Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/fda045ad48d3f899a89a7a655a5c5d/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_80B-N1-BDNA-1_A23NMNVLT4_1/1136_80B-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam
  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/fda045ad48d3f899a89a7a655a5c5d/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_80B-N1-BDNA-1_A23NMNVLT4_1/1136_80B-N1-BDNA-1_A23NMNVLT4_1.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: 1136_80B-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_80B-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_80B-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_80B-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: 65402914 total, 46913 skipped (flags/unmapped)
Fragments: 32765638 total (32561144 tlen-paired, 3451 hash-paired, 323 singletons, 9368 discordant, 191352 orphans, 8200 too large [>5000 bp], 7945142 duplicates)
Reads: 71284819 total, 36008 skipped (flags/unmapped)
Fragments: 35716557 total (35508895 tlen-paired, 2694 hash-paired, 342 singletons, 6759 discordant, 197867 orphans, 6953 too large [>5000 bp], 8514442 duplicates)
Reads: 77583034 total, 62956 skipped (flags/unmapped)
Fragments: 38948197 total (38368139 tlen-paired, 2275 hash-paired, 326 singletons, 110205 discordant, 467252 orphans, 45631 too large [>5000 bp], 9599476 duplicates)
Reads: 76787557 total, 40269 skipped (flags/unmapped)
Fragments: 38477434 total (38236134 tlen-paired, 4463 hash-paired, 309 singletons, 9571 discordant, 226957 orphans, 9843 too large [>5000 bp], 9497915 duplicates)