Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6c/906fd9225651343c95381f482ced43/.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/6c/906fd9225651343c95381f482ced43/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_ILG-N1-BDNA-1_B23L5TMLT4_1/1029_ILG-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_ILG-N1-BDNA-1_B23L5TMLT4_1/1029_ILG-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam
==> 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_ILG-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_ILG-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_ILG-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_ILG-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: 111219118 total, 65658 skipped (flags/unmapped)
Fragments: 55829261 total (55276543 tlen-paired, 4125 hash-paired, 706 singletons, 16079 discordant, 531808 orphans, 13726 too large [>5000 bp], 21384226 duplicates)
Reads: 103469744 total, 80354 skipped (flags/unmapped)
Fragments: 51938091 total (51395420 tlen-paired, 5599 hash-paired, 572 singletons, 22938 discordant, 513562 orphans, 13671 too large [>5000 bp], 20175970 duplicates)
Reads: 110100976 total, 70018 skipped (flags/unmapped)
Fragments: 55269527 total (54693384 tlen-paired, 5961 hash-paired, 532 singletons, 19478 discordant, 550172 orphans, 21304 too large [>5000 bp], 21616179 duplicates)
Reads: 121925444 total, 122267 skipped (flags/unmapped)
Fragments: 61405906 total (59833454 tlen-paired, 4434 hash-paired, 646 singletons, 307575 discordant, 1259797 orphans, 125904 too large [>5000 bp], 23906358 duplicates)