Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/659_dkd-N1-BDNA-1_B23KFG5LT4_1/659_dkd-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/659_dkd-N1-BDNA-1_B23KFG5LT4_1/659_dkd-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/02/f5eb253514432471995952cc879849/.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/02/f5eb253514432471995952cc879849/.command.run
==> 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: 659_dkd-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
The index file is older than the data file: 659_dkd-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 659_dkd-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
The index file is older than the data file: 659_dkd-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: 71445569 total, 60606 skipped (flags/unmapped)
Fragments: 35814555 total (35533000 tlen-paired, 3037 hash-paired, 339 singletons, 15187 discordant, 262992 orphans, 9592 too large [>5000 bp], 15103598 duplicates)
Reads: 78297886 total, 54542 skipped (flags/unmapped)
Fragments: 39251768 total (38932456 tlen-paired, 4454 hash-paired, 308 singletons, 14322 discordant, 300228 orphans, 20172 too large [>5000 bp], 16685281 duplicates)
Reads: 77439592 total, 49554 skipped (flags/unmapped)
Fragments: 38821446 total (38533821 tlen-paired, 2235 hash-paired, 330 singletons, 11370 discordant, 273690 orphans, 10583 too large [>5000 bp], 16017313 duplicates)
Reads: 86554975 total, 88337 skipped (flags/unmapped)
Fragments: 43471538 total (42734261 tlen-paired, 3600 hash-paired, 363 singletons, 142743 discordant, 590571 orphans, 57248 too large [>5000 bp], 18490118 duplicates)