Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/78/a4c8fc7cbec149b50dc5fe121ac3b9/.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/78/a4c8fc7cbec149b50dc5fe121ac3b9/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_Y2P-N1-BDNA-1_A23TY7KLT4_1/1241_Y2P-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_Y2P-N1-BDNA-1_A23TY7KLT4_1/1241_Y2P-N1-BDNA-1_A23TY7KLT4_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: 1241_Y2P-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_Y2P-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_Y2P-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_Y2P-N1-BDNA-1_A23TY7KLT4_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: 67707623 total, 50224 skipped (flags/unmapped)
Fragments: 33921831 total (33705427 tlen-paired, 3288 hash-paired, 279 singletons, 10137 discordant, 202700 orphans, 8358 too large [>5000 bp], 11983114 duplicates)
Reads: 72005898 total, 43742 skipped (flags/unmapped)
Fragments: 36081803 total (35840239 tlen-paired, 3229 hash-paired, 250 singletons, 8747 discordant, 229338 orphans, 14069 too large [>5000 bp], 12794030 duplicates)
Reads: 72940058 total, 39879 skipped (flags/unmapped)
Fragments: 36548843 total (36327186 tlen-paired, 2555 hash-paired, 299 singletons, 7175 discordant, 211628 orphans, 7210 too large [>5000 bp], 12604823 duplicates)
Reads: 79617779 total, 76517 skipped (flags/unmapped)
Fragments: 39963147 total (39356524 tlen-paired, 2754 hash-paired, 287 singletons, 119127 discordant, 484455 orphans, 49855 too large [>5000 bp], 14158524 duplicates)