Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/659_dES-N1-BDNA-1_B23KFG5LT4_1/659_dES-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/8ec650433b01cacd518f250d240071/.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/a4/8ec650433b01cacd518f250d240071/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/659_dES-N1-BDNA-1_B23KFG5LT4_1/659_dES-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
==> 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: 659_dES-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_dES-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai[W::hts_idx_load3] The index file is older than the data file: 659_dES-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 659_dES-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: 72316993 total, 60028 skipped (flags/unmapped)
Fragments: 36247154 total (35968501 tlen-paired, 3748 hash-paired, 316 singletons, 18040 discordant, 256549 orphans, 9761 too large [>5000 bp], 13865836 duplicates)
Reads: 77822495 total, 51671 skipped (flags/unmapped)
Fragments: 39003048 total (38730280 tlen-paired, 3214 hash-paired, 399 singletons, 12066 discordant, 257089 orphans, 11108 too large [>5000 bp], 14710056 duplicates)
Reads: 84997489 total, 87046 skipped (flags/unmapped)
Fragments: 42674032 total (42011627 tlen-paired, 3577 hash-paired, 333 singletons, 120941 discordant, 537554 orphans, 50133 too large [>5000 bp], 16536488 duplicates)
Reads: 84844360 total, 56282 skipped (flags/unmapped)
Fragments: 42527497 total (42200809 tlen-paired, 4026 hash-paired, 305 singletons, 18284 discordant, 304073 orphans, 18731 too large [>5000 bp], 16436976 duplicates)