Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d2/f5fc9831074525c47252211cf90782/.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/d2/f5fc9831074525c47252211cf90782/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1136_13-N1-BDNA-1_B23H2GYLT3_1/1136_13-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1136_13-N1-BDNA-1_B23H2GYLT3_1/1136_13-N1-BDNA-1_B23H2GYLT3_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: 1136_13-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.baiThe index file is older than the data file: 1136_13-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1136_13-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_13-N1-BDNA-1_B23H2GYLT3_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: 71801919 total, 55938 skipped (flags/unmapped)
Fragments: 36026330 total (35680147 tlen-paired, 14798 hash-paired, 6003 singletons, 6000 discordant, 319382 orphans, 9353 too large [>5000 bp], 6673249 duplicates)
Reads: 71006578 total, 64075 skipped (flags/unmapped)
Fragments: 35617967 total (35287167 tlen-paired, 15916 hash-paired, 6122 singletons, 6935 discordant, 301827 orphans, 7259 too large [>5000 bp], 6626592 duplicates)
Reads: 79725077 total, 91299 skipped (flags/unmapped)
Fragments: 40168310 total (39066439 tlen-paired, 16601 hash-paired, 6867 singletons, 215132 discordant, 863271 orphans, 83648 too large [>5000 bp], 7380851 duplicates)
Reads: 78299249 total, 55303 skipped (flags/unmapped)
Fragments: 39291587 total (38914521 tlen-paired, 16136 hash-paired, 6641 singletons, 5098 discordant, 349191 orphans, 8302 too large [>5000 bp], 7289627 duplicates)