Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_BDGT-N1-BDNA-1_A23TNVNLT4_1/1241_BDGT-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ae/77ced348bf5973b743b5437b8b1b1e/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_BDGT-N1-BDNA-1_A23TNVNLT4_1/1241_BDGT-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/ae/77ced348bf5973b743b5437b8b1b1e/.command.run
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1241_BDGT-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.baiThe index file is older than the data file: 1241_BDGT-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1241_BDGT-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BDGT-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: 83285903 total, 52209 skipped (flags/unmapped)
Fragments: 41759150 total (41441696 tlen-paired, 3056 hash-paired, 324 singletons, 13680 discordant, 300394 orphans, 8056 too large [>5000 bp], 14962473 duplicates)
Reads: 89602749 total, 45388 skipped (flags/unmapped)
Fragments: 44928959 total (44600901 tlen-paired, 2147 hash-paired, 434 singletons, 9066 discordant, 316411 orphans, 8144 too large [>5000 bp], 15842186 duplicates)
Reads: 98449177 total, 48897 skipped (flags/unmapped)
Fragments: 49365194 total (48981597 tlen-paired, 3103 hash-paired, 396 singletons, 14296 discordant, 365802 orphans, 18045 too large [>5000 bp], 17826021 duplicates)
Reads: 100462730 total, 86428 skipped (flags/unmapped)
Fragments: 50495759 total (49540832 tlen-paired, 3416 hash-paired, 396 singletons, 187135 discordant, 763980 orphans, 74580 too large [>5000 bp], 18220492 duplicates)