Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_B245-N1-BDNA-1_A23TNVNLT4_1/1241_B245-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/35/7c2ea97a8960220d6272af6c1e9a72/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_B245-N1-BDNA-1_A23TNVNLT4_1/1241_B245-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/35/7c2ea97a8960220d6272af6c1e9a72/.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: 1241_B245-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_B245-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_B245-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_B245-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: 80127838 total, 60191 skipped (flags/unmapped)
Fragments: 40201731 total (39833271 tlen-paired, 4081 hash-paired, 332 singletons, 14994 discordant, 349053 orphans, 6785 too large [>5000 bp], 15067851 duplicates)
Reads: 86702644 total, 51817 skipped (flags/unmapped)
Fragments: 43503093 total (43114737 tlen-paired, 2980 hash-paired, 436 singletons, 11003 discordant, 373937 orphans, 9507 too large [>5000 bp], 15931737 duplicates)
Reads: 96655536 total, 94633 skipped (flags/unmapped)
Fragments: 48645795 total (47511371 tlen-paired, 3264 hash-paired, 404 singletons, 223181 discordant, 907575 orphans, 88646 too large [>5000 bp], 18337175 duplicates)
Reads: 94830375 total, 56469 skipped (flags/unmapped)
Fragments: 47580937 total (47131080 tlen-paired, 3479 hash-paired, 377 singletons, 15686 discordant, 430315 orphans, 21362 too large [>5000 bp], 17941234 duplicates)