Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1029_4WW-N1-BDNA-1_A23MHW3LT4_1/1029_4WW-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4d/efc3f3489c5998140b1e533842a353/.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/4d/efc3f3489c5998140b1e533842a353/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1029_4WW-N1-BDNA-1_A23MHW3LT4_1/1029_4WW-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_4WW-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_4WW-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_4WW-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_4WW-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: 83336634 total, 61960 skipped (flags/unmapped)
Fragments: 41882381 total (41350949 tlen-paired, 3436 hash-paired, 589 singletons, 13972 discordant, 513435 orphans, 11968 too large [>5000 bp], 14940818 duplicates)
Reads: 88577777 total, 57276 skipped (flags/unmapped)
Fragments: 44512534 total (43966551 tlen-paired, 4131 hash-paired, 548 singletons, 10045 discordant, 531259 orphans, 13620 too large [>5000 bp], 15454188 duplicates)
Reads: 96572245 total, 59042 skipped (flags/unmapped)
Fragments: 48535786 total (47911941 tlen-paired, 4235 hash-paired, 498 singletons, 15125 discordant, 603987 orphans, 23058 too large [>5000 bp], 17334702 duplicates)
Reads: 98297360 total, 102343 skipped (flags/unmapped)
Fragments: 49659816 total (47898581 tlen-paired, 3914 hash-paired, 645 singletons, 345934 discordant, 1410742 orphans, 143386 too large [>5000 bp], 17617451 duplicates)