I tried to collect OxoG metrics, but less than 2% of my BAMs gave empty metrics as below. I have also updated my picard to 2.8.3. The example file I have is of normal size (14G). Also I saw from another thread asking about read group information, and it does.
@RG ID:0 CN:BCM DS:Wilms Tumor PI R Gibbs DT:2012-05-31T12:00:00+0000 LB:ING_WTSRG.PAKGZX01A-1_1pA PL:Illumina PU:110208_SN601_0075_A81K6MABXX_6 SM:TARGET-50-PAKGZX-01A-01D

htsjdk.samtools.metrics.StringHeader

picard.analysis.CollectOxoGMetrics INPUT=TARGET-50-PAKGZX-01A-01D_hg19_Illumina_gdc_realn.bam OUTPUT=temp REFERENCE_SEQUENCE=/home/ubuntu/SCRATCH/GRCh38.d1.vd1.fa MINIMUM_QUALITY_SCORE=20 MINIMUM_MAPPING_QUALITY=30 MINIMUM_INSERT_SIZE=60 MAXIMUM_INSERT_SIZE=600 INCLUDE_NON_PF_READS=true USE_OQ=tr

ue CONTEXT_SIZE=1 STOP_AFTER=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json

htsjdk.samtools.metrics.StringHeader

Started on: Mon Feb 20 18:44:42 UTC 2017

METRICS CLASS picard.analysis.CollectOxoGMetrics$CpcgMetrics

SAMPLE_ALIAS LIBRARY CONTEXT TOTAL_SITES TOTAL_BASES REF_NONOXO_BASES REF_OXO_BASES REF_TOTAL_BASES ALT_NONOXO_BASES ALT_OXO_BASES OXIDATION_ERROR_RATE OXIDATION_Q C_REF_REF_BASES G_REF_REF_BASES C_REF_ALT_BASES G_REF_ALT_BASES C_REF_OXO_ERROR_RATE C_REF_OXO_Q G_REF_OXO_ERROR_RATE G_REF_OXO_Q
TARGET-50-PAKGZX-01A-01D ING_WTSRG.PAKGZX01A-1_1pA CCA 0 0 0 0 0 0 0 ? -? 0 0 0 0 ? ? ? ?
TARGET-50-PAKGZX-01A-01D ING_WTSRG.PAKGZX01A-1_1pA ACC 0 0 0 0 0 0 0 ? -? 0 0 0 0 ? ? ? ?
TARGET-50-PAKGZX-01A-01D ING_WTSRG.PAKGZX01A-1_1pA CCC 0 0 0 0 0 0 0 ? -? 0 0 0 0 ? ? ? ?
TARGET-50-PAKGZX-01A-01D ING_WTSRG.PAKGZX01A-1_1pA GCA 0 0 0 0 0 0 0 ? -? 0 0 0 0 ? ? ? ?
TARGET-50-PAKGZX-01A-01D ING_WTSRG.PAKGZX01A-1_1pA TCT 0 0 0 0 0 0 0 ? -? 0 0 0 0 ? ? ? ?
TARGET-50-PAKGZX-01A-01D ING_WTSRG.PAKGZX01A-1_1pA ACG 0 0 0 0 0 0 0 ? -? 0 0 0 0 ? ? ? ?
TARGET-50-PAKGZX-01A-01D ING_WTSRG.PAKGZX01A-1_1pA CCG 0 0 0 0 0 0 0 ? -? 0 0 0 0 ? ? ? ?
TARGET-50-PAKGZX-01A-01D ING_WTSRG.PAKGZX01A-1_1pA GCC 0 0 0 0 0 0 0 ? -? 0 0 0 0 ? ? ? ?
TARGET-50-PAKGZX-01A-01D ING_WTSRG.PAKGZX01A-1_1pA GCG 0 0 0 0 0 0 0 ? -? 0 0 0 0 ? ? ? ?
TARGET-50-PAKGZX-01A-01D ING_WTSRG.PAKGZX01A-1_1pA ACT 0 0 0 0 0 0 0 ? -? 0 0 0 0 ? ? ? ?
TARGET-50-PAKGZX-01A-01D ING_WTSRG.PAKGZX01A-1_1pA TCA 0 0 0 0 0 0 0 ? -? 0 0 0 0 ? ? ? ?
TARGET-50-PAKGZX-01A-01D ING_WTSRG.PAKGZX01A-1_1pA CCT 0 0 0 0 0 0 0 ? -? 0 0 0 0 ? ? ? ?
TARGET-50-PAKGZX-01A-01D ING_WTSRG.PAKGZX01A-1_1pA TCC 0 0 0 0 0 0 0 ? -? 0 0 0 0 ? ? ? ?
TARGET-50-PAKGZX-01A-01D ING_WTSRG.PAKGZX01A-1_1pA GCT 0 0 0 0 0 0 0 ? -? 0 0 0 0 ? ? ? ?
TARGET-50-PAKGZX-01A-01D ING_WTSRG.PAKGZX01A-1_1pA TCG 0 0 0 0 0 0 0 ? -? 0 0 0 0 ? ? ? ?
TARGET-50-PAKGZX-01A-01D ING_WTSRG.PAKGZX01A-1_1pA ACA 0 0 0 0 0 0 0 ? -? 0 0 0 0 ? ? ? ?