Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/97/ff51cb0d97157593f1334e80880347/.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/97/ff51cb0d97157593f1334e80880347/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_6Q7-N1-BDNA-1_A23NLN3LT4_1/1136_6Q7-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_6Q7-N1-BDNA-1_A23NLN3LT4_1/1136_6Q7-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_6Q7-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_6Q7-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_6Q7-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_6Q7-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: 96272254 total, 72094 skipped (flags/unmapped)
Fragments: 48288660 total (47859467 tlen-paired, 3270 hash-paired, 414 singletons, 19999 discordant, 405510 orphans, 14382 too large [>5000 bp], 19401065 duplicates)
Reads: 103017651 total, 67604 skipped (flags/unmapped)
Fragments: 51674736 total (51227500 tlen-paired, 4043 hash-paired, 556 singletons, 14332 discordant, 428305 orphans, 14718 too large [>5000 bp], 20420025 duplicates)
Reads: 113031408 total, 70083 skipped (flags/unmapped)
Fragments: 56703054 total (56170423 tlen-paired, 4490 hash-paired, 403 singletons, 21300 discordant, 506438 orphans, 31029 too large [>5000 bp], 22947788 duplicates)
Reads: 114102326 total, 103789 skipped (flags/unmapped)
Fragments: 57402756 total (56166521 tlen-paired, 3131 hash-paired, 454 singletons, 237671 discordant, 994979 orphans, 94229 too large [>5000 bp], 23199491 duplicates)