Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0e/82a8572ee69db5eecec5e06684431e/.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/0e/82a8572ee69db5eecec5e06684431e/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_7K3-N1-BDNA-1_A23KFG7LT4_1/1136_7K3-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_7K3-N1-BDNA-1_A23KFG7LT4_1/1136_7K3-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1136_7K3-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7K3-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
The index file is older than the data file: 1136_7K3-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7K3-N1-BDNA-1_A23KFG7LT4_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: 79161154 total, 55951 skipped (flags/unmapped)
Fragments: 39669914 total (39386306 tlen-paired, 4949 hash-paired, 436 singletons, 16396 discordant, 261827 orphans, 13819 too large [>5000 bp], 13582527 duplicates)
Reads: 84753025 total, 47136 skipped (flags/unmapped)
Fragments: 42476286 total (42194017 tlen-paired, 2783 hash-paired, 451 singletons, 11047 discordant, 267988 orphans, 10878 too large [>5000 bp], 14151833 duplicates)
Reads: 83825850 total, 47736 skipped (flags/unmapped)
Fragments: 42014492 total (41695829 tlen-paired, 3882 hash-paired, 309 singletons, 13395 discordant, 301077 orphans, 25258 too large [>5000 bp], 14404938 duplicates)
Reads: 92670214 total, 75960 skipped (flags/unmapped)
Fragments: 46527724 total (45813937 tlen-paired, 2358 hash-paired, 370 singletons, 137231 discordant, 573828 orphans, 56502 too large [>5000 bp], 16000555 duplicates)