Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_7CR-N1-BDNA-1_A23NMNVLT4_1/1136_7CR-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c2/166a52c54c2e4fe0d59d756400a2cb/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_7CR-N1-BDNA-1_A23NMNVLT4_1/1136_7CR-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/c2/166a52c54c2e4fe0d59d756400a2cb/.command.run
==> 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_7CR-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7CR-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7CR-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7CR-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: 70222347 total, 54528 skipped (flags/unmapped)
Fragments: 35178738 total (34962310 tlen-paired, 2379 hash-paired, 254 singletons, 9598 discordant, 204197 orphans, 7397 too large [>5000 bp], 10705771 duplicates)
Reads: 76037172 total, 49140 skipped (flags/unmapped)
Fragments: 38098075 total (37843041 tlen-paired, 3868 hash-paired, 266 singletons, 8662 discordant, 242238 orphans, 17193 too large [>5000 bp], 11678836 duplicates)
Reads: 76403436 total, 44997 skipped (flags/unmapped)
Fragments: 38280211 total (38055571 tlen-paired, 2148 hash-paired, 324 singletons, 6745 discordant, 215423 orphans, 6882 too large [>5000 bp], 11368148 duplicates)
Reads: 84017327 total, 75521 skipped (flags/unmapped)
Fragments: 42169095 total (41544674 tlen-paired, 1908 hash-paired, 361 singletons, 123175 discordant, 498977 orphans, 51477 too large [>5000 bp], 12960543 duplicates)