Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_BD4M-N1-BDNA-1_A23TNVNLT4_1/1241_BD4M-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d1/ea921edd8ec6b73229df3c8ba74b56/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_BD4M-N1-BDNA-1_A23TNVNLT4_1/1241_BD4M-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/d1/ea921edd8ec6b73229df3c8ba74b56/.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_BD4M-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BD4M-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BD4M-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BD4M-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: 78878803 total, 46046 skipped (flags/unmapped)
Fragments: 39530148 total (39257192 tlen-paired, 6040 hash-paired, 334 singletons, 12015 discordant, 254567 orphans, 13681 too large [>5000 bp], 14014246 duplicates)
Reads: 78639463 total, 42871 skipped (flags/unmapped)
Fragments: 39411322 total (39156774 tlen-paired, 3841 hash-paired, 430 singletons, 9609 discordant, 240668 orphans, 7523 too large [>5000 bp], 13633152 duplicates)
Reads: 73915233 total, 53827 skipped (flags/unmapped)
Fragments: 37038955 total (36784957 tlen-paired, 3968 hash-paired, 431 singletons, 14040 discordant, 235559 orphans, 9743 too large [>5000 bp], 13060571 duplicates)
Reads: 86690542 total, 79780 skipped (flags/unmapped)
Fragments: 43518705 total (42860407 tlen-paired, 2966 hash-paired, 391 singletons, 125932 discordant, 529009 orphans, 51376 too large [>5000 bp], 15445537 duplicates)