Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b7/0a9facddbbcaf7b179dce79135a317/.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/b7/0a9facddbbcaf7b179dce79135a317/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_2TX-N1-BDNA-1_A23KFG7LT4_1/1136_2TX-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_2TX-N1-BDNA-1_A23KFG7LT4_1/1136_2TX-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam
==> 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: 1136_2TX-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2TX-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2TX-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2TX-N1-BDNA-1_A23KFG7LT4_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: 60280499 total, 45823 skipped (flags/unmapped)
Fragments: 30321268 total (29881418 tlen-paired, 3021 hash-paired, 284 singletons, 10777 discordant, 425768 orphans, 9096 too large [>5000 bp], 10812815 duplicates)
Reads: 64128606 total, 40394 skipped (flags/unmapped)
Fragments: 32258089 total (31798717 tlen-paired, 2983 hash-paired, 351 singletons, 7837 discordant, 448201 orphans, 10293 too large [>5000 bp], 11182810 duplicates)
Reads: 69993254 total, 41395 skipped (flags/unmapped)
Fragments: 35214237 total (34694799 tlen-paired, 3374 hash-paired, 309 singletons, 11359 discordant, 504396 orphans, 14045 too large [>5000 bp], 12560649 duplicates)
Reads: 71377405 total, 70762 skipped (flags/unmapped)
Fragments: 36130603 total (34637221 tlen-paired, 1920 hash-paired, 359 singletons, 293165 discordant, 1197938 orphans, 121867 too large [>5000 bp], 12791770 duplicates)