Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1136_2RU-N1-BDNA-1_B23KFG5LT4_1/1136_2RU-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/41/564dc32fdd41506dad5dded2c35af1/.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/41/564dc32fdd41506dad5dded2c35af1/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1136_2RU-N1-BDNA-1_B23KFG5LT4_1/1136_2RU-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam
==> 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_2RU-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2RU-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1136_2RU-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2RU-N1-BDNA-1_B23KFG5LT4_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: 62277275 total, 44877 skipped (flags/unmapped)
Fragments: 31202716 total (30999570 tlen-paired, 2181 hash-paired, 224 singletons, 10777 discordant, 189964 orphans, 8577 too large [>5000 bp], 11677572 duplicates)
Reads: 66040457 total, 37678 skipped (flags/unmapped)
Fragments: 33090616 total (32888264 tlen-paired, 2097 hash-paired, 267 singletons, 7330 discordant, 192658 orphans, 7236 too large [>5000 bp], 12033855 duplicates)
Reads: 73119168 total, 65105 skipped (flags/unmapped)
Fragments: 36704922 total (36158833 tlen-paired, 1768 hash-paired, 294 singletons, 102930 discordant, 441097 orphans, 42805 too large [>5000 bp], 13779808 duplicates)
Reads: 72795968 total, 41618 skipped (flags/unmapped)
Fragments: 36480038 total (36233187 tlen-paired, 3416 hash-paired, 217 singletons, 10919 discordant, 232299 orphans, 13395 too large [>5000 bp], 13649842 duplicates)