Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1029_BRU2-N1-BDNA-1_A23KFG7LT4_1/1029_BRU2-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f2/90316ee50cdb58167cd6221a77f7bd/.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/f2/90316ee50cdb58167cd6221a77f7bd/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1029_BRU2-N1-BDNA-1_A23KFG7LT4_1/1029_BRU2-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
==> 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: 1029_BRU2-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1029_BRU2-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1029_BRU2-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BRU2-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: 72552940 total, 56320 skipped (flags/unmapped)
Fragments: 36401653 total (36062830 tlen-paired, 3402 hash-paired, 363 singletons, 7609 discordant, 327449 orphans, 10563 too large [>5000 bp], 13044378 duplicates)
Reads: 79511155 total, 46512 skipped (flags/unmapped)
Fragments: 39914037 total (39521592 tlen-paired, 3429 hash-paired, 541 singletons, 5999 discordant, 382476 orphans, 9793 too large [>5000 bp], 13910120 duplicates)
Reads: 85839042 total, 52298 skipped (flags/unmapped)
Fragments: 43081400 total (42658189 tlen-paired, 5341 hash-paired, 364 singletons, 7558 discordant, 409948 orphans, 17128 too large [>5000 bp], 15334586 duplicates)
Reads: 86734955 total, 83870 skipped (flags/unmapped)
Fragments: 43722187 total (42492716 tlen-paired, 4661 hash-paired, 408 singletons, 245439 discordant, 978963 orphans, 93041 too large [>5000 bp], 15473011 duplicates)