Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1029_V9X-N1-BDNA-1_A23MHW3LT4_1/1029_V9X-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_V9X-N1-BDNA-1_A23MHW3LT4_1/1029_V9X-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9d/4725022cfa93899fe2dd9cd477c2c4/.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/9d/4725022cfa93899fe2dd9cd477c2c4/.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] The index file is older than the data file: 1029_V9X-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1029_V9X-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1029_V9X-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_V9X-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: 40154565 total, 57833 skipped (flags/unmapped)
Fragments: 20600336 total (19471480 tlen-paired, 3600 hash-paired, 328 singletons, 3468 discordant, 1121460 orphans, 8924 too large [>5000 bp], 9141943 duplicates)
Reads: 41906597 total, 56068 skipped (flags/unmapped)
Fragments: 21511947 total (20315928 tlen-paired, 3264 hash-paired, 491 singletons, 2828 discordant, 1189436 orphans, 8281 too large [>5000 bp], 9326712 duplicates)
Reads: 46333205 total, 54720 skipped (flags/unmapped)
Fragments: 23785404 total (22455570 tlen-paired, 4713 hash-paired, 295 singletons, 3592 discordant, 1321234 orphans, 14603 too large [>5000 bp], 10591501 duplicates)
Reads: 51115517 total, 103380 skipped (flags/unmapped)
Fragments: 26917517 total (22442661 tlen-paired, 2111 hash-paired, 463 singletons, 907922 discordant, 3564360 orphans, 370963 too large [>5000 bp], 11125159 duplicates)