Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/2818088a6ff9653b8b980fa3d71e27/.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/5d/2818088a6ff9653b8b980fa3d71e27/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1029_D5L-N1-BDNA-1_A23KFG7LT4_1/1029_D5L-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1029_D5L-N1-BDNA-1_A23KFG7LT4_1/1029_D5L-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam
==> 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_D5L-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_D5L-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_D5L-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_D5L-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: 63827226 total, 57209 skipped (flags/unmapped)
Fragments: 32040084 total (31698410 tlen-paired, 3908 hash-paired, 390 singletons, 6245 discordant, 331131 orphans, 10685 too large [>5000 bp], 12101077 duplicates)
Reads: 71608935 total, 50067 skipped (flags/unmapped)
Fragments: 35970901 total (35560943 tlen-paired, 3368 hash-paired, 457 singletons, 5208 discordant, 400925 orphans, 9224 too large [>5000 bp], 13323718 duplicates)
Reads: 69046434 total, 47106 skipped (flags/unmapped)
Fragments: 34679886 total (34272970 tlen-paired, 3098 hash-paired, 310 singletons, 6226 discordant, 397282 orphans, 18574 too large [>5000 bp], 13021065 duplicates)
Reads: 75864471 total, 89282 skipped (flags/unmapped)
Fragments: 38294069 total (37033010 tlen-paired, 2538 hash-paired, 472 singletons, 260080 discordant, 997969 orphans, 92746 too large [>5000 bp], 14195556 duplicates)