Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7c/ff85bea4211d54ca910cfc5b918574/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_B0RK-N1-BDNA-1_A23TY7KLT4_1/1241_B0RK-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/7c/ff85bea4211d54ca910cfc5b918574/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_B0RK-N1-BDNA-1_A23TY7KLT4_1/1241_B0RK-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] [W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1241_B0RK-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
The index file is older than the data file: 1241_B0RK-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
The index file is older than the data file: 1241_B0RK-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_B0RK-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: 75294849 total, 60369 skipped (flags/unmapped)
Fragments: 37736482 total (37466508 tlen-paired, 4211 hash-paired, 276 singletons, 11139 discordant, 254348 orphans, 8070 too large [>5000 bp], 13476741 duplicates)
Reads: 80656083 total, 51268 skipped (flags/unmapped)
Fragments: 40428885 total (40147767 tlen-paired, 3100 hash-paired, 391 singletons, 8285 discordant, 269342 orphans, 8389 too large [>5000 bp], 14139587 duplicates)
Reads: 80239348 total, 54798 skipped (flags/unmapped)
Fragments: 40219797 total (39903837 tlen-paired, 3439 hash-paired, 230 singletons, 10089 discordant, 302202 orphans, 23694 too large [>5000 bp], 14407244 duplicates)
Reads: 88785293 total, 88576 skipped (flags/unmapped)
Fragments: 44596976 total (43810715 tlen-paired, 4060 hash-paired, 309 singletons, 154346 discordant, 627546 orphans, 65310 too large [>5000 bp], 15958777 duplicates)