Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_3XT-N1-BDNA-1_A23NLN3LT4_1/1136_3XT-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6a/a27e3af47e3711b983ab8129503373/.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/6a/a27e3af47e3711b983ab8129503373/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_3XT-N1-BDNA-1_A23NLN3LT4_1/1136_3XT-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1136_3XT-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1136_3XT-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1136_3XT-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3XT-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: 98008209 total, 79132 skipped (flags/unmapped)
Fragments: 49154525 total (48721067 tlen-paired, 4787 hash-paired, 431 singletons, 19984 discordant, 408256 orphans, 14357 too large [>5000 bp], 19815056 duplicates)
Reads: 104799814 total, 63025 skipped (flags/unmapped)
Fragments: 52569236 total (52124878 tlen-paired, 3460 hash-paired, 478 singletons, 13359 discordant, 427061 orphans, 12928 too large [>5000 bp], 20861944 duplicates)
Reads: 115833198 total, 69134 skipped (flags/unmapped)
Fragments: 58105917 total (57589692 tlen-paired, 4282 hash-paired, 398 singletons, 19781 discordant, 491764 orphans, 22196 too large [>5000 bp], 23567893 duplicates)
Reads: 116313227 total, 113820 skipped (flags/unmapped)
Fragments: 58507169 total (57249641 tlen-paired, 2766 hash-paired, 474 singletons, 242387 discordant, 1011901 orphans, 98722 too large [>5000 bp], 23705602 duplicates)