Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/72/7adabc735801e23bfc102ee9609f8d/.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/72/7adabc735801e23bfc102ee9609f8d/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_4NM-N1-BDNA-1_A23NLN3LT4_1/1136_4NM-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_4NM-N1-BDNA-1_A23NLN3LT4_1/1136_4NM-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam
==> 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_4NM-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4NM-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai[W::hts_idx_load3] The index file is older than the data file: 1136_4NM-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1136_4NM-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: 88579020 total, 71012 skipped (flags/unmapped)
Fragments: 44412693 total (44042307 tlen-paired, 4691 hash-paired, 427 singletons, 20403 discordant, 344865 orphans, 13957 too large [>5000 bp], 16622882 duplicates)
Reads: 94339293 total, 54693 skipped (flags/unmapped)
Fragments: 47306464 total (46938080 tlen-paired, 3731 hash-paired, 498 singletons, 13935 discordant, 350220 orphans, 11195 too large [>5000 bp], 17497950 duplicates)
Reads: 105194028 total, 99384 skipped (flags/unmapped)
Fragments: 52863080 total (51894033 tlen-paired, 2688 hash-paired, 415 singletons, 182677 discordant, 783267 orphans, 76083 too large [>5000 bp], 20012315 duplicates)
Reads: 104443030 total, 61436 skipped (flags/unmapped)
Fragments: 52375298 total (51938082 tlen-paired, 5860 hash-paired, 454 singletons, 21100 discordant, 409802 orphans, 20627 too large [>5000 bp], 19811545 duplicates)