Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1029_PLR-N1-BDNA-1_A23KFG7LT4_1/1029_PLR-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/94/41834799a6528dd241f78fef3fbe02/.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/94/41834799a6528dd241f78fef3fbe02/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1029_PLR-N1-BDNA-1_A23KFG7LT4_1/1029_PLR-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
==> 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: 1029_PLR-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_PLR-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_PLR-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_PLR-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: 83925742 total, 60373 skipped (flags/unmapped)
Fragments: 42042639 total (41786653 tlen-paired, 3153 hash-paired, 438 singletons, 11504 discordant, 240891 orphans, 10710 too large [>5000 bp], 15628154 duplicates)
Reads: 89286351 total, 49797 skipped (flags/unmapped)
Fragments: 44736891 total (44471845 tlen-paired, 2426 hash-paired, 578 singletons, 7878 discordant, 254164 orphans, 8757 too large [>5000 bp], 16176029 duplicates)
Reads: 97784822 total, 57102 skipped (flags/unmapped)
Fragments: 48991693 total (48676446 tlen-paired, 3882 hash-paired, 376 singletons, 11555 discordant, 299434 orphans, 22072 too large [>5000 bp], 18297389 duplicates)
Reads: 98260421 total, 88865 skipped (flags/unmapped)
Fragments: 49326778 total (48590532 tlen-paired, 2538 hash-paired, 468 singletons, 139630 discordant, 593610 orphans, 56039 too large [>5000 bp], 18496378 duplicates)