Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8e/4fd62d33cb3c3bb01c52d434810237/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_Q4P-N1-BDNA-1_A23TNVNLT4_1/1241_Q4P-N1-BDNA-1_A23TNVNLT4_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/8e/4fd62d33cb3c3bb01c52d434810237/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_Q4P-N1-BDNA-1_A23TNVNLT4_1/1241_Q4P-N1-BDNA-1_A23TNVNLT4_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: 1241_Q4P-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_Q4P-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_Q4P-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_Q4P-N1-BDNA-1_A23TNVNLT4_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: 45170311 total, 54115 skipped (flags/unmapped)
Fragments: 23014867 total (22082804 tlen-paired, 2801 hash-paired, 281 singletons, 4016 discordant, 924965 orphans, 5854 too large [>5000 bp], 10516472 duplicates)
Reads: 53462006 total, 48614 skipped (flags/unmapped)
Fragments: 27261315 total (26113460 tlen-paired, 3418 hash-paired, 224 singletons, 4527 discordant, 1139686 orphans, 15336 too large [>5000 bp], 12455426 duplicates)
Reads: 48824296 total, 49129 skipped (flags/unmapped)
Fragments: 24920876 total (23830538 tlen-paired, 3123 hash-paired, 466 singletons, 3008 discordant, 1083741 orphans, 8811 too large [>5000 bp], 11077943 duplicates)
Reads: 57796262 total, 115733 skipped (flags/unmapped)
Fragments: 30078090 total (26206240 tlen-paired, 3444 hash-paired, 427 singletons, 790537 discordant, 3077442 orphans, 301109 too large [>5000 bp], 12956167 duplicates)