Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/69/b4e6807db5e926f919a9386bb15e0b/.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/69/b4e6807db5e926f919a9386bb15e0b/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1029_6A7-N1-BDNA-1_A23NLN3LT4_1/1029_6A7-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1029_6A7-N1-BDNA-1_A23NLN3LT4_1/1029_6A7-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
==> 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: 1029_6A7-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1029_6A7-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] 
[W::hts_idx_load3] The index file is older than the data file: 1029_6A7-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1029_6A7-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: 57242122 total, 41461 skipped (flags/unmapped)
Fragments: 28683360 total (28488105 tlen-paired, 2440 hash-paired, 309 singletons, 9388 discordant, 183118 orphans, 8684 too large [>5000 bp], 8686976 duplicates)
Reads: 61969214 total, 35118 skipped (flags/unmapped)
Fragments: 31054743 total (30849115 tlen-paired, 3304 hash-paired, 274 singletons, 8124 discordant, 193926 orphans, 9405 too large [>5000 bp], 9449020 duplicates)
Reads: 62296769 total, 33429 skipped (flags/unmapped)
Fragments: 31221660 total (31020092 tlen-paired, 1601 hash-paired, 272 singletons, 6681 discordant, 193014 orphans, 6653 too large [>5000 bp], 9265502 duplicates)
Reads: 67845197 total, 62573 skipped (flags/unmapped)
Fragments: 34065261 total (33522154 tlen-paired, 3206 hash-paired, 256 singletons, 105621 discordant, 434024 orphans, 43191 too large [>5000 bp], 10355471 duplicates)