Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_VHK-N1-BDNA-1_A23TY7KLT4_1/1241_VHK-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_VHK-N1-BDNA-1_A23TY7KLT4_1/1241_VHK-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/99/f96b8bd93104abb42e65104d7f0504/.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/99/f96b8bd93104abb42e65104d7f0504/.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: 1241_VHK-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_VHK-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_VHK-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_VHK-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: 80358065 total, 60647 skipped (flags/unmapped)
Fragments: 40258504 total (40006962 tlen-paired, 4103 hash-paired, 357 singletons, 10285 discordant, 236797 orphans, 8782 too large [>5000 bp], 14532903 duplicates)
Reads: 85654786 total, 49157 skipped (flags/unmapped)
Fragments: 42919380 total (42656655 tlen-paired, 3796 hash-paired, 427 singletons, 7284 discordant, 251218 orphans, 9257 too large [>5000 bp], 15202963 duplicates)
Reads: 93509660 total, 54355 skipped (flags/unmapped)
Fragments: 46861007 total (46543491 tlen-paired, 3985 hash-paired, 293 singletons, 10750 discordant, 302488 orphans, 18036 too large [>5000 bp], 16928784 duplicates)
Reads: 94549242 total, 87863 skipped (flags/unmapped)
Fragments: 47472865 total (46721434 tlen-paired, 2680 hash-paired, 393 singletons, 144710 discordant, 603648 orphans, 59845 too large [>5000 bp], 17160513 duplicates)