Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_21K-N1-BDNA-1_A23TY7KLT4_1/1241_21K-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_21K-N1-BDNA-1_A23TY7KLT4_1/1241_21K-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f1/a42bf31f29988b7106a2c8ea9fb878/.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/f1/a42bf31f29988b7106a2c8ea9fb878/.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_21K-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_21K-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_21K-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
The index file is older than the data file: 1241_21K-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: 91344168 total, 65589 skipped (flags/unmapped)
Fragments: 45778966 total (45453613 tlen-paired, 4005 hash-paired, 397 singletons, 16849 discordant, 304102 orphans, 12573 too large [>5000 bp], 16185307 duplicates)
Reads: 97005708 total, 57101 skipped (flags/unmapped)
Fragments: 48621881 total (48256617 tlen-paired, 5649 hash-paired, 305 singletons, 14536 discordant, 344774 orphans, 24962 too large [>5000 bp], 17357916 duplicates)
Reads: 98974018 total, 55262 skipped (flags/unmapped)
Fragments: 49602697 total (49276904 tlen-paired, 4486 hash-paired, 429 singletons, 11815 discordant, 309063 orphans, 11427 too large [>5000 bp], 17275165 duplicates)
Reads: 106965257 total, 94547 skipped (flags/unmapped)
Fragments: 53710560 total (52852123 tlen-paired, 3939 hash-paired, 403 singletons, 164286 discordant, 689809 orphans, 69901 too large [>5000 bp], 19180231 duplicates)