Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1029_BLVT-N1-BDNA-1_B23H2GYLT3_1/1029_BLVT-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/2259d37d412b668fc2991f14b3d356/.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/1e/2259d37d412b668fc2991f14b3d356/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1029_BLVT-N1-BDNA-1_B23H2GYLT3_1/1029_BLVT-N1-BDNA-1_B23H2GYLT3_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: 1029_BLVT-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BLVT-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BLVT-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BLVT-N1-BDNA-1_B23H2GYLT3_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: 62572790 total, 55527 skipped (flags/unmapped)
Fragments: 31414586 total (31071210 tlen-paired, 9484 hash-paired, 4895 singletons, 6501 discordant, 322496 orphans, 7741 too large [>5000 bp], 5668586 duplicates)
Reads: 63028502 total, 47096 skipped (flags/unmapped)
Fragments: 31655108 total (31292499 tlen-paired, 9947 hash-paired, 4610 singletons, 5550 discordant, 342502 orphans, 9151 too large [>5000 bp], 5678814 duplicates)
Reads: 70211992 total, 86976 skipped (flags/unmapped)
Fragments: 35446256 total (34253595 tlen-paired, 10765 hash-paired, 5296 singletons, 235190 discordant, 941410 orphans, 89605 too large [>5000 bp], 6290554 duplicates)
Reads: 69327570 total, 46779 skipped (flags/unmapped)
Fragments: 34825040 total (34427241 tlen-paired, 10290 hash-paired, 5145 singletons, 4774 discordant, 377590 orphans, 6723 too large [>5000 bp], 6257639 duplicates)