Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/9d5b4c92a360e4fa1b55fbe5715f5a/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_0Q7-N1-BDNA-1_A23MHW3LT4_1/1136_0Q7-N1-BDNA-1_A23MHW3LT4_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/77/9d5b4c92a360e4fa1b55fbe5715f5a/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_0Q7-N1-BDNA-1_A23MHW3LT4_1/1136_0Q7-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam
==> 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: 1136_0Q7-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
The index file is older than the data file: 1136_0Q7-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0Q7-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1136_0Q7-N1-BDNA-1_A23MHW3LT4_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: 75199900 total, 63363 skipped (flags/unmapped)
Fragments: 37861403 total (37235708 tlen-paired, 4944 hash-paired, 497 singletons, 11480 discordant, 608774 orphans, 11501 too large [>5000 bp], 14181843 duplicates)
Reads: 78934149 total, 53427 skipped (flags/unmapped)
Fragments: 39748262 total (39101698 tlen-paired, 2031 hash-paired, 476 singletons, 7895 discordant, 636162 orphans, 10418 too large [>5000 bp], 14484421 duplicates)
Reads: 86286146 total, 59347 skipped (flags/unmapped)
Fragments: 43450146 total (42717850 tlen-paired, 3607 hash-paired, 427 singletons, 11630 discordant, 716632 orphans, 21783 too large [>5000 bp], 16245072 duplicates)
Reads: 88405721 total, 98155 skipped (flags/unmapped)
Fragments: 44854862 total (42645803 tlen-paired, 3646 hash-paired, 544 singletons, 436991 discordant, 1767878 orphans, 183132 too large [>5000 bp], 16565977 duplicates)