Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_BXHM-N1-BDNA-1_A23TNVNLT4_1/1241_BXHM-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/b56186686af3dfce1e4b8b2c0e1e5a/.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/46/b56186686af3dfce1e4b8b2c0e1e5a/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_BXHM-N1-BDNA-1_A23TNVNLT4_1/1241_BXHM-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: 1241_BXHM-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BXHM-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BXHM-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BXHM-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: 110668379 total, 66660 skipped (flags/unmapped)
Fragments: 55448731 total (55114230 tlen-paired, 5144 hash-paired, 457 singletons, 13972 discordant, 314928 orphans, 9821 too large [>5000 bp], 20730975 duplicates)
Reads: 118592130 total, 57263 skipped (flags/unmapped)
Fragments: 59426325 total (59077232 tlen-paired, 3657 hash-paired, 623 singletons, 10035 discordant, 334778 orphans, 8809 too large [>5000 bp], 21841981 duplicates)
Reads: 129510784 total, 61013 skipped (flags/unmapped)
Fragments: 64894512 total (64494101 tlen-paired, 3879 hash-paired, 428 singletons, 14031 discordant, 382073 orphans, 21624 too large [>5000 bp], 24309130 duplicates)
Reads: 131694258 total, 109790 skipped (flags/unmapped)
Fragments: 66114557 total (65112353 tlen-paired, 4387 hash-paired, 502 singletons, 195027 discordant, 802288 orphans, 79072 too large [>5000 bp], 24812366 duplicates)