Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_064-N1-BDNA-1_A23MHW3LT4_1/1136_064-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/69/030c81ccaf035ebd4ad5acd9d6c7aa/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_064-N1-BDNA-1_A23MHW3LT4_1/1136_064-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/69/030c81ccaf035ebd4ad5acd9d6c7aa/.command.run
==> 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_064-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_064-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1136_064-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1136_064-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: 87254796 total, 71897 skipped (flags/unmapped)
Fragments: 43845481 total (43289707 tlen-paired, 3880 hash-paired, 453 singletons, 16443 discordant, 534998 orphans, 13694 too large [>5000 bp], 16616090 duplicates)
Reads: 92843571 total, 57612 skipped (flags/unmapped)
Fragments: 46656244 total (46091531 tlen-paired, 3322 hash-paired, 506 singletons, 11230 discordant, 549655 orphans, 11816 too large [>5000 bp], 17375333 duplicates)
Reads: 100979811 total, 66767 skipped (flags/unmapped)
Fragments: 50744272 total (50080153 tlen-paired, 3850 hash-paired, 590 singletons, 17009 discordant, 642670 orphans, 33880 too large [>5000 bp], 19302850 duplicates)
Reads: 102652986 total, 109747 skipped (flags/unmapped)
Fragments: 51845115 total (50039974 tlen-paired, 4268 hash-paired, 531 singletons, 353442 discordant, 1446900 orphans, 150220 too large [>5000 bp], 19598377 duplicates)