Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/10/482032ab4e8e8495401041b307d9c0/.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/10/482032ab4e8e8495401041b307d9c0/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1029_BGNP-N1-BDNA-1_A23MHW3LT4_1/1029_BGNP-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1029_BGNP-N1-BDNA-1_A23MHW3LT4_1/1029_BGNP-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam
==> 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: 1029_BGNP-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1029_BGNP-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BGNP-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BGNP-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: 91089377 total, 75377 skipped (flags/unmapped)
Fragments: 45813642 total (45145415 tlen-paired, 4517 hash-paired, 594 singletons, 20418 discordant, 642698 orphans, 15004 too large [>5000 bp], 17053910 duplicates)
Reads: 95790153 total, 64682 skipped (flags/unmapped)
Fragments: 48179660 total (47500247 tlen-paired, 4206 hash-paired, 617 singletons, 13318 discordant, 661272 orphans, 14020 too large [>5000 bp], 17536886 duplicates)
Reads: 105302725 total, 69111 skipped (flags/unmapped)
Fragments: 52972018 total (52178617 tlen-paired, 5969 hash-paired, 484 singletons, 20828 discordant, 766120 orphans, 28091 too large [>5000 bp], 19757941 duplicates)
Reads: 106618470 total, 112423 skipped (flags/unmapped)
Fragments: 53947490 total (51779260 tlen-paired, 3694 hash-paired, 565 singletons, 421767 discordant, 1742204 orphans, 176918 too large [>5000 bp], 20022982 duplicates)