Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_T6O-N1-BDNA-1_A23TNVNLT4_1/1241_T6O-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/67/a93c3ad04c8c1075853f2030f033ea/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_T6O-N1-BDNA-1_A23TNVNLT4_1/1241_T6O-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/67/a93c3ad04c8c1075853f2030f033ea/.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_T6O-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_T6O-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_T6O-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_T6O-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: 75365454 total, 52287 skipped (flags/unmapped)
Fragments: 37775756 total (37509703 tlen-paired, 2701 hash-paired, 403 singletons, 11007 discordant, 251942 orphans, 7000 too large [>5000 bp], 14607128 duplicates)
Reads: 80747617 total, 45864 skipped (flags/unmapped)
Fragments: 40478457 total (40186755 tlen-paired, 2557 hash-paired, 281 singletons, 9604 discordant, 279260 orphans, 12190 too large [>5000 bp], 15719375 duplicates)
Reads: 81473602 total, 45800 skipped (flags/unmapped)
Fragments: 40840879 total (40557811 tlen-paired, 3010 hash-paired, 413 singletons, 8068 discordant, 271577 orphans, 9017 too large [>5000 bp], 15448017 duplicates)
Reads: 89747363 total, 88341 skipped (flags/unmapped)
Fragments: 45081145 total (44286965 tlen-paired, 2894 hash-paired, 360 singletons, 158674 discordant, 632252 orphans, 64672 too large [>5000 bp], 17469253 duplicates)