[continued from previous message]

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

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