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Bug#1103009: genomicsdb: FTBFS in testing/arm64: tests failed (5/9)

From Lucas Nussbaum@21:1/5 to All on Sun Apr 13 18:50:03 2025

[continued from previous message]

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:

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Bug#1103009: genomicsdb: FTBFS in testing/arm64: tests failed (5/9)

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