Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/61/e01ad3636b954b5a92794d42688bbf/.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/61/e01ad3636b954b5a92794d42688bbf/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_0QB-N1-BDNA-1_A23MHW3LT4_1/1136_0QB-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/1136_0QB-N1-BDNA-1_A23MHW3LT4_1/1136_0QB-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_0QB-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0QB-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0QB-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0QB-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: 48791844 total, 55025 skipped (flags/unmapped)
Fragments: 25008712 total (23701949 tlen-paired, 2537 hash-paired, 388 singletons, 6133 discordant, 1297705 orphans, 8744 too large [>5000 bp], 10511939 duplicates)
Reads: 55048029 total, 58757 skipped (flags/unmapped)
Fragments: 28189894 total (26751766 tlen-paired, 3037 hash-paired, 282 singletons, 9509 discordant, 1425300 orphans, 17533 too large [>5000 bp], 12149366 duplicates)
Reads: 48161966 total, 59620 skipped (flags/unmapped)
Fragments: 24646996 total (23425984 tlen-paired, 2614 hash-paired, 277 singletons, 8842 discordant, 1209279 orphans, 8955 too large [>5000 bp], 10491481 duplicates)
Reads: 59914657 total, 109744 skipped (flags/unmapped)
Fragments: 31409761 total (26666737 tlen-paired, 3123 hash-paired, 434 singletons, 951352 discordant, 3788115 orphans, 386970 too large [>5000 bp], 12811400 duplicates)