Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_BJXJ-N1-BDNA-1_A23TY7KLT4_1/1241_BJXJ-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c9/81f6743e78f856cd5ad0c9df4db713/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_BJXJ-N1-BDNA-1_A23TY7KLT4_1/1241_BJXJ-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam
  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/c9/81f6743e78f856cd5ad0c9df4db713/.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_BJXJ-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BJXJ-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BJXJ-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BJXJ-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: 61744034 total, 46704 skipped (flags/unmapped)
Fragments: 30931810 total (30737726 tlen-paired, 3416 hash-paired, 299 singletons, 9220 discordant, 181149 orphans, 7579 too large [>5000 bp], 10159875 duplicates)
Reads: 65227456 total, 37742 skipped (flags/unmapped)
Fragments: 32681513 total (32487795 tlen-paired, 1685 hash-paired, 276 singletons, 6359 discordant, 185398 orphans, 6181 too large [>5000 bp], 10511123 duplicates)
Reads: 72094824 total, 65906 skipped (flags/unmapped)
Fragments: 36187446 total (35653696 tlen-paired, 1544 hash-paired, 326 singletons, 101216 discordant, 430664 orphans, 42508 too large [>5000 bp], 11927061 duplicates)
Reads: 72128115 total, 40600 skipped (flags/unmapped)
Fragments: 36140738 total (35910662 tlen-paired, 2605 hash-paired, 235 singletons, 9600 discordant, 217636 orphans, 11955 too large [>5000 bp], 11903777 duplicates)