Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/06/dc31c7afe8ba5e60aa75b4e9b3ee91/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1047_ES-N1-BDNA-1_B23KFG5LT4_1/1047_ES-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam
  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/06/dc31c7afe8ba5e60aa75b4e9b3ee91/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1047_ES-N1-BDNA-1_B23KFG5LT4_1/1047_ES-N1-BDNA-1_B23KFG5LT4_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_ES-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_ES-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1047_ES-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
The index file is older than the data file: 1047_ES-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: 71155314 total, 57397 skipped (flags/unmapped)
Fragments: 35664719 total (35393107 tlen-paired, 3432 hash-paired, 340 singletons, 12511 discordant, 255329 orphans, 12074 too large [>5000 bp], 14391363 duplicates)
Reads: 75463797 total, 50308 skipped (flags/unmapped)
Fragments: 37829910 total (37550036 tlen-paired, 3154 hash-paired, 398 singletons, 8813 discordant, 267509 orphans, 10788 too large [>5000 bp], 14913273 duplicates)
Reads: 83307718 total, 53951 skipped (flags/unmapped)
Fragments: 41767900 total (41433953 tlen-paired, 3701 hash-paired, 360 singletons, 12807 discordant, 317079 orphans, 17703 too large [>5000 bp], 16883278 duplicates)
Reads: 83538749 total, 82353 skipped (flags/unmapped)
Fragments: 41981890 total (41202235 tlen-paired, 3138 hash-paired, 339 singletons, 149343 discordant, 626835 orphans, 59895 too large [>5000 bp], 16965039 duplicates)