Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1173_RQT-N1-BDNA-01_A23KFG7LT4_1/1173_RQT-N1-BDNA-01_A23KFG7LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bc/702f09ab9a372aa1a32c37353881fc/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1173_RQT-N1-BDNA-01_A23KFG7LT4_1/1173_RQT-N1-BDNA-01_A23KFG7LT4_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/bc/702f09ab9a372aa1a32c37353881fc/.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: 1173_RQT-N1-BDNA-01_A23KFG7LT4_1.recalibrated.bam.bai
The index file is older than the data file: 1173_RQT-N1-BDNA-01_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_RQT-N1-BDNA-01_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_RQT-N1-BDNA-01_A23KFG7LT4_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: 112965713 total, 81559 skipped (flags/unmapped)
Fragments: 56620344 total (56207628 tlen-paired, 5300 hash-paired, 564 singletons, 23610 discordant, 383242 orphans, 13636 too large [>5000 bp], 21288042 duplicates)
Reads: 120349829 total, 67629 skipped (flags/unmapped)
Fragments: 60323168 total (59911008 tlen-paired, 3696 hash-paired, 728 singletons, 16288 discordant, 391448 orphans, 14020 too large [>5000 bp], 22155944 duplicates)
Reads: 119701039 total, 73457 skipped (flags/unmapped)
Fragments: 60002776 total (59549964 tlen-paired, 7149 hash-paired, 521 singletons, 19971 discordant, 425171 orphans, 23861 too large [>5000 bp], 22741706 duplicates)
Reads: 132548960 total, 115081 skipped (flags/unmapped)
Fragments: 66556888 total (65499806 tlen-paired, 4032 hash-paired, 568 singletons, 203461 discordant, 849021 orphans, 84846 too large [>5000 bp], 25257258 duplicates)