Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_D1V-N1-BDNA-1_A23TNVNLT4_1/1241_D1V-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/84/309193ece9a2fde6bb2012de441b62/.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/84/309193ece9a2fde6bb2012de441b62/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_D1V-N1-BDNA-1_A23TNVNLT4_1/1241_D1V-N1-BDNA-1_A23TNVNLT4_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: 1241_D1V-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_D1V-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_D1V-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_D1V-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: 64331232 total, 43909 skipped (flags/unmapped)
Fragments: 32250292 total (32012676 tlen-paired, 2348 hash-paired, 352 singletons, 10015 discordant, 224901 orphans, 5996 too large [>5000 bp], 10969644 duplicates)
Reads: 68954218 total, 38010 skipped (flags/unmapped)
Fragments: 34570654 total (34322700 tlen-paired, 2251 hash-paired, 327 singletons, 7185 discordant, 238191 orphans, 6709 too large [>5000 bp], 11556284 duplicates)
Reads: 75700040 total, 40342 skipped (flags/unmapped)
Fragments: 37956113 total (37661622 tlen-paired, 2281 hash-paired, 303 singletons, 10808 discordant, 281099 orphans, 14437 too large [>5000 bp], 12963624 duplicates)
Reads: 76740647 total, 73164 skipped (flags/unmapped)
Fragments: 38563360 total (37849231 tlen-paired, 2512 hash-paired, 298 singletons, 138990 discordant, 572329 orphans, 56695 too large [>5000 bp], 13143422 duplicates)