Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_66R-N1-BDNA-1_A23NLN3LT4_1/1136_66R-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bf/bc7e02c84e46fa56212c941ead7046/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_66R-N1-BDNA-1_A23NLN3LT4_1/1136_66R-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
  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/bf/bc7e02c84e46fa56212c941ead7046/.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_66R-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_66R-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_66R-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_66R-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: 97753494 total, 66750 skipped (flags/unmapped)
Fragments: 48987513 total (48653476 tlen-paired, 3702 hash-paired, 457 singletons, 16771 discordant, 313107 orphans, 12641 too large [>5000 bp], 17744671 duplicates)
Reads: 104779602 total, 55446 skipped (flags/unmapped)
Fragments: 52511986 total (52175645 tlen-paired, 3229 hash-paired, 480 singletons, 11376 discordant, 321256 orphans, 10960 too large [>5000 bp], 18710746 duplicates)
Reads: 115192677 total, 61935 skipped (flags/unmapped)
Fragments: 57732330 total (57342337 tlen-paired, 5339 hash-paired, 399 singletons, 16538 discordant, 367717 orphans, 17099 too large [>5000 bp], 21048293 duplicates)
Reads: 116320589 total, 102349 skipped (flags/unmapped)
Fragments: 58406961 total (57482576 tlen-paired, 3045 hash-paired, 418 singletons, 176570 discordant, 744352 orphans, 74544 too large [>5000 bp], 21314048 duplicates)