Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/659_dQk-N1-BDNA-1_B23KGCJLT4_1/659_dQk-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/56/685642ba3eb542fd00a46cf22dd262/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/659_dQk-N1-BDNA-1_B23KGCJLT4_1/659_dQk-N1-BDNA-1_B23KGCJLT4_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/56/685642ba3eb542fd00a46cf22dd262/.command.run
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 659_dQk-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.baiThe index file is older than the data file: 659_dQk-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.baiThe index file is older than the data file: 659_dQk-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai


[W::hts_idx_load3] The index file is older than the data file: 659_dQk-N1-BDNA-1_B23KGCJLT4_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: 68626772 total, 56999 skipped (flags/unmapped)
Fragments: 34387000 total (34141840 tlen-paired, 3587 hash-paired, 339 singletons, 16308 discordant, 224926 orphans, 10519 too large [>5000 bp], 12657354 duplicates)
Reads: 74584652 total, 44762 skipped (flags/unmapped)
Fragments: 37372439 total (37135914 tlen-paired, 2585 hash-paired, 372 singletons, 11874 discordant, 221694 orphans, 8539 too large [>5000 bp], 13583325 duplicates)
Reads: 74002938 total, 49501 skipped (flags/unmapped)
Fragments: 37084913 total (36798758 tlen-paired, 3744 hash-paired, 267 singletons, 14858 discordant, 267286 orphans, 25582 too large [>5000 bp], 13845137 duplicates)
Reads: 81399973 total, 74110 skipped (flags/unmapped)
Fragments: 40840963 total (40294379 tlen-paired, 2980 hash-paired, 328 singletons, 101119 discordant, 442157 orphans, 43211 too large [>5000 bp], 15307322 duplicates)