Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1029_OIL-N1-BDNA-1_B23MHTGLT4_1/1029_OIL-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1029_OIL-N1-BDNA-1_B23MHTGLT4_1/1029_OIL-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/98/25ea9f09e1c7fce30d8083af857a1f/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/foresight/xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/98/25ea9f09e1c7fce30d8083af857a1f/.command.run
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_OIL-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_OIL-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_OIL-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_OIL-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Reads: 66491364 total, 40169 skipped (flags/unmapped)
Fragments: 33385369 total (33019668 tlen-paired, 3465 hash-paired, 337 singletons, 10247 discordant, 351652 orphans, 16223 too large [>5000 bp], 9138009 duplicates)
Reads: 67187395 total, 36418 skipped (flags/unmapped)
Fragments: 33729581 total (33394883 tlen-paired, 1980 hash-paired, 314 singletons, 8567 discordant, 323837 orphans, 7983 too large [>5000 bp], 8979033 duplicates)
Reads: 63093556 total, 46290 skipped (flags/unmapped)
Fragments: 31674863 total (31342623 tlen-paired, 3443 hash-paired, 363 singletons, 11815 discordant, 316619 orphans, 7261 too large [>5000 bp], 8633160 duplicates)
Reads: 73486196 total, 67181 skipped (flags/unmapped)
Fragments: 37027258 total (36027561 tlen-paired, 2498 hash-paired, 369 singletons, 195966 discordant, 800864 orphans, 82866 too large [>5000 bp], 10141748 duplicates)