[continued from previous message]

21: 1807 {"HG00141":{"CHR":["1","1"],"POS":[12141,17385],"AD":[null,58],"BaseQRankSum":[null,-2.0959999561309816],"ClippingRankSum":[null,-1.8589999675750733],"DP":[null,null],"DP_FORMAT":[2,80],"DS":["1","1"],"FILTER":[null,0],"GQ":[0,99],"GT":["C/C","

G/A"],"HaplotypeScore":[null,null],"InbreedingCoeff":[null,null],"MIN_DP":[0,null],"MLEAC":[null,1],"MLEAF":[null,0.5],"MQ":[null,31.719999313354493],"MQ0":[null,8],"MQRankSum":[null,-0.32899999618530276],"PGT":[null,"0|1"],"PID":[null,"17385_G_A"],"PL":[
0,504],"QUAL":[null,475.7699890136719],"RAW_MQ":[null,5.5],"REF":["C","G"],"ReadPosRankSum":[null,0.004999999888241291],"SB":[null,"[58, 0, 22, 0]"]},"HG01530":{"CHR":["1"],"POS":[17385],"AD":[40],"BaseQRankSum":[1.0460000038146973],"ClippingRankSum":[-2.
242000102996826],"DP":[76],"DP_FORMAT":[76],"DS":["127"],"FILTER":[null],"GQ":[99],"GT":["G/A"],"HaplotypeScore":[null],"InbreedingCoeff":[null],"MIN_DP":[null],"MLEAC":[1],"MLEAF":[0.5],"MQ":[59.369998931884769],"MQ0":[0],"MQRankSum":[-0.
4320000112056732],"PGT":[null],"PID":[null],"PL":[1018],"QUAL":[989.77001953125],"RAW_MQ":[null],"REF":["G"],"ReadPosRankSum":[2.055000066757202],"SB":["[9, 31, 13, 23]"]},"HG01958":{"CHR":["1","1"],"POS":[12145,17385],"AD":[null,0],"BaseQRankSum":[null,-
2.0739998817443849],"ClippingRankSum":[null,0.5550000071525574],"DP":[null,120],"DP_FORMAT":[3,120],"DS":["1","127"],"FILTER":[null,0],"GQ":[0,99],"GT":["C/C","T/T"],"HaplotypeScore":[null,null],"InbreedingCoeff":[null,null],"MIN_DP":[0,null],"MLEAC":[
null,2],"MLEAF":[null,1.0],"MQ":[null,29.81999969482422],"MQ0":[null,3],"MQRankSum":[null,-1.36899995803833],"PGT":[null,"0|1"],"PID":[null,"17385_G_T"],"PL":[0,3336],"QUAL":[null,3302.77001953125],"RAW_MQ":[null,2.5],"REF":["C","G"],"ReadPosRankSum":[
null,-0.10100000351667404],"SB":[null,"[0, 0, 0, 0]"]}}

21:
21: 0.044 s: api query_variant_calls with JSONVariantCallProcessor
21: 0.000 s: Test genomicsdb demo test case
21: 0.039 s: api generate_vcf direct
21: 13:46:22.605 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].

begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn

21: 13:46:22.605 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
21: 13:46:22.605 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
21: 0.009 s: api generate_vcf with json
21: 13:46:22.614 DEBUG NativeGenomicsDB - pid=7318 tid=7322 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].

begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn

21: 13:46:22.614 WARN NativeGenomicsDB - pid=7318 tid=7322 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
21: 13:46:22.615 DEBUG NativeGenomicsDB - pid=7318 tid=7325 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].

begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn

21: 13:46:22.615 WARN NativeGenomicsDB - pid=7318 tid=7325 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
21: 13:46:22.615 DEBUG NativeGenomicsDB - pid=7318 tid=7322 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
21: 13:46:22.615 DEBUG NativeGenomicsDB - pid=7318 tid=7325 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
21: 13:46:22.618 DEBUG NativeGenomicsDB - pid=7318 tid=7326 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].

begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn

21: 13:46:22.618 WARN NativeGenomicsDB - pid=7318 tid=7326 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
21: 13:46:22.618 DEBUG NativeGenomicsDB - pid=7318 tid=7326 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
21: 13:46:22.614 DEBUG NativeGenomicsDB - pid=7318 tid=7324 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].

begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn

21: 13:46:22.618 WARN NativeGenomicsDB - pid=7318 tid=7324 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
21: 13:46:22.619 DEBUG NativeGenomicsDB - pid=7318 tid=7327 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].

begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn

21: 13:46:22.619 WARN NativeGenomicsDB - pid=7318 tid=7327 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
21: 13:46:22.619 DEBUG NativeGenomicsDB - pid=7318 tid=7329 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].

begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn

21: 13:46:22.619 WARN NativeGenomicsDB - pid=7318 tid=7329 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
21: 13:46:22.619 DEBUG NativeGenomicsDB - pid=7318 tid=7329 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
21: 13:46:22.619 DEBUG NativeGenomicsDB - pid=7318 tid=7324 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
21: 13:46:22.619 DEBUG NativeGenomicsDB - pid=7318 tid=7327 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
21: 13:46:22.622 DEBUG NativeGenomicsDB - pid=7318 tid=7323 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].

begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn

21: 13:46:22.622 WARN NativeGenomicsDB - pid=7318 tid=7323 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
21: 13:46:22.627 DEBUG NativeGenomicsDB - pid=7318 tid=7323 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
21: 13:46:22.648 DEBUG NativeGenomicsDB - pid=7318 tid=7328 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].

begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn

21: 13:46:22.648 WARN NativeGenomicsDB - pid=7318 tid=7328 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
21: 13:46:22.648 DEBUG NativeGenomicsDB - pid=7318 tid=7328 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
21: 0.051 s: api generate_vcf with json multiple threads
21: 13:46:22.665 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].

begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn

21: 13:46:22.665 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
21: 13:46:22.665 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
21: 13:46:22.666 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field

name

21: 13:46:22.666 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
21: 13:46:22.666 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets):

missing field sample_name

21: 13:46:22.666 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular

JSON file instead

21: 13:46:22.673 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].

begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn

21: 13:46:22.673 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
21: 13:46:22.673 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
21: 13:46:22.673 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field

name

21: 13:46:22.673 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
21: 13:46:22.674 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets):

missing field sample_name

21: 13:46:22.674 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular

JSON file instead

21: 13:46:22.680 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].

begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn

21: 13:46:22.680 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
21: 13:46:22.680 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
21: 13:46:22.681 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field

name

21: 13:46:22.681 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
21: 13:46:22.681 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets):

missing field sample_name

21: 13:46:22.681 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular

JSON file instead

21: ----------------
21: Interval:[0,1000000000]
21:
21: ----------------
21: Interval:[0,1000000000]
21:
21: 0.021 s: api annotate query_variant_calls with test datasource 0
21: ===============================================================================
21: test cases: 26 | 25 passed | 1 failed
21: assertions: 1531 | 1530 passed | 1 failed
21:
18/22 Test #21: api_tests ........................***Failed 0.71 sec Randomness seeded to: 2475962137
0.000 s: utils
0.000 s: api empty_args
0.017 s: api query_variants direct DP
0.007 s: api query_variants direct DP with huge row range
0.007 s: api query_variants direct DP with huge disjoint row ranges
0.010 s: api query_variants direct DP with range composed of multiple points 0.010 s: api query_variants direct DP with range composed of overlapping ranges
13:46:22.055 ERROR NativeGenomicsDB - pid=7318 tid=7318 Query interval 0:-100-1 is out of bounds
0.005 s: api query_variants direct DP with invalid row range
0.014 s: api query_variants direct DP and GT
0.014 s: api query_variants direct DP and GT with PP
13:46:22.085 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].

begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn

13:46:22.086 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
13:46:22.086 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
13:46:22.093 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].

begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn

13:46:22.093 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
13:46:22.093 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
13:46:22.101 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].

begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn

13:46:22.101 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
13:46:22.101 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
0.017 s: api query_variants with json
13:46:22.101 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].

begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn

13:46:22.101 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
13:46:22.102 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/ws/t0_1_2/.__consolidation_lock
13:46:22.109 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].

begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn

13:46:22.109 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
13:46:22.109 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
13:46:22.116 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].

begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn

13:46:22.116 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
13:46:22.117 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
0.016 s: api query variants with json string
13:46:22.139 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].

begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn

13:46:22.139 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
13:46:22.140 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
0.029 s: api query variants with enabled shared posixfs optimizations ----------------
Interval:[0,9223372036854775806]

sample=HG00141
row=0 position=12140
genomic_interval=1:12141,12295
genomic_fields
REF:C ALT:[<NON_REF>]
sample=HG01958
row=1 position=12144
genomic_interval=1:12145,12277
genomic_fields
REF:C ALT:[<NON_REF>]
sample=HG00141
row=0 position=17384
genomic_interval=1:17385,17385
genomic_fields
REF:G ALT:[A, <NON_REF>]
sample=HG01958
row=1 position=17384
genomic_interval=1:17385,17385
genomic_fields
REF:G ALT:[T, <NON_REF>] DP:120
sample=HG01530
row=2 position=17384
genomic_interval=1:17385,17385
genomic_fields
REF:G ALT:[A, <NON_REF>] DP:76 ----------------
Interval:[0,1000000000]

sample=HG00141
row=0 position=12140
genomic_interval=1:12141,12295
genomic_fields
REF:C ALT:[<NON_REF>]
sample=HG01958
row=1 position=12144
genomic_interval=1:12145,12277
genomic_fields
REF:C ALT:[<NON_REF>]
sample=HG00141
row=0 position=17384
genomic_interval=1:17385,17385
genomic_fields
REF:G ALT:[A, <NON_REF>]
sample=HG01958
row=1 position=17384
genomic_interval=1:17385,17385
genomic_fields
REF:G ALT:[T, <NON_REF>] DP:120
sample=HG01530
row=2 position=17384
genomic_interval=1:17385,17385
genomic_fields
REF:G ALT:[A, <NON_REF>] DP:76
0.017 s: api query_variant_calls direct
----------------
Interval:[0,1000000000]

sample=HG00141
row=0 position=12140
genomic_interval=1:12141,12295
genomic_fields
REF:C ALT:[<NON_REF>] GT:0/0
sample=HG01958
row=1 position=12144
genomic_interval=1:12145,12277
genomic_fields
REF:C ALT:[<NON_REF>] GT:0/0
sample=HG00141
row=0 position=17384
genomic_interval=1:17385,17385
genomic_fields
REF:G ALT:[A, <NON_REF>] GT:0/1
sample=HG01958
row=1 position=17384
genomic_interval=1:17385,17385
genomic_fields
REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
sample=HG01530
row=2 position=17384
genomic_interval=1:17385,17385
genomic_fields
REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
0.017 s: api query_variant_calls direct DP and GT
----------------
Interval:[0,1000000000]

sample=HG00141
row=0 position=12140
genomic_interval=1:12141,12295
genomic_fields
REF:C ALT:[<NON_REF>] GT:0/0
sample=HG01958
row=1 position=12144
genomic_interval=1:12145,12277
genomic_fields
REF:C ALT:[<NON_REF>] GT:0|0
sample=HG00141
row=0 position=17384
genomic_interval=1:17385,17385
genomic_fields
REF:G ALT:[A, <NON_REF>] GT:0/1
sample=HG01958
row=1 position=17384
genomic_interval=1:17385,17385
genomic_fields
REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
sample=HG01530
row=2 position=17384
genomic_interval=1:17385,17385
genomic_fields
REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
0.017 s: api query_variant_calls direct DP and GT with PP
13:46:22.197 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].

begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn

13:46:22.197 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
13:46:22.198 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
----------------
Interval:[0,1000000000]

sample=HG00141
row=0 position=12140
genomic_interval=1:12141,12295
genomic_fields
REF:C ALT:[<NON_REF>]
sample=HG01958
row=1 position=12144
genomic_interval=1:12145,12277
genomic_fields
REF:C ALT:[<NON_REF>]
sample=HG00141
row=0 position=17384
genomic_interval=1:17385,17385
genomic_fields
REF:G ALT:[A, <NON_REF>]
sample=HG01958
row=1 position=17384
genomic_interval=1:17385,17385
genomic_fields
REF:G ALT:[T, <NON_REF>] DP:120
sample=HG01530
row=2 position=17384
genomic_interval=1:17385,17385
genomic_fields
REF:G ALT:[A, <NON_REF>] DP:76 13:46:22.205 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].

begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn

13:46:22.205 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
13:46:22.205 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
13:46:22.211 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].

begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn

13:46:22.211 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
13:46:22.211 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
0.014 s: api query_variant_calls with json
13:46:22.211 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].

begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn

13:46:22.211 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
13:46:22.212 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
13:46:22.212 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
13:46:22.212 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
13:46:22.212 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets):

missing field sample_name

13:46:22.212 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON

file instead

----------------
Interval:[0,1000000000]

sample=HG00141
row=0 position=12140
genomic_interval=1:12141,12295
genomic_fields
REF:C ALT:[<NON_REF>] GT:0/0
sample=HG01958
row=1 position=12144
genomic_interval=1:12145,12277
genomic_fields
REF:C ALT:[<NON_REF>] GT:0/0
sample=HG00141
row=0 position=17384
genomic_interval=1:17385,17385
genomic_fields
REF:G ALT:[A, <NON_REF>] GT:0/1
sample=HG01958
row=1 position=17384
genomic_interval=1:17385,17385
genomic_fields
REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
sample=HG01530
row=2 position=17384
genomic_interval=1:17385,17385
genomic_fields
REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
13:46:22.219 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].

begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn

13:46:22.219 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
13:46:22.220 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
13:46:22.220 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
13:46:22.220 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
13:46:22.220 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets):

missing field sample_name

13:46:22.220 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON

file instead

----------------
Interval:[0,1000000000]

sample=HG00141
row=0 position=12140
genomic_interval=1:12141,12295
genomic_fields
REF:C ALT:[<NON_REF>] GT:0/0
sample=HG01958
row=1 position=12144
genomic_interval=1:12145,12277
genomic_fields
REF:C ALT:[<NON_REF>] GT:0/0
sample=HG00141
row=0 position=17384
genomic_interval=1:17385,17385
genomic_fields
REF:G ALT:[A, <NON_REF>] GT:0/1
sample=HG01958
row=1 position=17384
genomic_interval=1:17385,17385
genomic_fields

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