Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/35/bb8e5b3b342f3bae01cd3d8da00877/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_RMW-N1-BDNA-1_A23TNVNLT4_1/1241_RMW-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/35/bb8e5b3b342f3bae01cd3d8da00877/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_RMW-N1-BDNA-1_A23TNVNLT4_1/1241_RMW-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: 1241_RMW-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_RMW-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_RMW-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_RMW-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: 72057588 total, 44561 skipped (flags/unmapped)
Fragments: 36120201 total (35865615 tlen-paired, 2921 hash-paired, 327 singletons, 11136 discordant, 240202 orphans, 6577 too large [>5000 bp], 11854282 duplicates)
Reads: 77560417 total, 37245 skipped (flags/unmapped)
Fragments: 38881251 total (38617988 tlen-paired, 2331 hash-paired, 373 singletons, 7908 discordant, 252651 orphans, 6847 too large [>5000 bp], 12551452 duplicates)
Reads: 84477851 total, 42305 skipped (flags/unmapped)
Fragments: 42348487 total (42039593 tlen-paired, 2968 hash-paired, 296 singletons, 11756 discordant, 293874 orphans, 16371 too large [>5000 bp], 13968932 duplicates)
Reads: 85506284 total, 77391 skipped (flags/unmapped)
Fragments: 42957309 total (42207319 tlen-paired, 2695 hash-paired, 369 singletons, 145866 discordant, 601060 orphans, 57852 too large [>5000 bp], 14180476 duplicates)