Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9c/89b7b148c4b318fe08c6d709cc59ac/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1029_BMEZ-N1-BDNA-1_A23MHW3LT4_1/1029_BMEZ-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam
  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/9c/89b7b148c4b318fe08c6d709cc59ac/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1029_BMEZ-N1-BDNA-1_A23MHW3LT4_1/1029_BMEZ-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
==> 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: 1029_BMEZ-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BMEZ-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BMEZ-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BMEZ-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: 58076939 total, 59436 skipped (flags/unmapped)
Fragments: 29193860 total (28785160 tlen-paired, 3931 hash-paired, 397 singletons, 7440 discordant, 396932 orphans, 13556 too large [>5000 bp], 10936753 duplicates)
Reads: 62794626 total, 51760 skipped (flags/unmapped)
Fragments: 31597774 total (31115192 tlen-paired, 2872 hash-paired, 407 singletons, 5848 discordant, 473455 orphans, 10590 too large [>5000 bp], 11609135 duplicates)
Reads: 67916584 total, 53738 skipped (flags/unmapped)
Fragments: 34163486 total (33651186 tlen-paired, 3474 hash-paired, 383 singletons, 8642 discordant, 499801 orphans, 18029 too large [>5000 bp], 12727944 duplicates)
Reads: 68489457 total, 101187 skipped (flags/unmapped)
Fragments: 34695365 total (33166937 tlen-paired, 2749 hash-paired, 426 singletons, 304519 discordant, 1220734 orphans, 109350 too large [>5000 bp], 12707262 duplicates)