Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/92a9eccf7bc12bcaf16b980da8f6db/.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/3b/92a9eccf7bc12bcaf16b980da8f6db/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_WT5-N1-BDNA-1_A23TY7KLT4_1/1241_WT5-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_WT5-N1-BDNA-1_A23TY7KLT4_1/1241_WT5-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_WT5-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_WT5-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_WT5-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_WT5-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: 77380188 total, 53186 skipped (flags/unmapped)
Fragments: 38761595 total (38535851 tlen-paired, 3699 hash-paired, 286 singletons, 11735 discordant, 210024 orphans, 7061 too large [>5000 bp], 12563712 duplicates)
Reads: 89920164 total, 50653 skipped (flags/unmapped)
Fragments: 45045767 total (44776816 tlen-paired, 5241 hash-paired, 307 singletons, 11767 discordant, 251636 orphans, 14960 too large [>5000 bp], 14720994 duplicates)
Reads: 82156871 total, 45851 skipped (flags/unmapped)
Fragments: 41152070 total (40930311 tlen-paired, 3419 hash-paired, 365 singletons, 7976 discordant, 209999 orphans, 8622 too large [>5000 bp], 13135942 duplicates)
Reads: 90482825 total, 79060 skipped (flags/unmapped)
Fragments: 45393431 total (44800861 tlen-paired, 2750 hash-paired, 328 singletons, 110333 discordant, 479159 orphans, 48195 too large [>5000 bp], 14862716 duplicates)