Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1029_CE3-N1-BDNA-1_A23KFG7LT4_1/1029_CE3-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/505e568d8ebbbc12ef1629d4a5741e/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1029_CE3-N1-BDNA-1_A23KFG7LT4_1/1029_CE3-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
  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/cd/505e568d8ebbbc12ef1629d4a5741e/.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: 1029_CE3-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_CE3-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_CE3-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_CE3-N1-BDNA-1_A23KFG7LT4_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: 59028064 total, 43572 skipped (flags/unmapped)
Fragments: 29644280 total (29311261 tlen-paired, 2236 hash-paired, 343 singletons, 11599 discordant, 318841 orphans, 7558 too large [>5000 bp], 10104695 duplicates)
Reads: 63566972 total, 35637 skipped (flags/unmapped)
Fragments: 31923447 total (31583794 tlen-paired, 1973 hash-paired, 328 singletons, 8145 discordant, 329207 orphans, 6988 too large [>5000 bp], 10578691 duplicates)
Reads: 69068393 total, 39779 skipped (flags/unmapped)
Fragments: 34688924 total (34287484 tlen-paired, 2488 hash-paired, 280 singletons, 12218 discordant, 386454 orphans, 18750 too large [>5000 bp], 11849962 duplicates)
Reads: 70038091 total, 65643 skipped (flags/unmapped)
Fragments: 35320159 total (34277042 tlen-paired, 2447 hash-paired, 349 singletons, 203742 discordant, 836579 orphans, 84529 too large [>5000 bp], 12039057 duplicates)