Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/659_eAi-N1-BDNA-1_A23TY32LT4_1/659_eAi-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/02a82734207c7fe911722449b66bb2/.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/ea/02a82734207c7fe911722449b66bb2/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/659_eAi-N1-BDNA-1_A23TY32LT4_1/659_eAi-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
==> 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: 659_eAi-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eAi-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eAi-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eAi-N1-BDNA-1_A23TY32LT4_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: 92137891 total, 67766 skipped (flags/unmapped)
Fragments: 46181508 total (45842049 tlen-paired, 5066 hash-paired, 428 singletons, 13686 discordant, 320279 orphans, 13908 too large [>5000 bp], 18464249 duplicates)
Reads: 99576254 total, 55372 skipped (flags/unmapped)
Fragments: 49918886 total (49568186 tlen-paired, 4330 hash-paired, 416 singletons, 9590 discordant, 336364 orphans, 9945 too large [>5000 bp], 19701999 duplicates)
Reads: 110007481 total, 107903 skipped (flags/unmapped)
Fragments: 55279282 total (54258727 tlen-paired, 5336 hash-paired, 355 singletons, 198097 discordant, 816767 orphans, 79068 too large [>5000 bp], 22225216 duplicates)
Reads: 109302202 total, 63081 skipped (flags/unmapped)
Fragments: 54788105 total (54382803 tlen-paired, 4667 hash-paired, 284 singletons, 14200 discordant, 386151 orphans, 24673 too large [>5000 bp], 22043965 duplicates)