Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9e/35f93b688d5fe3000d9fa842b508a4/.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/9e/35f93b688d5fe3000d9fa842b508a4/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/659_cl5-N1-BDNA-1_A23TNVNLT4_1/659_cl5-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/659_cl5-N1-BDNA-1_A23TNVNLT4_1/659_cl5-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: 659_cl5-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_cl5-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 659_cl5-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.baiThe index file is older than the data file: 659_cl5-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: 86122991 total, 43500 skipped (flags/unmapped)
Fragments: 43163412 total (42871893 tlen-paired, 3052 hash-paired, 364 singletons, 10292 discordant, 277811 orphans, 15421 too large [>5000 bp], 14627580 duplicates)
Reads: 80489676 total, 52955 skipped (flags/unmapped)
Fragments: 40332833 total (40068779 tlen-paired, 3586 hash-paired, 423 singletons, 11657 discordant, 248388 orphans, 9933 too large [>5000 bp], 13580635 duplicates)
Reads: 87084201 total, 44679 skipped (flags/unmapped)
Fragments: 43642371 total (43366835 tlen-paired, 4062 hash-paired, 439 singletons, 8056 discordant, 262979 orphans, 9099 too large [>5000 bp], 14386920 duplicates)
Reads: 95444079 total, 81611 skipped (flags/unmapped)
Fragments: 47925579 total (47159385 tlen-paired, 4114 hash-paired, 386 singletons, 151728 discordant, 609966 orphans, 60831 too large [>5000 bp], 16229596 duplicates)