Forum: >>> Magnum BBS <<<

Bug#1103009: genomicsdb: FTBFS in testing/arm64: tests failed (8/9)

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

[continued from previous message]

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

[continued in next message]

--- SoupGate-Win32 v1.05
* Origin: fsxNet Usenet Gateway (21:1/5)

Who's Online
Recent Visitors
- Plume
  Sun Sep 14 09:34:52 2025
  from Uk via Raw
- Gretchiie
  Sun Sep 14 06:07:30 2025
  from Derry, Nh via Telnet
- Thlc
  Sat Sep 13 17:11:34 2025
  from Rognac, France via Telnet
- Thlc
  Sat Sep 13 17:04:03 2025
  from Rognac, France via Telnet
- Thlc
  Sat Sep 13 16:32:19 2025
  from Rognac, France via SSH
- Thlc
  Sat Sep 13 15:41:11 2025
  from Rognac, France via SSH
- Thlc
  Sat Sep 13 07:56:03 2025
  from Rognac, France via SSH
- Gretchiie
  Sat Sep 13 07:22:10 2025
  from Derry, Nh via Telnet

System Info

Sysop:	Keyop
Location:	Huddersfield, West Yorkshire, UK
Users:	546
Nodes:	16 (3 / 13)
Uptime:	02:42:51
Calls:	10,385
Calls today:	2
Files:	14,057
Messages:	6,416,584

Bug#1103009: genomicsdb: FTBFS in testing/arm64: tests failed (8/9)

Who's Online

Recent Visitors

System Info