Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/44/1568fa18c0d8081006ee55acf1f115/.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/44/1568fa18c0d8081006ee55acf1f115/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_5WF-N1-BDNA-1_A23NMNVLT4_1/1136_5WF-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_5WF-N1-BDNA-1_A23NMNVLT4_1/1136_5WF-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] [W::hts_idx_load3] The index file is older than the data file: 1136_5WF-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.baiThe index file is older than the data file: 1136_5WF-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1136_5WF-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5WF-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: 69866802 total, 51965 skipped (flags/unmapped)
Fragments: 34996069 total (34788553 tlen-paired, 2148 hash-paired, 305 singletons, 10523 discordant, 194540 orphans, 8772 too large [>5000 bp], 10194418 duplicates)
Reads: 75563168 total, 46157 skipped (flags/unmapped)
Fragments: 37856159 total (37612595 tlen-paired, 3711 hash-paired, 242 singletons, 9762 discordant, 229849 orphans, 17392 too large [>5000 bp], 11169067 duplicates)
Reads: 75509316 total, 43464 skipped (flags/unmapped)
Fragments: 37825722 total (37616468 tlen-paired, 2651 hash-paired, 329 singletons, 7487 discordant, 198787 orphans, 6762 too large [>5000 bp], 10848566 duplicates)
Reads: 83250537 total, 77671 skipped (flags/unmapped)
Fragments: 41763218 total (41209075 tlen-paired, 2131 hash-paired, 370 singletons, 107304 discordant, 444338 orphans, 45569 too large [>5000 bp], 12340611 duplicates)