Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1029_XIG-N1-BDNA-1_B23KFG5LT4_1/1029_XIG-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/56/eb2108ab460030c38ebf80d89567da/.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/56/eb2108ab460030c38ebf80d89567da/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1029_XIG-N1-BDNA-1_B23KFG5LT4_1/1029_XIG-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
==> 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: 1029_XIG-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_XIG-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_XIG-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_XIG-N1-BDNA-1_B23KFG5LT4_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: 80402126 total, 62443 skipped (flags/unmapped)
Fragments: 40332395 total (39962973 tlen-paired, 3554 hash-paired, 320 singletons, 17059 discordant, 348489 orphans, 11851 too large [>5000 bp], 17304017 duplicates)
Reads: 85880941 total, 50070 skipped (flags/unmapped)
Fragments: 43086882 total (42709422 tlen-paired, 2192 hash-paired, 411 singletons, 12199 discordant, 362658 orphans, 10088 too large [>5000 bp], 17979710 duplicates)
Reads: 86074897 total, 56506 skipped (flags/unmapped)
Fragments: 43178199 total (42756066 tlen-paired, 6088 hash-paired, 306 singletons, 14996 discordant, 400743 orphans, 31521 too large [>5000 bp], 18514160 duplicates)
Reads: 95323424 total, 91611 skipped (flags/unmapped)
Fragments: 47946856 total (46906981 tlen-paired, 4177 hash-paired, 382 singletons, 204413 discordant, 830903 orphans, 84693 too large [>5000 bp], 20559044 duplicates)