Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a9/82125462a885d0e1a3783bf7c9ceb9/.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/a9/82125462a885d0e1a3783bf7c9ceb9/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_5Z7-N1-BDNA-1_A23TY7KLT4_1/1241_5Z7-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_5Z7-N1-BDNA-1_A23TY7KLT4_1/1241_5Z7-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_5Z7-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_5Z7-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_5Z7-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_5Z7-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: 69918698 total, 58073 skipped (flags/unmapped)
Fragments: 35045201 total (34780940 tlen-paired, 3075 hash-paired, 266 singletons, 13049 discordant, 247871 orphans, 9180 too large [>5000 bp], 11353778 duplicates)
Reads: 74408913 total, 50993 skipped (flags/unmapped)
Fragments: 37303744 total (36998755 tlen-paired, 2892 hash-paired, 218 singletons, 12137 discordant, 289742 orphans, 20196 too large [>5000 bp], 12153572 duplicates)
Reads: 75491231 total, 49287 skipped (flags/unmapped)
Fragments: 37841011 total (37571146 tlen-paired, 3143 hash-paired, 386 singletons, 9520 discordant, 256816 orphans, 8562 too large [>5000 bp], 12019567 duplicates)
Reads: 81904511 total, 80724 skipped (flags/unmapped)
Fragments: 41142460 total (40427874 tlen-paired, 3459 hash-paired, 366 singletons, 137732 discordant, 573029 orphans, 56131 too large [>5000 bp], 13436122 duplicates)