Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1c/9f27a071b02f299bd5c005741f2cd5/.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/1c/9f27a071b02f299bd5c005741f2cd5/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1136_41F-N1-BDNA-1_B23KFG5LT4_1/1136_41F-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1136_41F-N1-BDNA-1_B23KFG5LT4_1/1136_41F-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam
==> 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_41F-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1136_41F-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1136_41F-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai[W::hts_idx_load3] The index file is older than the data file: 1136_41F-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: 70773288 total, 54671 skipped (flags/unmapped)
Fragments: 35492335 total (35188042 tlen-paired, 2716 hash-paired, 385 singletons, 15910 discordant, 285282 orphans, 9807 too large [>5000 bp], 14380015 duplicates)
Reads: 76806166 total, 44674 skipped (flags/unmapped)
Fragments: 38520851 total (38209833 tlen-paired, 2032 hash-paired, 347 singletons, 10856 discordant, 297783 orphans, 8960 too large [>5000 bp], 15313580 duplicates)
Reads: 84944053 total, 50469 skipped (flags/unmapped)
Fragments: 42601581 total (42226640 tlen-paired, 2682 hash-paired, 343 singletons, 16969 discordant, 354947 orphans, 22856 too large [>5000 bp], 17386323 duplicates)
Reads: 85845753 total, 77487 skipped (flags/unmapped)
Fragments: 43156518 total (42320332 tlen-paired, 2629 hash-paired, 342 singletons, 160117 discordant, 673098 orphans, 64335 too large [>5000 bp], 17634390 duplicates)