Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/cb57b53ace126a5653cfc558616f90/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1267_EM-N1-BDNA-1_A23TNVNLT4_1/1267_EM-N1-BDNA-1_A23TNVNLT4_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/46/cb57b53ace126a5653cfc558616f90/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1267_EM-N1-BDNA-1_A23TNVNLT4_1/1267_EM-N1-BDNA-1_A23TNVNLT4_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: 1267_EM-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1267_EM-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1267_EM-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1267_EM-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: 100114897 total, 78681 skipped (flags/unmapped)
Fragments: 50199148 total (49785530 tlen-paired, 5976 hash-paired, 510 singletons, 22298 discordant, 384834 orphans, 11632 too large [>5000 bp], 19428591 duplicates)
Reads: 107496412 total, 69970 skipped (flags/unmapped)
Fragments: 53901630 total (53480777 tlen-paired, 5319 hash-paired, 549 singletons, 15568 discordant, 399417 orphans, 11574 too large [>5000 bp], 20640185 duplicates)
Reads: 117520330 total, 73571 skipped (flags/unmapped)
Fragments: 58929630 total (58438143 tlen-paired, 6100 hash-paired, 425 singletons, 23376 discordant, 461586 orphans, 24755 too large [>5000 bp], 23013622 duplicates)
Reads: 119346817 total, 120669 skipped (flags/unmapped)
Fragments: 59979074 total (58862685 tlen-paired, 4541 hash-paired, 499 singletons, 212578 discordant, 898771 orphans, 83635 too large [>5000 bp], 23391400 duplicates)