Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_6E4-N1-BDNA-1_A23NLN3LT4_1/1136_6E4-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_6E4-N1-BDNA-1_A23NLN3LT4_1/1136_6E4-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8c/8b1f23a239ba6468fab982af5cdd98/.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/8c/8b1f23a239ba6468fab982af5cdd98/.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_6E4-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1136_6E4-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1136_6E4-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1136_6E4-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: 65847745 total, 43684 skipped (flags/unmapped)
Fragments: 32996971 total (32780816 tlen-paired, 2634 hash-paired, 316 singletons, 10166 discordant, 203039 orphans, 6737 too large [>5000 bp], 11147560 duplicates)
Reads: 70650857 total, 38913 skipped (flags/unmapped)
Fragments: 35402604 total (35181273 tlen-paired, 2655 hash-paired, 330 singletons, 6876 discordant, 211470 orphans, 9268 too large [>5000 bp], 11720874 duplicates)
Reads: 78300211 total, 67248 skipped (flags/unmapped)
Fragments: 39313998 total (38701087 tlen-paired, 1617 hash-paired, 286 singletons, 117399 discordant, 493609 orphans, 49431 too large [>5000 bp], 13348697 duplicates)
Reads: 77590867 total, 42673 skipped (flags/unmapped)
Fragments: 38883269 total (38614128 tlen-paired, 3348 hash-paired, 237 singletons, 10191 discordant, 255365 orphans, 18629 too large [>5000 bp], 13206288 duplicates)