Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_209-N1-BDNA-1_A23MHW3LT4_1/1136_209-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_209-N1-BDNA-1_A23MHW3LT4_1/1136_209-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f4/d5e88ce66e661cf00e4d4ecb653553/.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/f4/d5e88ce66e661cf00e4d4ecb653553/.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_209-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_209-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_209-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_209-N1-BDNA-1_A23MHW3LT4_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: 64981881 total, 47352 skipped (flags/unmapped)
Fragments: 32644527 total (32251012 tlen-paired, 2745 hash-paired, 419 singletons, 13963 discordant, 376388 orphans, 11141 too large [>5000 bp], 10877416 duplicates)
Reads: 69314119 total, 38111 skipped (flags/unmapped)
Fragments: 34823210 total (34424951 tlen-paired, 2218 hash-paired, 546 singletons, 9583 discordant, 385912 orphans, 8023 too large [>5000 bp], 11319431 duplicates)
Reads: 75542814 total, 48028 skipped (flags/unmapped)
Fragments: 37952507 total (37496383 tlen-paired, 4419 hash-paired, 440 singletons, 14333 discordant, 436932 orphans, 13572 too large [>5000 bp], 12692264 duplicates)
Reads: 76242790 total, 71738 skipped (flags/unmapped)
Fragments: 38480821 total (37256555 tlen-paired, 1891 hash-paired, 400 singletons, 236425 discordant, 985550 orphans, 97680 too large [>5000 bp], 12837506 duplicates)