Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1136_4M9-N1-BDNA-1_B23KFG5LT4_1/1136_4M9-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1136_4M9-N1-BDNA-1_B23KFG5LT4_1/1136_4M9-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4e/15fddcbef9d62dc91bdde7338d9c6b/.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/4e/15fddcbef9d62dc91bdde7338d9c6b/.command.run
==> 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_4M9-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
The index file is older than the data file: 1136_4M9-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4M9-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4M9-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: 70793393 total, 54650 skipped (flags/unmapped)
Fragments: 35504482 total (35198498 tlen-paired, 2423 hash-paired, 297 singletons, 13164 discordant, 290100 orphans, 10088 too large [>5000 bp], 15920977 duplicates)
Reads: 75745039 total, 44577 skipped (flags/unmapped)
Fragments: 37996410 total (37676939 tlen-paired, 1811 hash-paired, 369 singletons, 9302 discordant, 307989 orphans, 8000 too large [>5000 bp], 16680587 duplicates)
Reads: 85653823 total, 85495 skipped (flags/unmapped)
Fragments: 43082257 total (42161351 tlen-paired, 2558 hash-paired, 349 singletons, 178962 discordant, 739037 orphans, 71600 too large [>5000 bp], 19348047 duplicates)
Reads: 85070857 total, 53587 skipped (flags/unmapped)
Fragments: 42667548 total (42280946 tlen-paired, 3594 hash-paired, 349 singletons, 13710 discordant, 368949 orphans, 25736 too large [>5000 bp], 19185343 duplicates)