Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1029_ILZ-N1-BDNA-1_A23MHW3LT4_1/1029_ILZ-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1029_ILZ-N1-BDNA-1_A23MHW3LT4_1/1029_ILZ-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/03/2eb20ad6a064599c25847464fe98a4/.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/03/2eb20ad6a064599c25847464fe98a4/.command.run
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_ILZ-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1029_ILZ-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai

The index file is older than the data file: 1029_ILZ-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_ILZ-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: 79284328 total, 56478 skipped (flags/unmapped)
Fragments: 39832656 total (39347261 tlen-paired, 3158 hash-paired, 441 singletons, 20237 discordant, 461559 orphans, 12269 too large [>5000 bp], 12693831 duplicates)
Reads: 84385158 total, 48634 skipped (flags/unmapped)
Fragments: 42390992 total (41907498 tlen-paired, 2629 hash-paired, 526 singletons, 13991 discordant, 466348 orphans, 10707 too large [>5000 bp], 13222729 duplicates)
Reads: 91359700 total, 53756 skipped (flags/unmapped)
Fragments: 45899411 total (45338318 tlen-paired, 3229 hash-paired, 395 singletons, 20732 discordant, 536737 orphans, 22127 too large [>5000 bp], 14691583 duplicates)
Reads: 93160079 total, 85480 skipped (flags/unmapped)
Fragments: 46996614 total (45576140 tlen-paired, 1974 hash-paired, 483 singletons, 272793 discordant, 1145224 orphans, 113539 too large [>5000 bp], 15004694 duplicates)