Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7d/1ec40d3e4df208d98121c088ef6e1e/.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/7d/1ec40d3e4df208d98121c088ef6e1e/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1136_21Y-N1-BDNA-1_B23KFG5LT4_1/1136_21Y-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/1136_21Y-N1-BDNA-1_B23KFG5LT4_1/1136_21Y-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
==> 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_21Y-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_21Y-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_21Y-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_21Y-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: 75446926 total, 43447 skipped (flags/unmapped)
Fragments: 37848267 total (37525535 tlen-paired, 2290 hash-paired, 364 singletons, 10409 discordant, 309669 orphans, 8489 too large [>5000 bp], 15986080 duplicates)
Reads: 69292534 total, 52336 skipped (flags/unmapped)
Fragments: 34755047 total (34450107 tlen-paired, 2589 hash-paired, 346 singletons, 14485 discordant, 287520 orphans, 8985 too large [>5000 bp], 15064965 duplicates)
Reads: 75856876 total, 46136 skipped (flags/unmapped)
Fragments: 38053021 total (37702656 tlen-paired, 3390 hash-paired, 265 singletons, 12883 discordant, 333827 orphans, 19395 too large [>5000 bp], 16587456 duplicates)
Reads: 84285832 total, 78977 skipped (flags/unmapped)
Fragments: 42384585 total (41504437 tlen-paired, 3121 hash-paired, 354 singletons, 175164 discordant, 701509 orphans, 69774 too large [>5000 bp], 18475578 duplicates)