Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1029_79L-N1-BDNA-1_A23MHW3LT4_1/1029_79L-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1029_79L-N1-BDNA-1_A23MHW3LT4_1/1029_79L-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a5/560bd5f5930095fc6fa2b57d583750/.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/a5/560bd5f5930095fc6fa2b57d583750/.command.run
==> 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: 1029_79L-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1029_79L-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] 
The index file is older than the data file: 1029_79L-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_79L-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: 68941623 total, 51245 skipped (flags/unmapped)
Fragments: 34611486 total (34241976 tlen-paired, 3222 hash-paired, 385 singletons, 13136 discordant, 352767 orphans, 10279 too large [>5000 bp], 11413286 duplicates)
Reads: 72792840 total, 44261 skipped (flags/unmapped)
Fragments: 36544284 total (36172736 tlen-paired, 3060 hash-paired, 450 singletons, 9121 discordant, 358917 orphans, 9689 too large [>5000 bp], 11798980 duplicates)
Reads: 80644647 total, 80013 skipped (flags/unmapped)
Fragments: 40645799 total (39515063 tlen-paired, 2151 hash-paired, 457 singletons, 218431 discordant, 909697 orphans, 91595 too large [>5000 bp], 13386348 duplicates)
Reads: 79536948 total, 46767 skipped (flags/unmapped)
Fragments: 39933700 total (39501884 tlen-paired, 3763 hash-paired, 388 singletons, 13450 discordant, 414215 orphans, 18692 too large [>5000 bp], 13188925 duplicates)