Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/01/dba443a7babba825ff1445e79dbedc/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_5SM-N1-BDNA-1_A23NMNVLT4_1/1136_5SM-N1-BDNA-1_A23NMNVLT4_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/01/dba443a7babba825ff1445e79dbedc/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_5SM-N1-BDNA-1_A23NMNVLT4_1/1136_5SM-N1-BDNA-1_A23NMNVLT4_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: 1136_5SM-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5SM-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5SM-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5SM-N1-BDNA-1_A23NMNVLT4_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: 82058102 total, 55004 skipped (flags/unmapped)
Fragments: 41102491 total (40870585 tlen-paired, 3507 hash-paired, 317 singletons, 11951 discordant, 216131 orphans, 7282 too large [>5000 bp], 10177240 duplicates)
Reads: 88938834 total, 46609 skipped (flags/unmapped)
Fragments: 44547308 total (44315318 tlen-paired, 3673 hash-paired, 434 singletons, 8266 discordant, 219617 orphans, 8830 too large [>5000 bp], 10921261 duplicates)
Reads: 97458372 total, 78364 skipped (flags/unmapped)
Fragments: 48891046 total (48268389 tlen-paired, 2988 hash-paired, 383 singletons, 117087 discordant, 502199 orphans, 50249 too large [>5000 bp], 12362647 duplicates)
Reads: 96444311 total, 55184 skipped (flags/unmapped)
Fragments: 48307814 total (48016342 tlen-paired, 4810 hash-paired, 299 singletons, 12295 discordant, 274068 orphans, 23933 too large [>5000 bp], 12199493 duplicates)