Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/57/cbd1d87d1a7ee903b4f322d6393091/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_7WF-N1-BDNA-1_A23NMNVLT4_1/1136_7WF-N1-BDNA-1_A23NMNVLT4_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/57/cbd1d87d1a7ee903b4f322d6393091/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_7WF-N1-BDNA-1_A23NMNVLT4_1/1136_7WF-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] [W::hts_idx_load3] The index file is older than the data file: 1136_7WF-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
The index file is older than the data file: 1136_7WF-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7WF-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7WF-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: 36639336 total, 28420 skipped (flags/unmapped)
Fragments: 18358643 total (18234654 tlen-paired, 1745 hash-paired, 162 singletons, 6076 discordant, 116006 orphans, 4899 too large [>5000 bp], 4924564 duplicates)
Reads: 39357885 total, 22969 skipped (flags/unmapped)
Fragments: 19722539 total (19599745 tlen-paired, 921 hash-paired, 163 singletons, 4133 discordant, 117577 orphans, 3789 too large [>5000 bp], 5164755 duplicates)
Reads: 43575811 total, 26705 skipped (flags/unmapped)
Fragments: 21836722 total (21683962 tlen-paired, 1565 hash-paired, 153 singletons, 6359 discordant, 144683 orphans, 10249 too large [>5000 bp], 5871437 duplicates)
Reads: 43722366 total, 44384 skipped (flags/unmapped)
Fragments: 21950932 total (21606403 tlen-paired, 1624 hash-paired, 206 singletons, 65267 discordant, 277432 orphans, 26878 too large [>5000 bp], 5904194 duplicates)