Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6f/be86d774a0f7c097cdb4dd716268e8/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1136_2FV-N1-BDNA-1_B23KFG5LT4_1/1136_2FV-N1-BDNA-1_B23KFG5LT4_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/6f/be86d774a0f7c097cdb4dd716268e8/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1136_2FV-N1-BDNA-1_B23KFG5LT4_1/1136_2FV-N1-BDNA-1_B23KFG5LT4_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_2FV-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai[W::hts_idx_load3] The index file is older than the data file: 1136_2FV-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1136_2FV-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2FV-N1-BDNA-1_B23KFG5LT4_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: 71089249 total, 51444 skipped (flags/unmapped)
Fragments: 35633318 total (35366283 tlen-paired, 2897 hash-paired, 282 singletons, 16087 discordant, 247769 orphans, 9610 too large [>5000 bp], 13998346 duplicates)
Reads: 75885374 total, 54066 skipped (flags/unmapped)
Fragments: 38034318 total (37752166 tlen-paired, 3861 hash-paired, 272 singletons, 13907 discordant, 264112 orphans, 13528 too large [>5000 bp], 14964464 duplicates)
Reads: 75756005 total, 46648 skipped (flags/unmapped)
Fragments: 37969455 total (37702337 tlen-paired, 2773 hash-paired, 369 singletons, 11162 discordant, 252814 orphans, 11815 too large [>5000 bp], 14519324 duplicates)
Reads: 83382892 total, 77008 skipped (flags/unmapped)
Fragments: 41869261 total (41208881 tlen-paired, 2788 hash-paired, 331 singletons, 124704 discordant, 532557 orphans, 50125 too large [>5000 bp], 16503213 duplicates)