Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3e/8f571e457801297a7f17becb7f55ac/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_4LF-N1-BDNA-1_A23NMNVLT4_1/1136_4LF-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3e/8f571e457801297a7f17becb7f55ac/.command.run
  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-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_4LF-N1-BDNA-1_A23NMNVLT4_1/1136_4LF-N1-BDNA-1_A23NMNVLT4_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: 1136_4LF-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4LF-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4LF-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4LF-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: 79507113 total, 60624 skipped (flags/unmapped)
Fragments: 39837703 total (39579453 tlen-paired, 4037 hash-paired, 324 singletons, 11608 discordant, 242281 orphans, 6844 too large [>5000 bp], 12071724 duplicates)
Reads: 84778293 total, 48413 skipped (flags/unmapped)
Fragments: 42480215 total (42222196 tlen-paired, 2257 hash-paired, 381 singletons, 7694 discordant, 247687 orphans, 8759 too large [>5000 bp], 12697487 duplicates)
Reads: 94532708 total, 89527 skipped (flags/unmapped)
Fragments: 47460305 total (46720740 tlen-paired, 2868 hash-paired, 348 singletons, 141670 discordant, 594679 orphans, 58799 too large [>5000 bp], 14585297 duplicates)
Reads: 94124991 total, 56233 skipped (flags/unmapped)
Fragments: 47164901 total (46840124 tlen-paired, 4281 hash-paired, 293 singletons, 11842 discordant, 308361 orphans, 23805 too large [>5000 bp], 14473191 duplicates)