Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/57/9ee321e914b65c670a8c327fe14776/.command.sh
  Downloading: s3://ai-pipelines-experiment/chnobles/ref_data/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/57/9ee321e914b65c670a8c327fe14776/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260318_LH00519_0070_B23KFCWLT4__d7a6b981--20260320-092016/alignments/recalibrated/1029_11H-T1-TDNA-1_B23KFCWLT4_1/1029_11H-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260318_LH00519_0070_B23KFCWLT4__d7a6b981--20260320-092016/alignments/recalibrated/1029_11H-T1-TDNA-1_B23KFCWLT4_1/1029_11H-T1-TDNA-1_B23KFCWLT4_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_11H-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_11H-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.baiThe index file is older than the data file: 1029_11H-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1029_11H-T1-TDNA-1_B23KFCWLT4_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: 348335284 total, 1066490 skipped (flags/unmapped)
Fragments: 174562588 total (172300221 tlen-paired, 75262 hash-paired, 1970 singletons, 109853 discordant, 2075282 orphans, 110435 too large [>5000 bp], 109509317 duplicates)
Reads: 393481623 total, 1634905 skipped (flags/unmapped)
Fragments: 197182015 total (193837579 tlen-paired, 111531 hash-paired, 1876 singletons, 401685 discordant, 2829344 orphans, 156954 too large [>5000 bp], 122721619 duplicates)
Reads: 409028754 total, 1468501 skipped (flags/unmapped)
Fragments: 205008522 total (201731532 tlen-paired, 113613 hash-paired, 1727 singletons, 302140 discordant, 2859510 orphans, 202223 too large [>5000 bp], 130477054 duplicates)
Reads: 414747174 total, 1597055 skipped (flags/unmapped)
Fragments: 208109604 total (203719454 tlen-paired, 106427 hash-paired, 2071 singletons, 690630 discordant, 3591022 orphans, 262002 too large [>5000 bp], 132302117 duplicates)