Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_2OL-N1-BDNA-1_A23KFG7LT4_1/1136_2OL-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ee/a51872b4aa8360c1ee41f08798438a/.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/ee/a51872b4aa8360c1ee41f08798438a/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_2OL-N1-BDNA-1_A23KFG7LT4_1/1136_2OL-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_2OL-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_2OL-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2OL-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2OL-N1-BDNA-1_A23KFG7LT4_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: 67363172 total, 47924 skipped (flags/unmapped)
Fragments: 33836962 total (33444298 tlen-paired, 2493 hash-paired, 364 singletons, 12367 discordant, 377440 orphans, 9564 too large [>5000 bp], 11428251 duplicates)
Reads: 71594286 total, 41344 skipped (flags/unmapped)
Fragments: 35964781 total (35560013 tlen-paired, 2132 hash-paired, 399 singletons, 8298 discordant, 393939 orphans, 8859 too large [>5000 bp], 11811700 duplicates)
Reads: 78142365 total, 44969 skipped (flags/unmapped)
Fragments: 39258242 total (38790911 tlen-paired, 2937 hash-paired, 360 singletons, 12060 discordant, 451974 orphans, 16623 too large [>5000 bp], 13269068 duplicates)
Reads: 79550755 total, 71408 skipped (flags/unmapped)
Fragments: 40146710 total (38872109 tlen-paired, 2995 hash-paired, 419 singletons, 249271 discordant, 1021916 orphans, 104131 too large [>5000 bp], 13535896 duplicates)