Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1029_HST-N1-BDNA-1_A23NMNVLT4_1/1029_HST-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b6/108a0a65ee8f1ecd0be342f4d6ea14/.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/b6/108a0a65ee8f1ecd0be342f4d6ea14/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1029_HST-N1-BDNA-1_A23NMNVLT4_1/1029_HST-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam
==> 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: 1029_HST-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_HST-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_HST-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_HST-N1-BDNA-1_A23NMNVLT4_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: 85944412 total, 63064 skipped (flags/unmapped)
Fragments: 43048936 total (42798552 tlen-paired, 3305 hash-paired, 279 singletons, 12671 discordant, 234129 orphans, 8942 too large [>5000 bp], 13216021 duplicates)
Reads: 92985476 total, 53418 skipped (flags/unmapped)
Fragments: 46577972 total (46323150 tlen-paired, 2023 hash-paired, 458 singletons, 8809 discordant, 243532 orphans, 10052 too large [>5000 bp], 14088433 duplicates)
Reads: 93375390 total, 58898 skipped (flags/unmapped)
Fragments: 46774190 total (46492113 tlen-paired, 4973 hash-paired, 255 singletons, 10818 discordant, 266031 orphans, 17199 too large [>5000 bp], 14525494 duplicates)
Reads: 102834364 total, 93988 skipped (flags/unmapped)
Fragments: 51589395 total (50904391 tlen-paired, 2262 hash-paired, 422 singletons, 134052 discordant, 548268 orphans, 55138 too large [>5000 bp], 16032648 duplicates)