Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_0Q6-N1-BDNA-1_A23MHW3LT4_1/1136_0Q6-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7b/9c6a09680fc2fbef25992e0b36ee9d/.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/7b/9c6a09680fc2fbef25992e0b36ee9d/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_0Q6-N1-BDNA-1_A23MHW3LT4_1/1136_0Q6-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] The index file is older than the data file: 1136_0Q6-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0Q6-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0Q6-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0Q6-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: 92452085 total, 60366 skipped (flags/unmapped)
Fragments: 46482932 total (45863007 tlen-paired, 3929 hash-paired, 501 singletons, 12737 discordant, 602758 orphans, 14557 too large [>5000 bp], 16499552 duplicates)
Reads: 88103379 total, 66461 skipped (flags/unmapped)
Fragments: 44302112 total (43690448 tlen-paired, 3641 hash-paired, 542 singletons, 17953 discordant, 589528 orphans, 11382 too large [>5000 bp], 16029271 duplicates)
Reads: 102836373 total, 102808 skipped (flags/unmapped)
Fragments: 52000486 total (50019956 tlen-paired, 4013 hash-paired, 542 singletons, 386690 discordant, 1589285 orphans, 161210 too large [>5000 bp], 18737991 duplicates)
Reads: 101002462 total, 62275 skipped (flags/unmapped)
Fragments: 50790457 total (50085087 tlen-paired, 3376 hash-paired, 566 singletons, 17843 discordant, 683585 orphans, 21712 too large [>5000 bp], 18400332 duplicates)