Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5c/6d506d4ef577eb9d0e14c6ee3f27df/.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/5c/6d506d4ef577eb9d0e14c6ee3f27df/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_3LK-N1-BDNA-1_A23KFG7LT4_1/1136_3LK-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_3LK-N1-BDNA-1_A23KFG7LT4_1/1136_3LK-N1-BDNA-1_A23KFG7LT4_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: 1136_3LK-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3LK-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3LK-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3LK-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: 93908168 total, 60503 skipped (flags/unmapped)
Fragments: 47073067 total (46726935 tlen-paired, 3192 hash-paired, 500 singletons, 19005 discordant, 323435 orphans, 12733 too large [>5000 bp], 17500052 duplicates)
Reads: 99803593 total, 55839 skipped (flags/unmapped)
Fragments: 50029675 total (49664650 tlen-paired, 3484 hash-paired, 388 singletons, 15933 discordant, 345220 orphans, 17006 too large [>5000 bp], 18640639 duplicates)
Reads: 110251089 total, 94136 skipped (flags/unmapped)
Fragments: 55368221 total (54464180 tlen-paired, 4511 hash-paired, 464 singletons, 174513 discordant, 724553 orphans, 72764 too large [>5000 bp], 20662741 duplicates)
Reads: 100820188 total, 51551 skipped (flags/unmapped)
Fragments: 50538717 total (50190281 tlen-paired, 3495 hash-paired, 526 singletons, 13386 discordant, 331029 orphans, 11379 too large [>5000 bp], 18257530 duplicates)