Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a6/051304be0a4e87846836186487f20b/.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/a6/051304be0a4e87846836186487f20b/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_3TP-N1-BDNA-1_B23L5TMLT4_1/1029_3TP-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_3TP-N1-BDNA-1_B23L5TMLT4_1/1029_3TP-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] [W::hts_idx_load3] The index file is older than the data file: 1029_3TP-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
The index file is older than the data file: 1029_3TP-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_3TP-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_3TP-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: 76712212 total, 60416 skipped (flags/unmapped)
Fragments: 38472451 total (38142308 tlen-paired, 4465 hash-paired, 419 singletons, 13338 discordant, 311921 orphans, 9617 too large [>5000 bp], 12751413 duplicates)
Reads: 81056103 total, 54011 skipped (flags/unmapped)
Fragments: 40655406 total (40288939 tlen-paired, 4940 hash-paired, 443 singletons, 11909 discordant, 349175 orphans, 20449 too large [>5000 bp], 13503407 duplicates)
Reads: 82501092 total, 51474 skipped (flags/unmapped)
Fragments: 41375575 total (41043064 tlen-paired, 3524 hash-paired, 550 singletons, 9227 discordant, 319210 orphans, 9114 too large [>5000 bp], 13457834 duplicates)
Reads: 89479297 total, 86358 skipped (flags/unmapped)
Fragments: 44998275 total (44049773 tlen-paired, 4794 hash-paired, 501 singletons, 184437 discordant, 758770 orphans, 77830 too large [>5000 bp], 14920522 duplicates)