Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b4/eea73fdc2c505bdaa35eea481f89d5/.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/b4/eea73fdc2c505bdaa35eea481f89d5/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1136_7VY-N1-BDNA-1_B23L5TMLT4_1/1136_7VY-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1136_7VY-N1-BDNA-1_B23L5TMLT4_1/1136_7VY-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] [W::hts_idx_load3] The index file is older than the data file: 1136_7VY-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
The index file is older than the data file: 1136_7VY-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1136_7VY-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.baiThe index file is older than the data file: 1136_7VY-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: 81961515 total, 54630 skipped (flags/unmapped)
Fragments: 41144846 total (40726709 tlen-paired, 3954 hash-paired, 579 singletons, 9196 discordant, 404408 orphans, 11090 too large [>5000 bp], 15108324 duplicates)
Reads: 89263312 total, 57569 skipped (flags/unmapped)
Fragments: 44816075 total (44327977 tlen-paired, 4743 hash-paired, 463 singletons, 13574 discordant, 469318 orphans, 21687 too large [>5000 bp], 16773374 duplicates)
Reads: 76740897 total, 62324 skipped (flags/unmapped)
Fragments: 38517767 total (38116793 tlen-paired, 3604 hash-paired, 424 singletons, 13395 discordant, 383551 orphans, 13507 too large [>5000 bp], 14385846 duplicates)
Reads: 90534333 total, 96354 skipped (flags/unmapped)
Fragments: 45631350 total (44349316 tlen-paired, 2629 hash-paired, 449 singletons, 250150 discordant, 1028806 orphans, 102267 too large [>5000 bp], 17015061 duplicates)