Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2d/7c38ec87ffdb00ed47b7ded848fc96/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_0YE-N1-BDNA-1_A23NLN3LT4_1/1136_0YE-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam
  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/2d/7c38ec87ffdb00ed47b7ded848fc96/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_0YE-N1-BDNA-1_A23NLN3LT4_1/1136_0YE-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1136_0YE-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1136_0YE-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1136_0YE-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0YE-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: 75083206 total, 56265 skipped (flags/unmapped)
Fragments: 37631156 total (37356393 tlen-paired, 3996 hash-paired, 379 singletons, 13070 discordant, 257318 orphans, 11163 too large [>5000 bp], 12497909 duplicates)
Reads: 81156951 total, 46239 skipped (flags/unmapped)
Fragments: 40680489 total (40397658 tlen-paired, 3609 hash-paired, 368 singletons, 9240 discordant, 269614 orphans, 9858 too large [>5000 bp], 13224181 duplicates)
Reads: 88878115 total, 81540 skipped (flags/unmapped)
Fragments: 44643862 total (43875329 tlen-paired, 2832 hash-paired, 303 singletons, 151052 discordant, 614346 orphans, 61750 too large [>5000 bp], 14876631 duplicates)
Reads: 80663829 total, 48369 skipped (flags/unmapped)
Fragments: 40436890 total (40130391 tlen-paired, 4739 hash-paired, 328 singletons, 11330 discordant, 290102 orphans, 16055 too large [>5000 bp], 13482404 duplicates)