Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_6BT-N1-BDNA-1_A23NLN3LT4_1/1136_6BT-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1a/f7af9b3a919e7cf2258e90bda99bf4/.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/1a/f7af9b3a919e7cf2258e90bda99bf4/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_6BT-N1-BDNA-1_A23NLN3LT4_1/1136_6BT-N1-BDNA-1_A23NLN3LT4_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_6BT-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_6BT-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_6BT-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_6BT-N1-BDNA-1_A23NLN3LT4_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: 72746735 total, 50411 skipped (flags/unmapped)
Fragments: 36462909 total (36197689 tlen-paired, 2416 hash-paired, 325 singletons, 13996 discordant, 248483 orphans, 9657 too large [>5000 bp], 11794747 duplicates)
Reads: 77884947 total, 42418 skipped (flags/unmapped)
Fragments: 39038643 total (38773510 tlen-paired, 2317 hash-paired, 415 singletons, 9867 discordant, 252534 orphans, 9096 too large [>5000 bp], 12457945 duplicates)
Reads: 85589230 total, 46433 skipped (flags/unmapped)
Fragments: 42902716 total (42581241 tlen-paired, 4301 hash-paired, 350 singletons, 14595 discordant, 302229 orphans, 19972 too large [>5000 bp], 14002502 duplicates)
Reads: 86021188 total, 73516 skipped (flags/unmapped)
Fragments: 43204713 total (42499268 tlen-paired, 1835 hash-paired, 341 singletons, 133318 discordant, 569951 orphans, 54269 too large [>5000 bp], 14117575 duplicates)