Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/55f0ffbf6da4f440cfc8ec6f2cfd00/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/659_ciZ-N1-BDNA-1_B23KFG5LT4_1/659_ciZ-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
  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/a0/55f0ffbf6da4f440cfc8ec6f2cfd00/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/659_ciZ-N1-BDNA-1_B23KFG5LT4_1/659_ciZ-N1-BDNA-1_B23KFG5LT4_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: 659_ciZ-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 659_ciZ-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_ciZ-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_ciZ-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: 79535823 total, 63157 skipped (flags/unmapped)
Fragments: 39871531 total (39557179 tlen-paired, 3691 hash-paired, 321 singletons, 19669 discordant, 290671 orphans, 10298 too large [>5000 bp], 17295461 duplicates)
Reads: 87059078 total, 55911 skipped (flags/unmapped)
Fragments: 43646231 total (43317135 tlen-paired, 3914 hash-paired, 308 singletons, 17243 discordant, 307631 orphans, 9322 too large [>5000 bp], 19067975 duplicates)
Reads: 86270289 total, 52785 skipped (flags/unmapped)
Fragments: 43244713 total (42933272 tlen-paired, 3353 hash-paired, 369 singletons, 13910 discordant, 293809 orphans, 11128 too large [>5000 bp], 18286580 duplicates)
Reads: 96445722 total, 87868 skipped (flags/unmapped)
Fragments: 48427866 total (47661852 tlen-paired, 2861 hash-paired, 333 singletons, 146297 discordant, 616523 orphans, 59489 too large [>5000 bp], 21212120 duplicates)