Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_QAP-N1-BDNA-1_A23TNVNLT4_1/1241_QAP-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/76/f028f8fe57862454d8e35e044bcf3a/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_QAP-N1-BDNA-1_A23TNVNLT4_1/1241_QAP-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/76/f028f8fe57862454d8e35e044bcf3a/.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_QAP-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_QAP-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_QAP-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_QAP-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: 85908809 total, 62585 skipped (flags/unmapped)
Fragments: 43127943 total (42675799 tlen-paired, 4356 hash-paired, 457 singletons, 13330 discordant, 434001 orphans, 12398 too large [>5000 bp], 17553148 duplicates)
Reads: 91983821 total, 50674 skipped (flags/unmapped)
Fragments: 46193564 total (45708658 tlen-paired, 2777 hash-paired, 539 singletons, 9544 discordant, 472046 orphans, 9302 too large [>5000 bp], 18360901 duplicates)
Reads: 92378594 total, 54432 skipped (flags/unmapped)
Fragments: 46386536 total (45888520 tlen-paired, 3337 hash-paired, 345 singletons, 11361 discordant, 482973 orphans, 17204 too large [>5000 bp], 18882559 duplicates)
Reads: 103045740 total, 95981 skipped (flags/unmapped)
Fragments: 51951016 total (50447868 tlen-paired, 3136 hash-paired, 423 singletons, 307793 discordant, 1191796 orphans, 119973 too large [>5000 bp], 21032994 duplicates)