Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1029_SGO-N1-BDNA-1_A23MHW3LT4_1/1029_SGO-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e0/1b56bfb8a740b8e6936fe68c252be6/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1029_SGO-N1-BDNA-1_A23MHW3LT4_1/1029_SGO-N1-BDNA-1_A23MHW3LT4_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/e0/1b56bfb8a740b8e6936fe68c252be6/.command.run
==> 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_SGO-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_SGO-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_SGO-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_SGO-N1-BDNA-1_A23MHW3LT4_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: 68056144 total, 60252 skipped (flags/unmapped)
Fragments: 34277456 total (33684168 tlen-paired, 3345 hash-paired, 485 singletons, 11333 discordant, 578125 orphans, 9795 too large [>5000 bp], 13574662 duplicates)
Reads: 71903226 total, 50744 skipped (flags/unmapped)
Fragments: 36219813 total (35603489 tlen-paired, 2421 hash-paired, 425 singletons, 7879 discordant, 605599 orphans, 9440 too large [>5000 bp], 13988623 duplicates)
Reads: 79109288 total, 54744 skipped (flags/unmapped)
Fragments: 39854731 total (39144303 tlen-paired, 3573 hash-paired, 396 singletons, 11897 discordant, 694562 orphans, 20020 too large [>5000 bp], 15709624 duplicates)
Reads: 80855912 total, 90047 skipped (flags/unmapped)
Fragments: 41047897 total (38949536 tlen-paired, 2714 hash-paired, 422 singletons, 417732 discordant, 1677493 orphans, 173993 too large [>5000 bp], 16013185 duplicates)