Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/659_Pl-N1-BDNA-1_A23TNVNLT4_1/659_Pl-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_Pl-N1-BDNA-1_A23TNVNLT4_1/659_Pl-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/64/524c3357ad709ea3b598dfe291ed92/.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/64/524c3357ad709ea3b598dfe291ed92/.command.run
==> 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_Pl-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_Pl-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_Pl-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_Pl-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: 90029096 total, 55963 skipped (flags/unmapped)
Fragments: 45130165 total (44806538 tlen-paired, 3245 hash-paired, 408 singletons, 14939 discordant, 305035 orphans, 9123 too large [>5000 bp], 15971710 duplicates)
Reads: 96822365 total, 47036 skipped (flags/unmapped)
Fragments: 48537944 total (48206948 tlen-paired, 2941 hash-paired, 443 singletons, 10518 discordant, 317094 orphans, 8489 too large [>5000 bp], 16873558 duplicates)
Reads: 105014251 total, 53239 skipped (flags/unmapped)
Fragments: 52642847 total (52264166 tlen-paired, 3982 hash-paired, 369 singletons, 15135 discordant, 359195 orphans, 17441 too large [>5000 bp], 18762762 duplicates)
Reads: 107035851 total, 94131 skipped (flags/unmapped)
Fragments: 53770567 total (52843862 tlen-paired, 3598 hash-paired, 428 singletons, 179159 discordant, 743520 orphans, 72267 too large [>5000 bp], 19163766 duplicates)