Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/60/d98a5aabb6cdd99632477ba74f5718/.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/60/d98a5aabb6cdd99632477ba74f5718/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_7RQ-N1-BDNA-1_A23NMNVLT4_1/1136_7RQ-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_7RQ-N1-BDNA-1_A23NMNVLT4_1/1136_7RQ-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_7RQ-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7RQ-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7RQ-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7RQ-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: 63292041 total, 38041 skipped (flags/unmapped)
Fragments: 31712410 total (31518556 tlen-paired, 2244 hash-paired, 257 singletons, 6076 discordant, 185277 orphans, 7357 too large [>5000 bp], 8560144 duplicates)
Reads: 58866780 total, 44722 skipped (flags/unmapped)
Fragments: 29493460 total (29303427 tlen-paired, 1804 hash-paired, 262 singletons, 8781 discordant, 179186 orphans, 7293 too large [>5000 bp], 8092660 duplicates)
Reads: 70337491 total, 68050 skipped (flags/unmapped)
Fragments: 35308867 total (34765512 tlen-paired, 2697 hash-paired, 282 singletons, 104521 discordant, 435855 orphans, 43922 too large [>5000 bp], 9816104 duplicates)
Reads: 69800644 total, 41287 skipped (flags/unmapped)
Fragments: 34979534 total (34736776 tlen-paired, 3300 hash-paired, 217 singletons, 9427 discordant, 229814 orphans, 15160 too large [>5000 bp], 9712658 duplicates)