Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1136_3BQ-N1-BDNA-1_B23KFG5LT4_1/1136_3BQ-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/62/cbe5b6b44919396c4af124b1a62d10/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1136_3BQ-N1-BDNA-1_B23KFG5LT4_1/1136_3BQ-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
  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/62/cbe5b6b44919396c4af124b1a62d10/.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: 1136_3BQ-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3BQ-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3BQ-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3BQ-N1-BDNA-1_B23KFG5LT4_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: 64853179 total, 50257 skipped (flags/unmapped)
Fragments: 32522383 total (32246828 tlen-paired, 2187 hash-paired, 271 singletons, 13498 discordant, 259599 orphans, 9013 too large [>5000 bp], 13900603 duplicates)
Reads: 70930148 total, 41644 skipped (flags/unmapped)
Fragments: 35576353 total (35282709 tlen-paired, 1902 hash-paired, 373 singletons, 10600 discordant, 280769 orphans, 8470 too large [>5000 bp], 14823803 duplicates)
Reads: 71084172 total, 44503 skipped (flags/unmapped)
Fragments: 35653557 total (35327011 tlen-paired, 2899 hash-paired, 269 singletons, 12766 discordant, 310612 orphans, 21718 too large [>5000 bp], 15292421 duplicates)
Reads: 78616770 total, 74944 skipped (flags/unmapped)
Fragments: 39521770 total (38745332 tlen-paired, 2997 hash-paired, 326 singletons, 151873 discordant, 621242 orphans, 59927 too large [>5000 bp], 16971256 duplicates)