Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/83/f1da56fea248c7e280d515b528d5a6/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1029_BJVV-N1-BDNA-1_A23NMNVLT4_1/1029_BJVV-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/83/f1da56fea248c7e280d515b528d5a6/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1029_BJVV-N1-BDNA-1_A23NMNVLT4_1/1029_BJVV-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
==> 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_BJVV-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_BJVV-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BJVV-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BJVV-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: 79937427 total, 61763 skipped (flags/unmapped)
Fragments: 40081941 total (39760606 tlen-paired, 3266 hash-paired, 299 singletons, 11015 discordant, 306755 orphans, 9418 too large [>5000 bp], 11804517 duplicates)
Reads: 86097142 total, 54885 skipped (flags/unmapped)
Fragments: 43173686 total (42837033 tlen-paired, 3334 hash-paired, 491 singletons, 8040 discordant, 324788 orphans, 10082 too large [>5000 bp], 12534689 duplicates)
Reads: 95886854 total, 93991 skipped (flags/unmapped)
Fragments: 48226152 total (47195464 tlen-paired, 1506 hash-paired, 437 singletons, 203489 discordant, 825256 orphans, 83126 too large [>5000 bp], 14473109 duplicates)
Reads: 95032253 total, 57098 skipped (flags/unmapped)
Fragments: 47658350 total (47277990 tlen-paired, 3473 hash-paired, 351 singletons, 11454 discordant, 365082 orphans, 11944 too large [>5000 bp], 14360612 duplicates)