Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f4/5b0f434de198407e70cc74dfe5dcbe/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1029_9N5-N1-BDNA-1_A23NMNVLT4_1/1029_9N5-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/f4/5b0f434de198407e70cc74dfe5dcbe/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1029_9N5-N1-BDNA-1_A23NMNVLT4_1/1029_9N5-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_9N5-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_9N5-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_9N5-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_9N5-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: 87542650 total, 57212 skipped (flags/unmapped)
Fragments: 43842871 total (43612630 tlen-paired, 3825 hash-paired, 315 singletons, 12104 discordant, 213997 orphans, 7004 too large [>5000 bp], 11041765 duplicates)
Reads: 95383238 total, 48060 skipped (flags/unmapped)
Fragments: 47769549 total (47537970 tlen-paired, 2901 hash-paired, 468 singletons, 8844 discordant, 219366 orphans, 7957 too large [>5000 bp], 11931041 duplicates)
Reads: 103967656 total, 88164 skipped (flags/unmapped)
Fragments: 52138691 total (51526231 tlen-paired, 3096 hash-paired, 424 singletons, 115568 discordant, 493372 orphans, 47953 too large [>5000 bp], 13463685 duplicates)
Reads: 103487934 total, 52500 skipped (flags/unmapped)
Fragments: 51833808 total (51547604 tlen-paired, 4237 hash-paired, 336 singletons, 12607 discordant, 269024 orphans, 18589 too large [>5000 bp], 13366089 duplicates)