Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_3F-N1-BDNA-1_A23KFG7LT4_1/1136_3F-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ae/c1d8c86aa65b7ae1ffbec323cc82cc/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_3F-N1-BDNA-1_A23KFG7LT4_1/1136_3F-N1-BDNA-1_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/ae/c1d8c86aa65b7ae1ffbec323cc82cc/.command.run
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_3F-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3F-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_3F-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3F-N1-BDNA-1_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: 92933815 total, 67517 skipped (flags/unmapped)
Fragments: 46677762 total (46136596 tlen-paired, 4637 hash-paired, 584 singletons, 16831 discordant, 519114 orphans, 15236 too large [>5000 bp], 18812529 duplicates)
Reads: 98096448 total, 55421 skipped (flags/unmapped)
Fragments: 49276732 total (48726016 tlen-paired, 2707 hash-paired, 524 singletons, 11488 discordant, 535997 orphans, 12042 too large [>5000 bp], 19370442 duplicates)
Reads: 107810169 total, 61406 skipped (flags/unmapped)
Fragments: 54160562 total (53511815 tlen-paired, 5335 hash-paired, 409 singletons, 18169 discordant, 624834 orphans, 26441 too large [>5000 bp], 21885824 duplicates)
Reads: 110125438 total, 93660 skipped (flags/unmapped)
Fragments: 55571694 total (53829110 tlen-paired, 3787 hash-paired, 511 singletons, 343493 discordant, 1394793 orphans, 141847 too large [>5000 bp], 22348881 duplicates)