Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_229-N1-BDNA-1_A23MHW3LT4_1/1136_229-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ab/8f79f8bee04f7b5df774702abe9ea2/.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/ab/8f79f8bee04f7b5df774702abe9ea2/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_229-N1-BDNA-1_A23MHW3LT4_1/1136_229-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_229-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_229-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_229-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_229-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: 78655791 total, 46239 skipped (flags/unmapped)
Fragments: 39527881 total (39050310 tlen-paired, 2544 hash-paired, 428 singletons, 9501 discordant, 465098 orphans, 9658 too large [>5000 bp], 13589572 duplicates)
Reads: 73474466 total, 51818 skipped (flags/unmapped)
Fragments: 36926713 total (36462667 tlen-paired, 2681 hash-paired, 375 singletons, 13713 discordant, 447277 orphans, 8437 too large [>5000 bp], 12973425 duplicates)
Reads: 85658325 total, 50417 skipped (flags/unmapped)
Fragments: 43053462 total (42501947 tlen-paired, 4794 hash-paired, 315 singletons, 13911 discordant, 532495 orphans, 16897 too large [>5000 bp], 15176420 duplicates)
Reads: 87209072 total, 86607 skipped (flags/unmapped)
Fragments: 44046654 total (42524356 tlen-paired, 1858 hash-paired, 406 singletons, 298781 discordant, 1221253 orphans, 125408 too large [>5000 bp], 15442149 duplicates)