Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_16Z-N1-BDNA-1_A23KFG7LT4_1/1136_16Z-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5e/7bd782de08f2e72b3468757c547a31/.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/5e/7bd782de08f2e72b3468757c547a31/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_16Z-N1-BDNA-1_A23KFG7LT4_1/1136_16Z-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam
==> 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_16Z-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_16Z-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_16Z-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_16Z-N1-BDNA-1_A23KFG7LT4_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: 70743819 total, 46768 skipped (flags/unmapped)
Fragments: 35461601 total (35203415 tlen-paired, 2970 hash-paired, 342 singletons, 11727 discordant, 243147 orphans, 8669 too large [>5000 bp], 12708106 duplicates)
Reads: 74470206 total, 40370 skipped (flags/unmapped)
Fragments: 37333652 total (37071736 tlen-paired, 2160 hash-paired, 334 singletons, 7930 discordant, 251492 orphans, 7179 too large [>5000 bp], 13065740 duplicates)
Reads: 82956527 total, 70482 skipped (flags/unmapped)
Fragments: 41684801 total (40940086 tlen-paired, 1652 hash-paired, 398 singletons, 143574 discordant, 599091 orphans, 57966 too large [>5000 bp], 14964313 duplicates)
Reads: 82254134 total, 44682 skipped (flags/unmapped)
Fragments: 41236933 total (40924495 tlen-paired, 3539 hash-paired, 332 singletons, 12403 discordant, 296164 orphans, 16041 too large [>5000 bp], 14794040 duplicates)