Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_CZM-N1-BDNA-1_A23TY7KLT4_1/1241_CZM-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1d/7a6c57929c359e375ed3568351bac4/.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/1d/7a6c57929c359e375ed3568351bac4/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_CZM-N1-BDNA-1_A23TY7KLT4_1/1241_CZM-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_CZM-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_CZM-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_CZM-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_CZM-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: 82624676 total, 61673 skipped (flags/unmapped)
Fragments: 41379479 total (41148674 tlen-paired, 3096 hash-paired, 322 singletons, 11508 discordant, 215879 orphans, 10123 too large [>5000 bp], 14088954 duplicates)
Reads: 87984411 total, 59638 skipped (flags/unmapped)
Fragments: 44070641 total (43794319 tlen-paired, 6227 hash-paired, 283 singletons, 10132 discordant, 259680 orphans, 21727 too large [>5000 bp], 15078369 duplicates)
Reads: 90041244 total, 50696 skipped (flags/unmapped)
Fragments: 45099029 total (44859540 tlen-paired, 3425 hash-paired, 411 singletons, 8330 discordant, 227323 orphans, 10112 too large [>5000 bp], 15063290 duplicates)
Reads: 96872683 total, 96262 skipped (flags/unmapped)
Fragments: 48590564 total (47962620 tlen-paired, 3780 hash-paired, 366 singletons, 120899 discordant, 502899 orphans, 49279 too large [>5000 bp], 16654220 duplicates)