Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/521e8f5d99922f366fb2a9ed65270c/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_WWM-N1-BDNA-1_A23TNVNLT4_1/1241_WWM-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/4f/521e8f5d99922f366fb2a9ed65270c/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_WWM-N1-BDNA-1_A23TNVNLT4_1/1241_WWM-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_WWM-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_WWM-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_WWM-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_WWM-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: 73873828 total, 47095 skipped (flags/unmapped)
Fragments: 37017960 total (36779318 tlen-paired, 3001 hash-paired, 275 singletons, 11014 discordant, 224352 orphans, 7720 too large [>5000 bp], 11865445 duplicates)
Reads: 79946246 total, 39143 skipped (flags/unmapped)
Fragments: 40064214 total (39818166 tlen-paired, 2307 hash-paired, 351 singletons, 7598 discordant, 235792 orphans, 7409 too large [>5000 bp], 12617483 duplicates)
Reads: 88264338 total, 78615 skipped (flags/unmapped)
Fragments: 44317525 total (43622232 tlen-paired, 3236 hash-paired, 296 singletons, 134994 discordant, 556767 orphans, 53868 too large [>5000 bp], 14343942 duplicates)
Reads: 87129784 total, 42572 skipped (flags/unmapped)
Fragments: 43666597 total (43373965 tlen-paired, 4650 hash-paired, 276 singletons, 11652 discordant, 276054 orphans, 15174 too large [>5000 bp], 14117782 duplicates)