Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_5Z-N1-BDNA-1_B2377KTLT3_3/869_5Z-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/04/8764e8fde77b562157ba272e052e57/.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/04/8764e8fde77b562157ba272e052e57/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_5Z-N1-BDNA-1_B2377KTLT3_3/869_5Z-N1-BDNA-1_B2377KTLT3_3.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: 869_5Z-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_5Z-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_5Z-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_5Z-N1-BDNA-1_B2377KTLT3_3.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: 108221960 total, 88677 skipped (flags/unmapped)
Fragments: 54254252 total (53805025 tlen-paired, 40300 hash-paired, 8101 singletons, 9624 discordant, 391202 orphans, 12041 too large [>5000 bp], 14371346 duplicates)
Reads: 119199414 total, 78825 skipped (flags/unmapped)
Fragments: 59772956 total (59273801 tlen-paired, 42149 hash-paired, 8476 singletons, 7169 discordant, 441361 orphans, 12257 too large [>5000 bp], 15876055 duplicates)
Reads: 119215680 total, 78794 skipped (flags/unmapped)
Fragments: 59789283 total (59259335 tlen-paired, 44549 hash-paired, 8535 singletons, 9737 discordant, 467127 orphans, 16991 too large [>5000 bp], 15697285 duplicates)
Reads: 122256994 total, 141572 skipped (flags/unmapped)
Fragments: 61507967 total (60065166 tlen-paired, 46759 hash-paired, 9031 singletons, 268366 discordant, 1118645 orphans, 113582 too large [>5000 bp], 16111896 duplicates)