[continued from previous message]

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

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