Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/35/40c690e5eb004415f2e288f0723075/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_2QN-N1-BDNA-1_A23NMNVLT4_1/1136_2QN-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/35/40c690e5eb004415f2e288f0723075/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_2QN-N1-BDNA-1_A23NMNVLT4_1/1136_2QN-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_2QN-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2QN-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2QN-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2QN-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: 55621427 total, 43046 skipped (flags/unmapped)
Fragments: 27875866 total (27681060 tlen-paired, 2425 hash-paired, 257 singletons, 9542 discordant, 182582 orphans, 4744 too large [>5000 bp], 6512940 duplicates)
Reads: 60214974 total, 36054 skipped (flags/unmapped)
Fragments: 30176664 total (29980441 tlen-paired, 2700 hash-paired, 264 singletons, 6635 discordant, 186624 orphans, 6240 too large [>5000 bp], 6894515 duplicates)
Reads: 66018592 total, 60430 skipped (flags/unmapped)
Fragments: 33153955 total (32613666 tlen-paired, 3156 hash-paired, 267 singletons, 102581 discordant, 434285 orphans, 42402 too large [>5000 bp], 7858338 duplicates)
Reads: 65459028 total, 39905 skipped (flags/unmapped)
Fragments: 32808690 total (32570914 tlen-paired, 3342 hash-paired, 202 singletons, 9913 discordant, 224319 orphans, 13132 too large [>5000 bp], 7763384 duplicates)