Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8f/c9159722af06c9481b3010a9ef7004/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/659_dKM-N1-BDNA-1_B23KFG5LT4_1/659_dKM-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/659_dKM-N1-BDNA-1_B23KFG5LT4_1/659_dKM-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
  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/8f/c9159722af06c9481b3010a9ef7004/.command.run
==> 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: 659_dKM-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 659_dKM-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_dKM-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_dKM-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: 74654652 total, 56789 skipped (flags/unmapped)
Fragments: 37411325 total (37154117 tlen-paired, 2186 hash-paired, 408 singletons, 14837 discordant, 239777 orphans, 7699 too large [>5000 bp], 14992954 duplicates)
Reads: 81269695 total, 46927 skipped (flags/unmapped)
Fragments: 40726714 total (40467100 tlen-paired, 2308 hash-paired, 343 singletons, 10066 discordant, 246897 orphans, 8290 too large [>5000 bp], 16021885 duplicates)
Reads: 90236318 total, 89241 skipped (flags/unmapped)
Fragments: 45293024 total (44618359 tlen-paired, 3963 hash-paired, 364 singletons, 127041 discordant, 543297 orphans, 52345 too large [>5000 bp], 18339383 duplicates)
Reads: 89432988 total, 53848 skipped (flags/unmapped)
Fragments: 44819005 total (44491904 tlen-paired, 5109 hash-paired, 330 singletons, 15782 discordant, 305880 orphans, 23670 too large [>5000 bp], 18097584 duplicates)