Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_8E7-N1-BDNA-1_A23NLN3LT4_1/1136_8E7-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_8E7-N1-BDNA-1_A23NLN3LT4_1/1136_8E7-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/49/aefc5045cd2da3c20d014c22e647f4/.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/49/aefc5045cd2da3c20d014c22e647f4/.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: 1136_8E7-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_8E7-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_8E7-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_8E7-N1-BDNA-1_A23NLN3LT4_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: 61441566 total, 48699 skipped (flags/unmapped)
Fragments: 30859701 total (30502441 tlen-paired, 2624 hash-paired, 316 singletons, 11271 discordant, 343049 orphans, 8415 too large [>5000 bp], 11201308 duplicates)
Reads: 66294255 total, 42613 skipped (flags/unmapped)
Fragments: 33301342 total (32923714 tlen-paired, 2215 hash-paired, 374 singletons, 8057 discordant, 366982 orphans, 8157 too large [>5000 bp], 11722006 duplicates)
Reads: 65706685 total, 44821 skipped (flags/unmapped)
Fragments: 33010886 total (32606540 tlen-paired, 3501 hash-paired, 228 singletons, 9777 discordant, 390840 orphans, 15580 too large [>5000 bp], 12020456 duplicates)
Reads: 73047492 total, 72328 skipped (flags/unmapped)
Fragments: 36850567 total (35701907 tlen-paired, 1879 hash-paired, 294 singletons, 231973 discordant, 914514 orphans, 94419 too large [>5000 bp], 13344265 duplicates)