Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/aa/8741ca5ffdf9e31a213db63674e152/.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/aa/8741ca5ffdf9e31a213db63674e152/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_KBQ-N1-BDNA-1_B23L5TMLT4_1/1029_KBQ-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_KBQ-N1-BDNA-1_B23L5TMLT4_1/1029_KBQ-N1-BDNA-1_B23L5TMLT4_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_KBQ-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_KBQ-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_KBQ-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_KBQ-N1-BDNA-1_B23L5TMLT4_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: 71119001 total, 48797 skipped (flags/unmapped)
Fragments: 35681279 total (35357658 tlen-paired, 2697 hash-paired, 492 singletons, 9422 discordant, 311010 orphans, 9574 too large [>5000 bp], 12519258 duplicates)
Reads: 72079048 total, 60291 skipped (flags/unmapped)
Fragments: 36160801 total (35819514 tlen-paired, 3851 hash-paired, 438 singletons, 14457 discordant, 322541 orphans, 10067 too large [>5000 bp], 12848084 duplicates)
Reads: 80337343 total, 95030 skipped (flags/unmapped)
Fragments: 40428440 total (39464927 tlen-paired, 4142 hash-paired, 417 singletons, 170596 discordant, 788358 orphans, 87104 too large [>5000 bp], 14300659 duplicates)
Reads: 85093766 total, 56933 skipped (flags/unmapped)
Fragments: 42693359 total (42284513 tlen-paired, 5944 hash-paired, 489 singletons, 15297 discordant, 387116 orphans, 18860 too large [>5000 bp], 15177754 duplicates)