Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0a/0b0227dc80a39ce2f250e896af3dd3/.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/0a/0b0227dc80a39ce2f250e896af3dd3/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_5JI-N1-BDNA-1_A23NLN3LT4_1/1136_5JI-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_5JI-N1-BDNA-1_A23NLN3LT4_1/1136_5JI-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

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_5JI-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1136_5JI-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] 
The index file is older than the data file: 1136_5JI-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_5JI-N1-BDNA-1_A23NLN3LT4_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: 79735381 total, 59210 skipped (flags/unmapped)
Fragments: 39968138 total (39665001 tlen-paired, 3145 hash-paired, 334 singletons, 19741 discordant, 279917 orphans, 10073 too large [>5000 bp], 13774947 duplicates)
Reads: 86361817 total, 50489 skipped (flags/unmapped)
Fragments: 43286570 total (42986919 tlen-paired, 2513 hash-paired, 341 singletons, 14084 discordant, 282713 orphans, 10621 too large [>5000 bp], 14698361 duplicates)
Reads: 85771840 total, 55083 skipped (flags/unmapped)
Fragments: 42994248 total (42669194 tlen-paired, 6202 hash-paired, 326 singletons, 16447 discordant, 302079 orphans, 15333 too large [>5000 bp], 14991821 duplicates)
Reads: 94622437 total, 92189 skipped (flags/unmapped)
Fragments: 47499224 total (46780739 tlen-paired, 2991 hash-paired, 364 singletons, 134884 discordant, 580246 orphans, 56205 too large [>5000 bp], 16589776 duplicates)