Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_211-N1-BDNA-1_A23MHW3LT4_1/1136_211-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/31/aa965ff9c0fb919f0077b268912eab/.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/31/aa965ff9c0fb919f0077b268912eab/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_211-N1-BDNA-1_A23MHW3LT4_1/1136_211-N1-BDNA-1_A23MHW3LT4_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_211-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1136_211-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] 
The index file is older than the data file: 1136_211-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_211-N1-BDNA-1_A23MHW3LT4_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: 105655017 total, 79205 skipped (flags/unmapped)
Fragments: 53047706 total (52469261 tlen-paired, 4143 hash-paired, 678 singletons, 24280 discordant, 549344 orphans, 15211 too large [>5000 bp], 20080808 duplicates)
Reads: 112217508 total, 67551 skipped (flags/unmapped)
Fragments: 56338980 total (55761065 tlen-paired, 4101 hash-paired, 672 singletons, 16533 discordant, 556609 orphans, 14639 too large [>5000 bp], 20988094 duplicates)
Reads: 122839190 total, 70167 skipped (flags/unmapped)
Fragments: 61677713 total (61014495 tlen-paired, 3849 hash-paired, 545 singletons, 24482 discordant, 634342 orphans, 24242 too large [>5000 bp], 23586818 duplicates)
Reads: 124881614 total, 119073 skipped (flags/unmapped)
Fragments: 62935287 total (61218482 tlen-paired, 3602 hash-paired, 624 singletons, 330790 discordant, 1381789 orphans, 137190 too large [>5000 bp], 23981629 duplicates)