Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f8/a91a5b166232ae7ad699014a6e5702/.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/f8/a91a5b166232ae7ad699014a6e5702/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_2HR-N1-BDNA-1_A23MHW3LT4_1/1136_2HR-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_2HR-N1-BDNA-1_A23MHW3LT4_1/1136_2HR-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] [W::hts_idx_load3] The index file is older than the data file: 1136_2HR-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1136_2HR-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1136_2HR-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2HR-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: 72643291 total, 43069 skipped (flags/unmapped)
Fragments: 36495204 total (36072640 tlen-paired, 3201 hash-paired, 500 singletons, 9829 discordant, 409034 orphans, 9674 too large [>5000 bp], 11676106 duplicates)
Reads: 68263764 total, 48951 skipped (flags/unmapped)
Fragments: 34299193 total (33882966 tlen-paired, 2634 hash-paired, 416 singletons, 14468 discordant, 398709 orphans, 7776 too large [>5000 bp], 11194736 duplicates)
Reads: 79409408 total, 45822 skipped (flags/unmapped)
Fragments: 39899798 total (39422388 tlen-paired, 4983 hash-paired, 364 singletons, 14187 discordant, 457876 orphans, 11115 too large [>5000 bp], 13093692 duplicates)
Reads: 80676249 total, 73847 skipped (flags/unmapped)
Fragments: 40721765 total (39411510 tlen-paired, 1494 hash-paired, 441 singletons, 255297 discordant, 1053023 orphans, 106168 too large [>5000 bp], 13309315 duplicates)