Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_738-N1-BDNA-1_A23TY7KLT4_1/1241_738-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/68/79736d0c58291521bbf7afdc1fd50a/.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/68/79736d0c58291521bbf7afdc1fd50a/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_738-N1-BDNA-1_A23TY7KLT4_1/1241_738-N1-BDNA-1_A23TY7KLT4_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: 1241_738-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_738-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_738-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_738-N1-BDNA-1_A23TY7KLT4_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: 87739285 total, 61461 skipped (flags/unmapped)
Fragments: 43966606 total (43672844 tlen-paired, 2670 hash-paired, 462 singletons, 13880 discordant, 276750 orphans, 10912 too large [>5000 bp], 15774047 duplicates)
Reads: 93677498 total, 51354 skipped (flags/unmapped)
Fragments: 46946617 total (46649028 tlen-paired, 2116 hash-paired, 451 singletons, 10091 discordant, 284931 orphans, 9146 too large [>5000 bp], 16523713 duplicates)
Reads: 93116045 total, 55372 skipped (flags/unmapped)
Fragments: 46667365 total (46320148 tlen-paired, 5358 hash-paired, 310 singletons, 12182 discordant, 329367 orphans, 27810 too large [>5000 bp], 16808120 duplicates)
Reads: 103263396 total, 93786 skipped (flags/unmapped)
Fragments: 51841770 total (51030284 tlen-paired, 3711 hash-paired, 402 singletons, 157713 discordant, 649660 orphans, 68066 too large [>5000 bp], 18671100 duplicates)