Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/659_c95-N1-BDNA-1_B23KFG5LT4_1/659_c95-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bd/07ffd39c7a8a0c5106b8d706eb0cf7/.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/bd/07ffd39c7a8a0c5106b8d706eb0cf7/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/659_c95-N1-BDNA-1_B23KFG5LT4_1/659_c95-N1-BDNA-1_B23KFG5LT4_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: 659_c95-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_c95-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_c95-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_c95-N1-BDNA-1_B23KFG5LT4_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: 72975491 total, 60014 skipped (flags/unmapped)
Fragments: 36612825 total (36260831 tlen-paired, 2566 hash-paired, 322 singletons, 17853 discordant, 331253 orphans, 10701 too large [>5000 bp], 15361851 duplicates)
Reads: 78339727 total, 48728 skipped (flags/unmapped)
Fragments: 39307572 total (38947345 tlen-paired, 2163 hash-paired, 425 singletons, 11965 discordant, 345674 orphans, 10977 too large [>5000 bp], 16180293 duplicates)
Reads: 88471405 total, 86077 skipped (flags/unmapped)
Fragments: 44516095 total (43518420 tlen-paired, 3673 hash-paired, 385 singletons, 192424 discordant, 801193 orphans, 77358 too large [>5000 bp], 18805074 duplicates)
Reads: 87516190 total, 55410 skipped (flags/unmapped)
Fragments: 43913485 total (43481162 tlen-paired, 2940 hash-paired, 405 singletons, 18653 discordant, 410325 orphans, 22270 too large [>5000 bp], 18527738 duplicates)