Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_1MH-N1-BDNA-1_A23MHW3LT4_1/1136_1MH-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/eb/e33550e316c338eaa595f23e5a5bda/.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/eb/e33550e316c338eaa595f23e5a5bda/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_1MH-N1-BDNA-1_A23MHW3LT4_1/1136_1MH-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: 1136_1MH-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_1MH-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_1MH-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_1MH-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: 71838964 total, 54466 skipped (flags/unmapped)
Fragments: 36125275 total (35621936 tlen-paired, 3782 hash-paired, 446 singletons, 14729 discordant, 484382 orphans, 9388 too large [>5000 bp], 12461629 duplicates)
Reads: 76238315 total, 49921 skipped (flags/unmapped)
Fragments: 38336430 total (37777998 tlen-paired, 3744 hash-paired, 354 singletons, 13258 discordant, 541076 orphans, 28482 too large [>5000 bp], 13244810 duplicates)
Reads: 77380499 total, 48039 skipped (flags/unmapped)
Fragments: 38909379 total (38388586 tlen-paired, 2485 hash-paired, 453 singletons, 10416 discordant, 507439 orphans, 10797 too large [>5000 bp], 13085402 duplicates)
Reads: 84860579 total, 87057 skipped (flags/unmapped)
Fragments: 42900170 total (41279486 tlen-paired, 2502 hash-paired, 405 singletons, 323960 discordant, 1293817 orphans, 133702 too large [>5000 bp], 14729502 duplicates)