid=7318 tid=7325 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.618 DEBUG NativeGenomicsDB - pid=7318 tid=7326 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 21: 13:46:22.618 WARN NativeGenomicsDB - pid=7318 tid=7326 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.618 DEBUG NativeGenomicsDB - pid=7318 tid=7326 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.614 DEBUG NativeGenomicsDB - pid=7318 tid=7324 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 21: 13:46:22.618 WARN NativeGenomicsDB - pid=7318 tid=7324 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.619 DEBUG NativeGenomicsDB - pid=7318 tid=7327 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 21: 13:46:22.619 WARN NativeGenomicsDB - pid=7318 tid=7327 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.619 DEBUG NativeGenomicsDB - pid=7318 tid=7329 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 21: 13:46:22.619 WARN NativeGenomicsDB - pid=7318 tid=7329 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.619 DEBUG NativeGenomicsDB - pid=7318 tid=7329 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.619 DEBUG NativeGenomicsDB - pid=7318 tid=7324 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.619 DEBUG NativeGenomicsDB - pid=7318 tid=7327 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.622 DEBUG NativeGenomicsDB - pid=7318 tid=7323 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 21: 13:46:22.622 WARN NativeGenomicsDB - pid=7318 tid=7323 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.627 DEBUG NativeGenomicsDB - pid=7318 tid=7323 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.648 DEBUG NativeGenomicsDB - pid=7318 tid=7328 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 21: 13:46:22.648 WARN NativeGenomicsDB - pid=7318 tid=7328 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.648 DEBUG NativeGenomicsDB - pid=7318 tid=7328 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 0.051 s: api generate_vcf with json multiple threads
> 21: 13:46:22.665 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 21: 13:46:22.665 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.665 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.666 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.666 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.666 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 21: 13:46:22.666 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.673 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 21: 13:46:22.673 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.673 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.673 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.673 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.674 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 21: 13:46:22.674 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.680 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 21: 13:46:22.680 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.680 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.681 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 21: 13:46:22.681 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 21: 13:46:22.681 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 21: 13:46:22.681 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> 21: ----------------
> 21: Interval:[0,1000000000]
> 21:
> 21: ----------------
> 21: Interval:[0,1000000000]
> 21:
> 21: 0.021 s: api annotate query_variant_calls with test datasource 0
> 21: ===============================================================================
> 21: test cases: 26 | 25 passed | 1 failed
> 21: assertions: 1531 | 1530 passed | 1 failed
> 21:
> 18/22 Test #21: api_tests ........................***Failed 0.71 sec
> Randomness seeded to: 2475962137
> 0.000 s: utils
> 0.000 s: api empty_args
> 0.017 s: api query_variants direct DP
> 0.007 s: api query_variants direct DP with huge row range
> 0.007 s: api query_variants direct DP with huge disjoint row ranges
> 0.010 s: api query_variants direct DP with range composed of multiple points
> 0.010 s: api query_variants direct DP with range composed of overlapping ranges
> 13:46:22.055 ERROR NativeGenomicsDB - pid=7318 tid=7318 Query interval 0:-100-1 is out of bounds
> 0.005 s: api query_variants direct DP with invalid row range
> 0.014 s: api query_variants direct DP and GT
> 0.014 s: api query_variants direct DP and GT with PP
> 13:46:22.085 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:22.086 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.086 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.093 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:22.093 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.093 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.101 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:22.101 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.101 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 0.017 s: api query_variants with json
> 13:46:22.101 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:22.101 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.102 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/ws/t0_1_2/.__consolidation_lock
> 13:46:22.109 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:22.109 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.109 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.116 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:22.116 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.117 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 0.016 s: api query variants with json string
> 13:46:22.139 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:22.139 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.140 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 0.029 s: api query variants with enabled shared posixfs optimizations
> ----------------
> Interval:[0,9223372036854775806]
>
> sample=HG00141
> row=0 position=12140
> genomic_interval=1:12141,12295
> genomic_fields
> REF:C ALT:[<NON_REF>]
> sample=HG01958
> row=1 position=12144
> genomic_interval=1:12145,12277
> genomic_fields
> REF:C ALT:[<NON_REF>]
> sample=HG00141
> row=0 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[A, <NON_REF>]
> sample=HG01958
> row=1 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[T, <NON_REF>] DP:120
> sample=HG01530
> row=2 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[A, <NON_REF>] DP:76
> ----------------
> Interval:[0,1000000000]
>
> sample=HG00141
> row=0 position=12140
> genomic_interval=1:12141,12295
> genomic_fields
> REF:C ALT:[<NON_REF>]
> sample=HG01958
> row=1 position=12144
> genomic_interval=1:12145,12277
> genomic_fields
> REF:C ALT:[<NON_REF>]
> sample=HG00141
> row=0 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[A, <NON_REF>]
> sample=HG01958
> row=1 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[T, <NON_REF>] DP:120
> sample=HG01530
> row=2 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[A, <NON_REF>] DP:76
> 0.017 s: api query_variant_calls direct
> ----------------
> Interval:[0,1000000000]
>
> sample=HG00141
> row=0 position=12140
> genomic_interval=1:12141,12295
> genomic_fields
> REF:C ALT:[<NON_REF>] GT:0/0
> sample=HG01958
> row=1 position=12144
> genomic_interval=1:12145,12277
> genomic_fields
> REF:C ALT:[<NON_REF>] GT:0/0
> sample=HG00141
> row=0 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[A, <NON_REF>] GT:0/1
> sample=HG01958
> row=1 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
> sample=HG01530
> row=2 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
> 0.017 s: api query_variant_calls direct DP and GT
> ----------------
> Interval:[0,1000000000]
>
> sample=HG00141
> row=0 position=12140
> genomic_interval=1:12141,12295
> genomic_fields
> REF:C ALT:[<NON_REF>] GT:0/0
> sample=HG01958
> row=1 position=12144
> genomic_interval=1:12145,12277
> genomic_fields
> REF:C ALT:[<NON_REF>] GT:0|0
> sample=HG00141
> row=0 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[A, <NON_REF>] GT:0/1
> sample=HG01958
> row=1 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
> sample=HG01530
> row=2 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
> 0.017 s: api query_variant_calls direct DP and GT with PP
> 13:46:22.197 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:22.197 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.198 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> ----------------
> Interval:[0,1000000000]
>
> sample=HG00141
> row=0 position=12140
> genomic_interval=1:12141,12295
> genomic_fields
> REF:C ALT:[<NON_REF>]
> sample=HG01958
> row=1 position=12144
> genomic_interval=1:12145,12277
> genomic_fields
> REF:C ALT:[<NON_REF>]
> sample=HG00141
> row=0 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[A, <NON_REF>]
> sample=HG01958
> row=1 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[T, <NON_REF>] DP:120
> sample=HG01530
> row=2 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[A, <NON_REF>] DP:76
> 13:46:22.205 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:22.205 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.205 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.211 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:22.211 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.211 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 0.014 s: api query_variant_calls with json
> 13:46:22.211 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:22.211 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.212 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.212 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.212 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.212 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 13:46:22.212 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> ----------------
> Interval:[0,1000000000]
>
> sample=HG00141
> row=0 position=12140
> genomic_interval=1:12141,12295
> genomic_fields
> REF:C ALT:[<NON_REF>] GT:0/0
> sample=HG01958
> row=1 position=12144
> genomic_interval=1:12145,12277
> genomic_fields
> REF:C ALT:[<NON_REF>] GT:0/0
> sample=HG00141
> row=0 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[A, <NON_REF>] GT:0/1
> sample=HG01958
> row=1 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
> sample=HG01530
> row=2 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
> 13:46:22.219 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:22.219 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.220 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.220 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.220 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.220 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 13:46:22.220 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> ----------------
> Interval:[0,1000000000]
>
> sample=HG00141
> row=0 position=12140
> genomic_interval=1:12141,12295
> genomic_fields
> REF:C ALT:[<NON_REF>] GT:0/0
> sample=HG01958
> row=1 position=12144
> genomic_interval=1:12145,12277
> genomic_fields
> REF:C ALT:[<NON_REF>] GT:0/0
> sample=HG00141
> row=0 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[A, <NON_REF>] GT:0/1
> sample=HG01958
> row=1 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
> sample=HG01530
> row=2 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
> 13:46:22.228 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:22.228 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.228 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.228 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.228 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.229 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 13:46:22.229 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> 0.007 s: Try query with contig intervals instead of tiledb column intervals
> 0.023 s: api query_variant_calls with protobuf
> 13:46:22.234 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:22.234 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.235 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.235 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.235 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.235 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 13:46:22.235 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> ----------------
> Interval:[0,1000000000]
>
> sample=HG00141
> row=0 position=12140
> genomic_interval=1:12141,12295
> genomic_fields
> REF:C ALT:[<NON_REF>] GT:0/0
> sample=HG01958
> row=1 position=12144
> genomic_interval=1:12145,12277
> genomic_fields
> REF:C ALT:[<NON_REF>] GT:0/0
> sample=HG00141
> row=0 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[A, <NON_REF>] GT:0/1
> sample=HG01958
> row=1 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
> sample=HG01530
> row=2 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
> 13:46:22.243 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:22.243 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.243 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.244 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.244 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.244 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 13:46:22.244 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> ----------------
> Interval:[0,1000000000]
>
> sample=HG00141
> row=0 position=12140
> genomic_interval=1:12141,12295
> genomic_fields
> REF:C ALT:[<NON_REF>] GT:0/0
> sample=HG01958
> row=1 position=12144
> genomic_interval=1:12145,12277
> genomic_fields
> REF:C ALT:[<NON_REF>] GT:0/0
> sample=HG00141
> row=0 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[A, <NON_REF>] GT:0/1
> sample=HG01958
> row=1 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
> sample=HG01530
> row=2 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
> 13:46:22.251 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:22.251 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.251 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.252 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.252 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.252 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 13:46:22.252 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> 0.007 s: Try query with a filter
> 0.024 s: api query_variant_calls with protobuf
> 13:46:22.258 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:22.258 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.258 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.259 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.259 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.259 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 13:46:22.259 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> ----------------
> Interval:[0,1000000000]
>
> sample=HG00141
> row=0 position=12140
> genomic_interval=1:12141,12295
> genomic_fields
> REF:C ALT:[<NON_REF>] GT:0/0
> sample=HG01958
> row=1 position=12144
> genomic_interval=1:12145,12277
> genomic_fields
> REF:C ALT:[<NON_REF>] GT:0/0
> sample=HG00141
> row=0 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[A, <NON_REF>] GT:0/1
> sample=HG01958
> row=1 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
> sample=HG01530
> row=2 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
> 13:46:22.267 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:22.267 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.267 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.268 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.268 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.268 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 13:46:22.268 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> ----------------
> Interval:[0,1000000000]
>
> sample=HG00141
> row=0 position=12140
> genomic_interval=1:12141,12295
> genomic_fields
> REF:C ALT:[<NON_REF>] GT:0/0
> sample=HG01958
> row=1 position=12144
> genomic_interval=1:12145,12277
> genomic_fields
> REF:C ALT:[<NON_REF>] GT:0/0
> sample=HG00141
> row=0 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[A, <NON_REF>] GT:0/1
> sample=HG01958
> row=1 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
> sample=HG01530
> row=2 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
> 13:46:22.275 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:22.275 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.276 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.276 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.276 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.276 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 13:46:22.276 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> 0.007 s: Try query with a filter and workspace with GT ploidy
> 0.024 s: api query_variant_calls with protobuf
> 13:46:22.282 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:22.282 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.282 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.283 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.283 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.283 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 13:46:22.283 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> ----------------
> Interval:[0,1000000000]
>
> sample=HG00141
> row=0 position=12140
> genomic_interval=1:12141,12295
> genomic_fields
> REF:C ALT:[<NON_REF>] GT:0/0
> sample=HG01958
> row=1 position=12144
> genomic_interval=1:12145,12277
> genomic_fields
> REF:C ALT:[<NON_REF>] GT:0/0
> sample=HG00141
> row=0 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[A, <NON_REF>] GT:0/1
> sample=HG01958
> row=1 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
> sample=HG01530
> row=2 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
> 13:46:22.290 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:22.290 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.291 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.291 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.291 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.292 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 13:46:22.292 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> ----------------
> Interval:[0,1000000000]
>
> sample=HG00141
> row=0 position=12140
> genomic_interval=1:12141,12295
> genomic_fields
> REF:C ALT:[<NON_REF>] GT:0/0
> sample=HG01958
> row=1 position=12144
> genomic_interval=1:12145,12277
> genomic_fields
> REF:C ALT:[<NON_REF>] GT:0/0
> sample=HG00141
> row=0 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[A, <NON_REF>] GT:0/1
> sample=HG01958
> row=1 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
> sample=HG01530
> row=2 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
> 13:46:22.299 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:22.299 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.300 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.301 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.301 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.301 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 13:46:22.301 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> 0.008 s: Try query with a filter and a small segment size to force TileDB buffers overflow
> 0.025 s: api query_variant_calls with protobuf
> 13:46:22.307 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:22.307 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.307 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.308 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.308 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.308 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 13:46:22.308 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> ----------------
> Interval:[0,1000000000]
>
> sample=HG00141
> row=0 position=12140
> genomic_interval=1:12141,12295
> genomic_fields
> REF:C ALT:[<NON_REF>] GT:0/0
> sample=HG01958
> row=1 position=12144
> genomic_interval=1:12145,12277
> genomic_fields
> REF:C ALT:[<NON_REF>] GT:0/0
> sample=HG00141
> row=0 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[A, <NON_REF>] GT:0/1
> sample=HG01958
> row=1 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
> sample=HG01530
> row=2 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
> 13:46:22.316 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:22.316 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.317 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.317 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.317 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.317 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 13:46:22.317 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> ----------------
> Interval:[0,1000000000]
>
> sample=HG00141
> row=0 position=12140
> genomic_interval=1:12141,12295
> genomic_fields
> REF:C ALT:[<NON_REF>] GT:0/0
> sample=HG01958
> row=1 position=12144
> genomic_interval=1:12145,12277
> genomic_fields
> REF:C ALT:[<NON_REF>] GT:0/0
> sample=HG00141
> row=0 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[A, <NON_REF>] GT:0/1
> sample=HG01958
> row=1 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
> sample=HG01530
> row=2 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
> 13:46:22.325 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:22.325 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.325 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.326 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.326 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.326 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 13:46:22.326 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> 0.007 s: Try query with POS and ROW with no match
> 0.025 s: api query_variant_calls with protobuf
> 13:46:22.332 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:22.332 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.333 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.333 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.333 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.333 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 13:46:22.333 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> ----------------
> Interval:[0,1000000000]
>
> sample=HG00141
> row=0 position=12140
> genomic_interval=1:12141,12295
> genomic_fields
> REF:C ALT:[<NON_REF>] GT:0/0
> sample=HG01958
> row=1 position=12144
> genomic_interval=1:12145,12277
> genomic_fields
> REF:C ALT:[<NON_REF>] GT:0/0
> sample=HG00141
> row=0 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[A, <NON_REF>] GT:0/1
> sample=HG01958
> row=1 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
> sample=HG01530
> row=2 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
> 13:46:22.340 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:22.340 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.341 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.341 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.341 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.341 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 13:46:22.341 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> ----------------
> Interval:[0,1000000000]
>
> sample=HG00141
> row=0 position=12140
> genomic_interval=1:12141,12295
> genomic_fields
> REF:C ALT:[<NON_REF>] GT:0/0
> sample=HG01958
> row=1 position=12144
> genomic_interval=1:12145,12277
> genomic_fields
> REF:C ALT:[<NON_REF>] GT:0/0
> sample=HG00141
> row=0 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[A, <NON_REF>] GT:0/1
> sample=HG01958
> row=1 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
> sample=HG01530
> row=2 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
> 13:46:22.349 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:22.349 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.349 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.349 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.349 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.350 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 13:46:22.350 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> 0.007 s: Try query with POS and ROW
> 0.023 s: api query_variant_calls with protobuf
> 13:46:22.355 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:22.355 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.356 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.356 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.356 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.356 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 13:46:22.357 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> ----------------
> Interval:[0,1000000000]
>
> sample=HG00141
> row=0 position=12140
> genomic_interval=1:12141,12295
> genomic_fields
> REF:C ALT:[<NON_REF>] GT:0/0
> sample=HG01958
> row=1 position=12144
> genomic_interval=1:12145,12277
> genomic_fields
> REF:C ALT:[<NON_REF>] GT:0/0
> sample=HG00141
> row=0 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[A, <NON_REF>] GT:0/1
> sample=HG01958
> row=1 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
> sample=HG01530
> row=2 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
> 13:46:22.364 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:22.364 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.364 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.365 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.365 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.365 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 13:46:22.365 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> ----------------
> Interval:[0,1000000000]
>
> sample=HG00141
> row=0 position=12140
> genomic_interval=1:12141,12295
> genomic_fields
> REF:C ALT:[<NON_REF>] GT:0/0
> sample=HG01958
> row=1 position=12144
> genomic_interval=1:12145,12277
> genomic_fields
> REF:C ALT:[<NON_REF>] GT:0/0
> sample=HG00141
> row=0 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[A, <NON_REF>] GT:0/1
> sample=HG01958
> row=1 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
> sample=HG01530
> row=2 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
> 13:46:22.372 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:22.372 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.372 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.373 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.373 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.373 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 13:46:22.373 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> 0.007 s: Try query with ISHOMREF
> 0.023 s: api query_variant_calls with protobuf
> 13:46:22.379 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:22.379 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.379 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.379 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.380 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.380 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 13:46:22.380 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> ----------------
> Interval:[0,1000000000]
>
> sample=HG00141
> row=0 position=12140
> genomic_interval=1:12141,12295
> genomic_fields
> REF:C ALT:[<NON_REF>] GT:0/0
> sample=HG01958
> row=1 position=12144
> genomic_interval=1:12145,12277
> genomic_fields
> REF:C ALT:[<NON_REF>] GT:0/0
> sample=HG00141
> row=0 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[A, <NON_REF>] GT:0/1
> sample=HG01958
> row=1 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
> sample=HG01530
> row=2 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
> 13:46:22.387 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:22.387 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.387 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.388 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.388 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.388 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 13:46:22.388 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> ----------------
> Interval:[0,1000000000]
>
> sample=HG00141
> row=0 position=12140
> genomic_interval=1:12141,12295
> genomic_fields
> REF:C ALT:[<NON_REF>] GT:0/0
> sample=HG01958
> row=1 position=12144
> genomic_interval=1:12145,12277
> genomic_fields
> REF:C ALT:[<NON_REF>] GT:0/0
> sample=HG00141
> row=0 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[A, <NON_REF>] GT:0/1
> sample=HG01958
> row=1 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
> sample=HG01530
> row=2 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
> 13:46:22.395 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:22.395 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.395 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.396 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.396 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.396 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 13:46:22.396 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> 0.007 s: Try query with ISHOMREF
> 0.023 s: api query_variant_calls with protobuf
> 13:46:22.401 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:22.401 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.402 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.402 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.402 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.402 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 13:46:22.402 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> ----------------
> Interval:[0,1000000000]
>
> sample=HG00141
> row=0 position=12140
> genomic_interval=1:12141,12295
> genomic_fields
> REF:C ALT:[<NON_REF>] GT:0/0
> sample=HG01958
> row=1 position=12144
> genomic_interval=1:12145,12277
> genomic_fields
> REF:C ALT:[<NON_REF>] GT:0/0
> sample=HG00141
> row=0 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[A, <NON_REF>] GT:0/1
> sample=HG01958
> row=1 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
> sample=HG01530
> row=2 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
> 13:46:22.409 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:22.409 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.410 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.410 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.410 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.410 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 13:46:22.410 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> ----------------
> Interval:[0,1000000000]
>
> sample=HG00141
> row=0 position=12140
> genomic_interval=1:12141,12295
> genomic_fields
> REF:C ALT:[<NON_REF>] GT:0/0
> sample=HG01958
> row=1 position=12144
> genomic_interval=1:12145,12277
> genomic_fields
> REF:C ALT:[<NON_REF>] GT:0/0
> sample=HG00141
> row=0 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[A, <NON_REF>] GT:0/1
> sample=HG01958
> row=1 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
> sample=HG01530
> row=2 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
> 13:46:22.417 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:22.418 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.418 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.418 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.418 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.419 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 13:46:22.419 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> 0.007 s: Try query with ISHOMREF
> 0.023 s: api query_variant_calls with protobuf
> 13:46:22.424 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:22.424 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.425 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.425 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.425 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.425 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 13:46:22.425 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> ----------------
> Interval:[0,1000000000]
>
> sample=HG00141
> row=0 position=12140
> genomic_interval=1:12141,12295
> genomic_fields
> REF:C ALT:[<NON_REF>] GT:0/0
> sample=HG01958
> row=1 position=12144
> genomic_interval=1:12145,12277
> genomic_fields
> REF:C ALT:[<NON_REF>] GT:0/0
> sample=HG00141
> row=0 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[A, <NON_REF>] GT:0/1
> sample=HG01958
> row=1 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
> sample=HG01530
> row=2 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
> 13:46:22.433 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:22.433 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.433 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.434 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.434 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.434 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 13:46:22.434 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> ----------------
> Interval:[0,1000000000]
>
> sample=HG00141
> row=0 position=12140
> genomic_interval=1:12141,12295
> genomic_fields
> REF:C ALT:[<NON_REF>] GT:0/0
> sample=HG01958
> row=1 position=12144
> genomic_interval=1:12145,12277
> genomic_fields
> REF:C ALT:[<NON_REF>] GT:0/0
> sample=HG00141
> row=0 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[A, <NON_REF>] GT:0/1
> sample=HG01958
> row=1 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
> sample=HG01530
> row=2 position=17384
> genomic_interval=1:17385,17385
> genomic_fields
> REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
> 13:46:22.441 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:22.441 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.442 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.442 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.442 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.442 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 13:46:22.443 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> 0.007 s: Try query with ISHOMREF
> 0.024 s: api query_variant_calls with protobuf
> 0.004 s: Base configuration
> 0.006 s: api query_variant_calls with protobuf and config
> 13:46:22.455 ERROR NativeGenomicsDB - pid=7318 tid=7318 Could not parse query_configuration. Only protobuf QueryConfiguration binary strings accepted as input argument
> 0.000 s: Subset Array with pb string that is not Query or ExportConfiguration
> 0.001 s: api query_variant_calls with protobuf and config
> 0.004 s: Subset Array using QueryConfiguration
> 0.006 s: api query_variant_calls with protobuf and config
> 0.004 s: Subset Array using ExportConfiguration
> 0.006 s: api query_variant_calls with protobuf and config
> 0.004 s: Subset Array using QueryConfiguration - two intervals
> 0.006 s: api query_variant_calls with protobuf and config
> 0.006 s: Subset Array using QueryConfiguration - multiple queries
> 0.007 s: api query_variant_calls with protobuf and config
> 0.025 s: Test filter test for 0
> 0.026 s: api query_variant_calls with protobuf new
> 0.006 s: Test filter test for 1
> 0.006 s: api query_variant_calls with protobuf new
> 0.006 s: Test filter test for 2
> 0.006 s: api query_variant_calls with protobuf new
> 0.006 s: Test filter test for 3
> 0.006 s: api query_variant_calls with protobuf new
> 273 {"HG00141":{"CHR":["1","1"],"POS":[12141,17385],"DP":[null,null],"GT":["C/C","G/A"],"REF":["C","G"]},"HG01530":{"CHR":["1"],"POS":[17385],"DP":[76],"GT":["G/A"],"REF":["G"]},"HG01958":{"CHR":["1","1"],"POS":[12145,17385],"DP":[null,120],"GT":["C/C","T/T"],"REF":["C","G"]}}
>
> 207 {"FIELD":["CHR","POS","DP","GT","REF"],"HG00141":[["1",12141,null,"C/C","C"],["1",17385,null,"G/A","G"]],"HG01530":[["1",17385,76,"G/A","G"]],"HG01958":[["1",12145,null,"C/C","C"],["1",17385,120,"T/T","G"]]}
>
> 37 {"HG00141":2,"HG01530":1,"HG01958":2}
>
> 15 {"num_calls":5}
>
> 15 {"num_calls":5}
>
> 31 ["HG00141","HG01530","HG01958"]
>
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> api_tests is a Catch2 v3.7.1 host application.
> Run with -? for options
>
> -------------------------------------------------------------------------------
> api query_variant_calls with JSONVariantCallProcessor
> -------------------------------------------------------------------------------
> ./src/test/cpp/src/test_genomicsdb_api.cc:887
> ...............................................................................
>
> ./src/test/cpp/src/test_genomicsdb_api.cc:997: FAILED:
> CHECK( output.length() == 1805 )
> with expansion:
> 1807 (0x70f) == 1805 (0x70d)
>
> 1807 {"HG00141":{"CHR":["1","1"],"POS":[12141,17385],"AD":[null,58],"BaseQRankSum":[null,-2.0959999561309816],"ClippingRankSum":[null,-1.8589999675750733],"DP":[null,null],"DP_FORMAT":[2,80],"DS":["1","1"],"FILTER":[null,0],"GQ":[0,99],"GT":["C/C","G/A"],"HaplotypeScore":[null,null],"InbreedingCoeff":[null,null],"MIN_DP":[0,null],"MLEAC":[null,1],"MLEAF":[null,0.5],"MQ":[null,31.719999313354493],"MQ0":[null,8],"MQRankSum":[null,-0.32899999618530276],"PGT":[null,"0|1"],"PID":[null,"17385_G_A"],"PL":[0,504],"QUAL":[null,475.7699890136719],"RAW_MQ":[null,5.5],"REF":["C","G"],"ReadPosRankSum":[null,0.004999999888241291],"SB":[null,"[58, 0, 22, 0]"]},"HG01530":{"CHR":["1"],"POS":[17385],"AD":[40],"BaseQRankSum":[1.0460000038146973],"ClippingRankSum":[-2.242000102996826],"DP":[76],"DP_FORMAT":[76],"DS":["127"],"FILTER":[null],"GQ":[99],"GT":["G/A"],"HaplotypeScore":[null],"InbreedingCoeff":[null],"MIN_DP":[null],"MLEAC":[1],"MLEAF":[0.5],"MQ":[59.369998931884769],"MQ0":[0],"MQRankSum":[-0.4320000112056732],"PGT":[null],"PID":[null],"PL":[1018],"QUAL":[989.77001953125],"RAW_MQ":[null],"REF":["G"],"ReadPosRankSum":[2.055000066757202],"SB":["[9, 31, 13, 23]"]},"HG01958":{"CHR":["1","1"],"POS":[12145,17385],"AD":[null,0],"BaseQRankSum":[null,-2.0739998817443849],"ClippingRankSum":[null,0.5550000071525574],"DP":[null,120],"DP_FORMAT":[3,120],"DS":["1","127"],"FILTER":[null,0],"GQ":[0,99],"GT":["C/C","T/T"],"HaplotypeScore":[null,null],"InbreedingCoeff":[null,null],"MIN_DP":[0,null],"MLEAC":[null,2],"MLEAF":[null,1.0],"MQ":[null,29.81999969482422],"MQ0":[null,3],"MQRankSum":[null,-1.36899995803833],"PGT":[null,"0|1"],"PID":[null,"17385_G_T"],"PL":[0,3336],"QUAL":[null,3302.77001953125],"RAW_MQ":[null,2.5],"REF":["C","G"],"ReadPosRankSum":[null,-0.10100000351667404],"SB":[null,"[0, 0, 0, 0]"]}}
>
> 0.044 s: api query_variant_calls with JSONVariantCallProcessor
> 0.000 s: Test genomicsdb demo test case
> 0.039 s: api generate_vcf direct
> 13:46:22.605 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:22.605 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.605 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 0.009 s: api generate_vcf with json
> 13:46:22.614 DEBUG NativeGenomicsDB - pid=7318 tid=7322 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:22.614 WARN NativeGenomicsDB - pid=7318 tid=7322 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.615 DEBUG NativeGenomicsDB - pid=7318 tid=7325 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:22.615 WARN NativeGenomicsDB - pid=7318 tid=7325 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.615 DEBUG NativeGenomicsDB - pid=7318 tid=7322 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.615 DEBUG NativeGenomicsDB - pid=7318 tid=7325 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.618 DEBUG NativeGenomicsDB - pid=7318 tid=7326 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:22.618 WARN NativeGenomicsDB - pid=7318 tid=7326 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.618 DEBUG NativeGenomicsDB - pid=7318 tid=7326 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.614 DEBUG NativeGenomicsDB - pid=7318 tid=7324 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:22.618 WARN NativeGenomicsDB - pid=7318 tid=7324 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.619 DEBUG NativeGenomicsDB - pid=7318 tid=7327 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:22.619 WARN NativeGenomicsDB - pid=7318 tid=7327 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.619 DEBUG NativeGenomicsDB - pid=7318 tid=7329 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:22.619 WARN NativeGenomicsDB - pid=7318 tid=7329 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.619 DEBUG NativeGenomicsDB - pid=7318 tid=7329 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.619 DEBUG NativeGenomicsDB - pid=7318 tid=7324 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.619 DEBUG NativeGenomicsDB - pid=7318 tid=7327 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.622 DEBUG NativeGenomicsDB - pid=7318 tid=7323 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:22.622 WARN NativeGenomicsDB - pid=7318 tid=7323 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.627 DEBUG NativeGenomicsDB - pid=7318 tid=7323 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.648 DEBUG NativeGenomicsDB - pid=7318 tid=7328 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:22.648 WARN NativeGenomicsDB - pid=7318 tid=7328 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.648 DEBUG NativeGenomicsDB - pid=7318 tid=7328 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 0.051 s: api generate_vcf with json multiple threads
> 13:46:22.665 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:22.665 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.665 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.666 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.666 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.666 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 13:46:22.666 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.673 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:22.673 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.673 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.673 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.673 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.674 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 13:46:22.674 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.680 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
> 13:46:22.680 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.680 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.681 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
> 13:46:22.681 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
> 13:46:22.681 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name
> 13:46:22.681 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead
> ----------------
> Interval:[0,1000000000]
>
> ----------------
> Interval:[0,1000000000]
>
> 0.021 s: api annotate query_variant_calls with test datasource 0
> ===============================================================================
> test cases: 26 | 25 passed | 1 failed
> assertions: 1531 | 1530 passed | 1 failed
>
>
> test 22
> Start 22: tools_tests
>
> 22: Test command: /build/reproducible-path/genomicsdb-1.5.4/tests/test_tools.sh "/build/reproducible-path/genomicsdb-1.5.4/tests/inputs/vcfs" "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/tools" "1"
> 22: Working Directory: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/tools
> 22: Test timeout computed to be: 10000000
> 22: 13:46:23.103 INFO NativeGenomicsDB - pid=7400 tid=7400 Reading 1 vcfs
> 22: 13:46:23.104 INFO NativeGenomicsDB - pid=7400 tid=7400 [STAGE 1 / 3] Reading 1 / 1 = 100.00%
> 22: 13:46:23.153 INFO NativeGenomicsDB - pid=7400 tid=7400 [STAGE 2 / 3] read_next_batch 0 / 1 = 0.00%
> 22: 13:46:23.154 INFO NativeGenomicsDB - pid=7400 tid=7400 [STAGE 3 / 3] progress: 12140 / 249250620 = 0.00%
> 22: [TileDB::utils] Error: (gzip_handle_error) Cannot compress with GZIP: deflateInit error: Z_STREAM_ERROR
> 22: [TileDB::Codec] Error: Could not compress with GZIP.
> 22: [TileDB::WriteState] Error: Cannot compress tile for /tmp/test_tools-GenomicsDB-1BhoXmDpmj/ws_7004/1$1$249250621/.__71a412e3-fcd4-435b-9805-42df13759a33281473768824864_1744551983141/END.tdb.
> 22: 13:46:23.159 ERROR NativeGenomicsDB - pid=7400 tid=7400 VariantStorageManagerException exception : Error while finalizing GenomicsDB array 1$1$249250621 : [TileDB::WriteState] Error: Cannot compress tile for /tmp/test_tools-GenomicsDB-1BhoXmDpmj/ws_7004/1$1$249250621/.__71a412e3-fcd4-435b-9805-42df13759a33281473768824864_1744551983141/END.tdb
> 22: command 'vcf2genomicsdb --progress /tmp/test_tools-GenomicsDB-1BhoXmDpmj/ws_7004/loader.json' returned 139 unexpectedly
> 19/22 Test #22: tools_tests ......................***Failed 0.47 sec
> 13:46:23.103 INFO NativeGenomicsDB - pid=7400 tid=7400 Reading 1 vcfs
> 13:46:23.104 INFO NativeGenomicsDB - pid=7400 tid=7400 [STAGE 1 / 3] Reading 1 / 1 = 100.00%
> 13:46:23.153 INFO NativeGenomicsDB - pid=7400 tid=7400 [STAGE 2 / 3] read_next_batch 0 / 1 = 0.00%
> 13:46:23.154 INFO NativeGenomicsDB - pid=7400 tid=7400 [STAGE 3 / 3] progress: 12140 / 249250620 = 0.00%
> [TileDB::utils] Error: (gzip_handle_error) Cannot compress with GZIP: deflateInit error: Z_STREAM_ERROR
> [TileDB::Codec] Error: Could not compress with GZIP.
> [TileDB::WriteState] Error: Cannot compress tile for /tmp/test_tools-GenomicsDB-1BhoXmDpmj/ws_7004/1$1$249250621/.__71a412e3-fcd4-435b-9805-42df13759a33281473768824864_1744551983141/END.tdb.
> 13:46:23.159 ERROR NativeGenomicsDB - pid=7400 tid=7400 VariantStorageManagerException exception : Error while finalizing GenomicsDB array 1$1$249250621 : [TileDB::WriteState] Error: Cannot compress tile for /tmp/test_tools-GenomicsDB-1BhoXmDpmj/ws_7004/1$1$249250621/.__71a412e3-fcd4-435b-9805-42df13759a33281473768824864_1744551983141/END.tdb
> command 'vcf2genomicsdb --progress /tmp/test_tools-GenomicsDB-1BhoXmDpmj/ws_7004/loader.json' returned 139 unexpectedly
>
> 18: ===============================================================================
> 18: All tests passed (450703 assertions in 3 test cases)
> 18:
> 20/22 Test #18: test_storage_buffer .............. Passed 1.59 sec
> 8: Randomness seeded to: 2127700894
> 8: 10% [=== ]
> 20% [====== ]
> 30% [========= ]
> 40% [============ ]
> 50% [=============== ]
> 60% [================== ]
> 70% [===================== ]
> 80% [======================= ]
> 89% [========================== ]
> 99% [============================= ]
> ===============================================================================
> 8: All tests passed (16578158 assertions in 15 test cases)
> 8:
> 21/22 Test #8: test_sparse_array_api ............ Passed 5.08 sec
> 7: 10% [=== ]
> 20% [====== ]
> 30% [========= ]
> 40% [============ ]
> 50% [=============== ]
> 60% [================== ]
> 70% [===================== ]
> 80% [======================= ]
> 89% [========================== ]
> 99% [============================= ]
> 10% [=== ]
> 20% [====== ]
> 30% [========= ]
> 40% [============ ]
> 50% [=============== ]
> 60% [================== ]
> 70% [===================== ]
> 80% [======================= ]
> 89% [========================== ]
> 99% [============================= ]
> ===============================================================================
> 7: All tests passed (174824580 assertions in 4 test cases)
> 7:
> 22/22 Test #7: test_dense_array_api ............. Passed 6.95 sec
>
> 73% tests passed, 6 tests failed out of 22
>
> Total Test time (real) = 6.96 sec
>
> The following tests FAILED:
> 5 - test_array_iterator (SEGFAULT)
> 6 - test_array_schema_api (Failed)
> 19 - ci_tests (Failed)
> 20 - ctests (Failed)
> 21 - api_tests (Failed)
> 22 - tools_tests (Failed)
> Errors while running CTest
> make[2]: *** [Makefile:74: test] Error 8
> make[2]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu'
> dh_auto_test: error: cd obj-aarch64-linux-gnu && make -j4 test ARGS\+=--verbose ARGS\+=-j4 returned exit code 2
The full build log is available from:
http://qa-logs.debian.net/2025/04/13/genomicsdb_1.5.4-5_testing.log
All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20250413;users=lucas@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20250413&fusertaguser=lucas@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
If you reassign this bug to another package, please mark it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects
If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.
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