Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8d/3aa8cb5b8b3ccbbf678e2611bf6bf8/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_PD2-N1-BDNA-1_A23TY7KLT4_1/1241_PD2-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
  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/8d/3aa8cb5b8b3ccbbf678e2611bf6bf8/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_PD2-N1-BDNA-1_A23TY7KLT4_1/1241_PD2-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam
==> 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_PD2-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_PD2-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_PD2-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_PD2-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: 69865935 total, 47378 skipped (flags/unmapped)
Fragments: 35002376 total (34787056 tlen-paired, 2270 hash-paired, 347 singletons, 10907 discordant, 201796 orphans, 7974 too large [>5000 bp], 11837632 duplicates)
Reads: 74880260 total, 39488 skipped (flags/unmapped)
Fragments: 37516109 total (37299883 tlen-paired, 2646 hash-paired, 355 singletons, 7516 discordant, 205709 orphans, 7309 too large [>5000 bp], 12433380 duplicates)
Reads: 74338958 total, 42796 skipped (flags/unmapped)
Fragments: 37243494 total (37001011 tlen-paired, 3744 hash-paired, 237 singletons, 9411 discordant, 229091 orphans, 19251 too large [>5000 bp], 12647815 duplicates)
Reads: 81633764 total, 71239 skipped (flags/unmapped)
Fragments: 40964611 total (40392420 tlen-paired, 1870 hash-paired, 314 singletons, 110246 discordant, 459761 orphans, 46689 too large [>5000 bp], 13944447 duplicates)