Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_3LF-N1-BDNA-1_A23TY7KLT4_1/1241_3LF-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/8bd42fd2d03b0027ac5d98d9642803/.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/de/8bd42fd2d03b0027ac5d98d9642803/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_3LF-N1-BDNA-1_A23TY7KLT4_1/1241_3LF-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_3LF-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_3LF-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_3LF-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_3LF-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: 73304537 total, 51821 skipped (flags/unmapped)
Fragments: 36717726 total (36507028 tlen-paired, 2532 hash-paired, 338 singletons, 8940 discordant, 198888 orphans, 8245 too large [>5000 bp], 12897138 duplicates)
Reads: 78975003 total, 45109 skipped (flags/unmapped)
Fragments: 39561711 total (39341188 tlen-paired, 3295 hash-paired, 323 singletons, 6740 discordant, 210165 orphans, 8480 too large [>5000 bp], 13636232 duplicates)
Reads: 78279730 total, 46929 skipped (flags/unmapped)
Fragments: 39216494 total (38975977 tlen-paired, 5111 hash-paired, 273 singletons, 8351 discordant, 226782 orphans, 13434 too large [>5000 bp], 13823523 duplicates)
Reads: 86260796 total, 74346 skipped (flags/unmapped)
Fragments: 43286128 total (42682603 tlen-paired, 2378 hash-paired, 384 singletons, 118211 discordant, 482552 orphans, 48565 too large [>5000 bp], 15264952 duplicates)