Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/a96f89010f0c53941017825a49bd2c/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1029_8TK-N1-BDNA-1_A23MHW3LT4_1/1029_8TK-N1-BDNA-1_A23MHW3LT4_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/79/a96f89010f0c53941017825a49bd2c/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1029_8TK-N1-BDNA-1_A23MHW3LT4_1/1029_8TK-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
==> 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_8TK-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai[W::hts_idx_load3] The index file is older than the data file: 1029_8TK-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1029_8TK-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_8TK-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: 107144698 total, 85632 skipped (flags/unmapped)
Fragments: 53840632 total (53162888 tlen-paired, 5335 hash-paired, 656 singletons, 21711 discordant, 650042 orphans, 14250 too large [>5000 bp], 19388352 duplicates)
Reads: 112988947 total, 72684 skipped (flags/unmapped)
Fragments: 56776873 total (56086986 tlen-paired, 4272 hash-paired, 723 singletons, 15118 discordant, 669774 orphans, 16507 too large [>5000 bp], 20110227 duplicates)
Reads: 124567584 total, 75510 skipped (flags/unmapped)
Fragments: 62597992 total (61844657 tlen-paired, 7338 hash-paired, 607 singletons, 20471 discordant, 724919 orphans, 10808 too large [>5000 bp], 22691676 duplicates)
Reads: 126289947 total, 122280 skipped (flags/unmapped)
Fragments: 63778499 total (61614812 tlen-paired, 2211 hash-paired, 615 singletons, 422711 discordant, 1738150 orphans, 174717 too large [>5000 bp], 23002940 duplicates)