Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/12/b311165d33f0f7a606119e50e3812e/.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/12/b311165d33f0f7a606119e50e3812e/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1047_KF-N1-BDNA-1_B23MHTGLT4_1/1047_KF-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1047_KF-N1-BDNA-1_B23MHTGLT4_1/1047_KF-N1-BDNA-1_B23MHTGLT4_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: 1047_KF-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1047_KF-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.baiThe index file is older than the data file: 1047_KF-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.baiThe index file is older than the data file: 1047_KF-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: 98194955 total, 75623 skipped (flags/unmapped)
Fragments: 49349258 total (48716730 tlen-paired, 3948 hash-paired, 622 singletons, 17322 discordant, 610636 orphans, 16037 too large [>5000 bp], 17551379 duplicates)
Reads: 104582830 total, 64585 skipped (flags/unmapped)
Fragments: 52565852 total (51909369 tlen-paired, 3921 hash-paired, 617 singletons, 11985 discordant, 639960 orphans, 13559 too large [>5000 bp], 18374274 duplicates)
Reads: 113604840 total, 67280 skipped (flags/unmapped)
Fragments: 57107213 total (56355867 tlen-paired, 4077 hash-paired, 579 singletons, 17343 discordant, 729347 orphans, 26530 too large [>5000 bp], 20472729 duplicates)
Reads: 115876416 total, 113506 skipped (flags/unmapped)
Fragments: 58559393 total (56443330 tlen-paired, 3856 hash-paired, 648 singletons, 415429 discordant, 1696130 orphans, 170451 too large [>5000 bp], 20901013 duplicates)