Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/15/84bd05ca8ba27fcd992fe73bc5cc50/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_2UQ-N1-BDNA-1_A23KFG7LT4_1/1136_2UQ-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam
  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/15/84bd05ca8ba27fcd992fe73bc5cc50/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_2UQ-N1-BDNA-1_A23KFG7LT4_1/1136_2UQ-N1-BDNA-1_A23KFG7LT4_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_2UQ-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2UQ-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2UQ-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2UQ-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: 83931570 total, 57134 skipped (flags/unmapped)
Fragments: 42152646 total (41681697 tlen-paired, 2775 hash-paired, 468 singletons, 14926 discordant, 452780 orphans, 11196 too large [>5000 bp], 15228027 duplicates)
Reads: 89240042 total, 49272 skipped (flags/unmapped)
Fragments: 44818691 total (44336892 tlen-paired, 2618 hash-paired, 454 singletons, 10507 discordant, 468220 orphans, 11031 too large [>5000 bp], 15811404 duplicates)
Reads: 97539042 total, 52831 skipped (flags/unmapped)
Fragments: 48989516 total (48420138 tlen-paired, 4010 hash-paired, 402 singletons, 15673 discordant, 549293 orphans, 28437 too large [>5000 bp], 17743341 duplicates)
Reads: 99225576 total, 85376 skipped (flags/unmapped)
Fragments: 50056390 total (48542882 tlen-paired, 2808 hash-paired, 505 singletons, 296476 discordant, 1213719 orphans, 120822 too large [>5000 bp], 18095704 duplicates)