Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/29/fe561ce018eec6ec02ded9fb3f87a0/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_2SK-N1-BDNA-1_A23KFG7LT4_1/1136_2SK-N1-BDNA-1_A23KFG7LT4_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/29/fe561ce018eec6ec02ded9fb3f87a0/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_2SK-N1-BDNA-1_A23KFG7LT4_1/1136_2SK-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_2SK-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2SK-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2SK-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_2SK-N1-BDNA-1_A23KFG7LT4_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: 81524289 total, 60494 skipped (flags/unmapped)
Fragments: 40972841 total (40449765 tlen-paired, 3306 hash-paired, 525 singletons, 13527 discordant, 505718 orphans, 12178 too large [>5000 bp], 15685583 duplicates)
Reads: 86875981 total, 52130 skipped (flags/unmapped)
Fragments: 43670303 total (43117788 tlen-paired, 2785 hash-paired, 615 singletons, 9619 discordant, 539496 orphans, 11678 too large [>5000 bp], 16266166 duplicates)
Reads: 95120018 total, 52727 skipped (flags/unmapped)
Fragments: 47818970 total (47187633 tlen-paired, 2624 hash-paired, 416 singletons, 13942 discordant, 614355 orphans, 22061 too large [>5000 bp], 18281276 duplicates)
Reads: 97055141 total, 88027 skipped (flags/unmapped)
Fragments: 49058029 total (47269771 tlen-paired, 2622 hash-paired, 492 singletons, 353478 discordant, 1431666 orphans, 141607 too large [>5000 bp], 18691996 duplicates)