Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_0N-N1-BDNA-1_A23MHW3LT4_1/1136_0N-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e8/321caab4228d79fc4c05c363d4998e/.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/e8/321caab4228d79fc4c05c363d4998e/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_0N-N1-BDNA-1_A23MHW3LT4_1/1136_0N-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: 1136_0N-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0N-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0N-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0N-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: 80489730 total, 55543 skipped (flags/unmapped)
Fragments: 40443506 total (39935419 tlen-paired, 5549 hash-paired, 463 singletons, 14229 discordant, 487846 orphans, 17742 too large [>5000 bp], 13409004 duplicates)
Reads: 77112834 total, 61850 skipped (flags/unmapped)
Fragments: 38741463 total (38262849 tlen-paired, 4066 hash-paired, 511 singletons, 17140 discordant, 456897 orphans, 12733 too large [>5000 bp], 12810699 duplicates)
Reads: 81188147 total, 53061 skipped (flags/unmapped)
Fragments: 40789109 total (40306171 tlen-paired, 3434 hash-paired, 489 singletons, 11742 discordant, 467273 orphans, 12315 too large [>5000 bp], 13173225 duplicates)
Reads: 88701193 total, 85466 skipped (flags/unmapped)
Fragments: 44767512 total (43322801 tlen-paired, 2187 hash-paired, 529 singletons, 282279 discordant, 1159716 orphans, 120474 too large [>5000 bp], 14806217 duplicates)