Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1029_G6L-N1-BDNA-1_A23NLN3LT4_1/1029_G6L-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/e3b50c62706d1a169b4b4f870093b0/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1029_G6L-N1-BDNA-1_A23NLN3LT4_1/1029_G6L-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam
  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/17/e3b50c62706d1a169b4b4f870093b0/.command.run
==> 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: 1029_G6L-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_G6L-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_G6L-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_G6L-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: 79060130 total, 83274 skipped (flags/unmapped)
Fragments: 39594865 total (39328420 tlen-paired, 4765 hash-paired, 444 singletons, 17108 discordant, 244128 orphans, 15849 too large [>5000 bp], 13438031 duplicates)
Reads: 89202581 total, 71268 skipped (flags/unmapped)
Fragments: 44687356 total (44397839 tlen-paired, 5247 hash-paired, 348 singletons, 13579 discordant, 270343 orphans, 13646 too large [>5000 bp], 14950729 duplicates)
Reads: 85791501 total, 71332 skipped (flags/unmapped)
Fragments: 42981330 total (42672316 tlen-paired, 3809 hash-paired, 335 singletons, 15032 discordant, 289838 orphans, 23841 too large [>5000 bp], 14548019 duplicates)
Reads: 93470803 total, 107202 skipped (flags/unmapped)
Fragments: 46895600 total (46251789 tlen-paired, 4305 hash-paired, 394 singletons, 121779 discordant, 517333 orphans, 45064 too large [>5000 bp], 15914370 duplicates)