Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_XRA-N1-BDNA-1_A23TY7KLT4_1/1241_XRA-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/60/d5fbdc306e6cf505b4f6ae11b47c68/.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/60/d5fbdc306e6cf505b4f6ae11b47c68/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_XRA-N1-BDNA-1_A23TY7KLT4_1/1241_XRA-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_XRA-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1241_XRA-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.baiThe index file is older than the data file: 1241_XRA-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1241_XRA-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: 86482484 total, 64631 skipped (flags/unmapped)
Fragments: 43302168 total (43077249 tlen-paired, 3738 hash-paired, 366 singletons, 13366 discordant, 207449 orphans, 10666 too large [>5000 bp], 15111492 duplicates)
Reads: 92142013 total, 52808 skipped (flags/unmapped)
Fragments: 46140852 total (45917953 tlen-paired, 3684 hash-paired, 382 singletons, 9508 discordant, 209325 orphans, 8604 too large [>5000 bp], 15828058 duplicates)
Reads: 101131868 total, 90328 skipped (flags/unmapped)
Fragments: 50700313 total (50149811 tlen-paired, 3380 hash-paired, 328 singletons, 101172 discordant, 445622 orphans, 43432 too large [>5000 bp], 17813625 duplicates)
Reads: 100624507 total, 58988 skipped (flags/unmapped)
Fragments: 50392463 total (50124315 tlen-paired, 3099 hash-paired, 287 singletons, 14064 discordant, 250698 orphans, 15789 too large [>5000 bp], 17653903 duplicates)