Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/72/f3889ad70630fb427036bbc5bd94d3/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_BF1H-N1-BDNA-1_A23TY7KLT4_1/1241_BF1H-N1-BDNA-1_A23TY7KLT4_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/72/f3889ad70630fb427036bbc5bd94d3/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_BF1H-N1-BDNA-1_A23TY7KLT4_1/1241_BF1H-N1-BDNA-1_A23TY7KLT4_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: 1241_BF1H-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BF1H-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BF1H-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1241_BF1H-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: 68500245 total, 39061 skipped (flags/unmapped)
Fragments: 34320611 total (34086478 tlen-paired, 3593 hash-paired, 246 singletons, 8456 discordant, 221838 orphans, 21023 too large [>5000 bp], 11098600 duplicates)
Reads: 64234558 total, 47422 skipped (flags/unmapped)
Fragments: 32178931 total (31981750 tlen-paired, 3359 hash-paired, 230 singletons, 9444 discordant, 184148 orphans, 6826 too large [>5000 bp], 10360638 duplicates)
Reads: 69148830 total, 36494 skipped (flags/unmapped)
Fragments: 34645253 total (34444909 tlen-paired, 1963 hash-paired, 355 singletons, 6655 discordant, 191371 orphans, 6778 too large [>5000 bp], 10968100 duplicates)
Reads: 75280298 total, 65660 skipped (flags/unmapped)
Fragments: 37780427 total (37236272 tlen-paired, 3178 hash-paired, 249 singletons, 105175 discordant, 435553 orphans, 44793 too large [>5000 bp], 12244340 duplicates)