Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260318_LH00166_0269_A23H3W5LT3__d7a6b981--20260320-054016/alignments/recalibrated/1136_4VV-N1-BDNA-1_A23H3W5LT3_1/1136_4VV-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4a/816e5c9d8fc5e447557341d983e533/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260318_LH00166_0269_A23H3W5LT3__d7a6b981--20260320-054016/alignments/recalibrated/1136_4VV-N1-BDNA-1_A23H3W5LT3_1/1136_4VV-N1-BDNA-1_A23H3W5LT3_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/4a/816e5c9d8fc5e447557341d983e533/.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: 1136_4VV-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4VV-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4VV-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4VV-N1-BDNA-1_A23H3W5LT3_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: 69065975 total, 47600 skipped (flags/unmapped)
Fragments: 34671259 total (34319483 tlen-paired, 8562 hash-paired, 4395 singletons, 4743 discordant, 334076 orphans, 7164 too large [>5000 bp], 6521009 duplicates)
Reads: 63215930 total, 55971 skipped (flags/unmapped)
Fragments: 31722296 total (31406248 tlen-paired, 8678 hash-paired, 4250 singletons, 6337 discordant, 296783 orphans, 8200 too large [>5000 bp], 5952652 duplicates)
Reads: 69879514 total, 51455 skipped (flags/unmapped)
Fragments: 35076268 total (34708971 tlen-paired, 10602 hash-paired, 4592 singletons, 6372 discordant, 345731 orphans, 12923 too large [>5000 bp], 6552165 duplicates)
Reads: 71420527 total, 81362 skipped (flags/unmapped)
Fragments: 36020902 total (34931992 tlen-paired, 7972 hash-paired, 4598 singletons, 211447 discordant, 864893 orphans, 83426 too large [>5000 bp], 6671995 duplicates)