Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_573-N1-BDNA-1_A23NMNVLT4_1/1136_573-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3c/da6a8fb497cfc8c584a14b26e8dd54/.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/3c/da6a8fb497cfc8c584a14b26e8dd54/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_573-N1-BDNA-1_A23NMNVLT4_1/1136_573-N1-BDNA-1_A23NMNVLT4_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: 1136_573-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_573-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_573-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_573-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: 98282403 total, 67833 skipped (flags/unmapped)
Fragments: 49228668 total (48949306 tlen-paired, 3977 hash-paired, 393 singletons, 12851 discordant, 262141 orphans, 9884 too large [>5000 bp], 14275958 duplicates)
Reads: 106766729 total, 55585 skipped (flags/unmapped)
Fragments: 53484409 total (53194867 tlen-paired, 3577 hash-paired, 490 singletons, 9511 discordant, 275964 orphans, 9390 too large [>5000 bp], 15307103 duplicates)
Reads: 105595273 total, 58021 skipped (flags/unmapped)
Fragments: 52906079 total (52582733 tlen-paired, 3361 hash-paired, 330 singletons, 11209 discordant, 308446 orphans, 16935 too large [>5000 bp], 15687042 duplicates)
Reads: 116315571 total, 103048 skipped (flags/unmapped)
Fragments: 58359341 total (57564546 tlen-paired, 3982 hash-paired, 442 singletons, 156136 discordant, 634235 orphans, 64259 too large [>5000 bp], 17356440 duplicates)