Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_5UV-N1-BDNA-1_A23NMNVLT4_1/1136_5UV-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/27/d3467e924b3520176d2b7da2aead93/.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/27/d3467e924b3520176d2b7da2aead93/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_5UV-N1-BDNA-1_A23NMNVLT4_1/1136_5UV-N1-BDNA-1_A23NMNVLT4_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_5UV-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5UV-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5UV-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5UV-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: 45115036 total, 28549 skipped (flags/unmapped)
Fragments: 22599845 total (22470614 tlen-paired, 1460 hash-paired, 165 singletons, 5652 discordant, 121954 orphans, 4458 too large [>5000 bp], 5217013 duplicates)
Reads: 48504994 total, 25419 skipped (flags/unmapped)
Fragments: 24302108 total (24150837 tlen-paired, 1709 hash-paired, 172 singletons, 5079 discordant, 144311 orphans, 9921 too large [>5000 bp], 5668451 duplicates)
Reads: 53555609 total, 44896 skipped (flags/unmapped)
Fragments: 26874901 total (26501128 tlen-paired, 1327 hash-paired, 220 singletons, 73647 discordant, 298579 orphans, 29855 too large [>5000 bp], 6274789 duplicates)
Reads: 49325779 total, 24150 skipped (flags/unmapped)
Fragments: 24711123 total (24576184 tlen-paired, 1766 hash-paired, 211 singletons, 4106 discordant, 128856 orphans, 4225 too large [>5000 bp], 5576731 duplicates)