Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cb/2b9d207469637a1b74b1a31ac274e7/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_VMF-N1-BDNA-1_B23L5TMLT4_1/1029_VMF-N1-BDNA-1_B23L5TMLT4_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/cb/2b9d207469637a1b74b1a31ac274e7/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_VMF-N1-BDNA-1_B23L5TMLT4_1/1029_VMF-N1-BDNA-1_B23L5TMLT4_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: 1029_VMF-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_VMF-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_VMF-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_VMF-N1-BDNA-1_B23L5TMLT4_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: 109778367 total, 68786 skipped (flags/unmapped)
Fragments: 55132426 total (54501099 tlen-paired, 5847 hash-paired, 560 singletons, 16459 discordant, 608461 orphans, 26875 too large [>5000 bp], 20911120 duplicates)
Reads: 104131749 total, 76118 skipped (flags/unmapped)
Fragments: 52283822 total (51715846 tlen-paired, 5236 hash-paired, 625 singletons, 18761 discordant, 543354 orphans, 15983 too large [>5000 bp], 19739224 duplicates)
Reads: 111857801 total, 65933 skipped (flags/unmapped)
Fragments: 56171524 total (55574873 tlen-paired, 3979 hash-paired, 767 singletons, 13304 discordant, 578601 orphans, 14094 too large [>5000 bp], 20765576 duplicates)
Reads: 122285190 total, 121142 skipped (flags/unmapped)
Fragments: 61648766 total (59864380 tlen-paired, 5234 hash-paired, 680 singletons, 356028 discordant, 1422444 orphans, 144820 too large [>5000 bp], 23264908 duplicates)