Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1136_0YX-N1-BDNA-1_B23KFG5LT4_1/1136_0YX-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1136_0YX-N1-BDNA-1_B23KFG5LT4_1/1136_0YX-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5a/9fc3102714c0d856e0c0ed4b00cac3/.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/5a/9fc3102714c0d856e0c0ed4b00cac3/.command.run
==> 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_0YX-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0YX-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0YX-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0YX-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: 74084133 total, 54768 skipped (flags/unmapped)
Fragments: 37141376 total (36848762 tlen-paired, 2465 hash-paired, 421 singletons, 18396 discordant, 271332 orphans, 9183 too large [>5000 bp], 15354568 duplicates)
Reads: 79630427 total, 45508 skipped (flags/unmapped)
Fragments: 39922430 total (39628083 tlen-paired, 1831 hash-paired, 453 singletons, 12799 discordant, 279264 orphans, 9888 too large [>5000 bp], 16080219 duplicates)
Reads: 80157318 total, 51824 skipped (flags/unmapped)
Fragments: 40188401 total (39855375 tlen-paired, 3310 hash-paired, 314 singletons, 16322 discordant, 313080 orphans, 21043 too large [>5000 bp], 16689164 duplicates)
Reads: 88260382 total, 86754 skipped (flags/unmapped)
Fragments: 44320226 total (43598268 tlen-paired, 3042 hash-paired, 374 singletons, 137390 discordant, 581152 orphans, 57351 too large [>5000 bp], 18425791 duplicates)