Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ed/302ca7aa2e37201a6f4a8d2daea917/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/659_dz-N1-BDNA-1_A23TNVNLT4_1/659_dz-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
  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/ed/302ca7aa2e37201a6f4a8d2daea917/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/659_dz-N1-BDNA-1_A23TNVNLT4_1/659_dz-N1-BDNA-1_A23TNVNLT4_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: 659_dz-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_dz-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_dz-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_dz-N1-BDNA-1_A23TNVNLT4_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: 105672865 total, 67011 skipped (flags/unmapped)
Fragments: 52945377 total (52617269 tlen-paired, 4835 hash-paired, 532 singletons, 15741 discordant, 307000 orphans, 11316 too large [>5000 bp], 18624411 duplicates)
Reads: 113503818 total, 61595 skipped (flags/unmapped)
Fragments: 56866811 total (56535224 tlen-paired, 6148 hash-paired, 561 singletons, 10814 discordant, 314064 orphans, 11613 too large [>5000 bp], 19748957 duplicates)
Reads: 123032808 total, 62422 skipped (flags/unmapped)
Fragments: 61647795 total (61251232 tlen-paired, 7105 hash-paired, 456 singletons, 16792 discordant, 372210 orphans, 23731 too large [>5000 bp], 21906092 duplicates)
Reads: 125136097 total, 110860 skipped (flags/unmapped)
Fragments: 62808754 total (61890157 tlen-paired, 6083 hash-paired, 504 singletons, 174633 discordant, 737377 orphans, 72805 too large [>5000 bp], 22329807 duplicates)