Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/82/ea620e7454451811c6958817914d09/.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/82/ea620e7454451811c6958817914d09/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_BY40-N1-BDNA-1_A23TY7KLT4_1/1241_BY40-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_BY40-N1-BDNA-1_A23TY7KLT4_1/1241_BY40-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] [W::hts_idx_load3] The index file is older than the data file: 1241_BY40-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
The index file is older than the data file: 1241_BY40-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BY40-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BY40-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: 86366458 total, 55937 skipped (flags/unmapped)
Fragments: 43254096 total (43030162 tlen-paired, 2577 hash-paired, 350 singletons, 11382 discordant, 209625 orphans, 6152 too large [>5000 bp], 14611726 duplicates)
Reads: 92609194 total, 47426 skipped (flags/unmapped)
Fragments: 46379265 total (46154511 tlen-paired, 2735 hash-paired, 366 singletons, 7885 discordant, 213768 orphans, 8686 too large [>5000 bp], 15435446 duplicates)
Reads: 101311905 total, 87028 skipped (flags/unmapped)
Fragments: 50808605 total (50200985 tlen-paired, 4415 hash-paired, 359 singletons, 113756 discordant, 489090 orphans, 48558 too large [>5000 bp], 17317391 duplicates)
Reads: 100944673 total, 53939 skipped (flags/unmapped)
Fragments: 50552589 total (50278793 tlen-paired, 3260 hash-paired, 297 singletons, 11208 discordant, 259031 orphans, 22442 too large [>5000 bp], 17181505 duplicates)