Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_R7Z-N1-BDNA-1_A23TY7KLT4_1/1241_R7Z-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a7/3511d472869e4362cf4135ea0ceee9/.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-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_R7Z-N1-BDNA-1_A23TY7KLT4_1/1241_R7Z-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a7/3511d472869e4362cf4135ea0ceee9/.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_R7Z-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_R7Z-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_R7Z-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_R7Z-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: 88296142 total, 64707 skipped (flags/unmapped)
Fragments: 44216220 total (43975697 tlen-paired, 2837 hash-paired, 334 singletons, 13041 discordant, 224311 orphans, 11820 too large [>5000 bp], 14964387 duplicates)
Reads: 95038438 total, 54825 skipped (flags/unmapped)
Fragments: 47596494 total (47354244 tlen-paired, 4170 hash-paired, 491 singletons, 9169 discordant, 228420 orphans, 9768 too large [>5000 bp], 15769404 duplicates)
Reads: 93651735 total, 57968 skipped (flags/unmapped)
Fragments: 46907187 total (46636058 tlen-paired, 4964 hash-paired, 280 singletons, 11018 discordant, 254867 orphans, 17270 too large [>5000 bp], 15930970 duplicates)
Reads: 103198670 total, 90871 skipped (flags/unmapped)
Fragments: 51754704 total (51129109 tlen-paired, 2593 hash-paired, 335 singletons, 119871 discordant, 502796 orphans, 50761 too large [>5000 bp], 17595459 duplicates)