Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1136_2M6-N1-BDNA-1_B23KFG5LT4_1/1136_2M6-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2a/d60a68e0417e3cb13ff5c4ec25a1f6/.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/2a/d60a68e0417e3cb13ff5c4ec25a1f6/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1136_2M6-N1-BDNA-1_B23KFG5LT4_1/1136_2M6-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: 1136_2M6-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2M6-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2M6-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2M6-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: 69710690 total, 53882 skipped (flags/unmapped)
Fragments: 34939514 total (34677788 tlen-paired, 2467 hash-paired, 340 singletons, 14791 discordant, 244128 orphans, 11124 too large [>5000 bp], 13422545 duplicates)
Reads: 74561817 total, 46704 skipped (flags/unmapped)
Fragments: 37374770 total (37105596 tlen-paired, 3210 hash-paired, 404 singletons, 10033 discordant, 255527 orphans, 10752 too large [>5000 bp], 14003074 duplicates)
Reads: 83013708 total, 75393 skipped (flags/unmapped)
Fragments: 41698985 total (40998489 tlen-paired, 2895 hash-paired, 372 singletons, 132112 discordant, 565117 orphans, 52917 too large [>5000 bp], 16131073 duplicates)
Reads: 82421601 total, 50792 skipped (flags/unmapped)
Fragments: 41317747 total (40997859 tlen-paired, 3781 hash-paired, 319 singletons, 15222 discordant, 300566 orphans, 18100 too large [>5000 bp], 15956307 duplicates)