Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/930fc79ee172cec9b2d86456e365a9/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/930fc79ee172cec9b2d86456e365a9/.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_7L7-N1-BDNA-1_A23NMNVLT4_1/1136_7L7-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_7L7-N1-BDNA-1_A23NMNVLT4_1/1136_7L7-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] [W::hts_idx_load3] The index file is older than the data file: 1136_7L7-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.baiThe index file is older than the data file: 1136_7L7-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1136_7L7-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7L7-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: 78086982 total, 60189 skipped (flags/unmapped)
Fragments: 39124799 total (38870293 tlen-paired, 2688 hash-paired, 333 singletons, 12775 discordant, 238710 orphans, 8119 too large [>5000 bp], 11662039 duplicates)
Reads: 84172005 total, 49404 skipped (flags/unmapped)
Fragments: 42173945 total (41918488 tlen-paired, 3378 hash-paired, 403 singletons, 8860 discordant, 242816 orphans, 8965 too large [>5000 bp], 12399403 duplicates)
Reads: 93118674 total, 91460 skipped (flags/unmapped)
Fragments: 46740366 total (46039852 tlen-paired, 3199 hash-paired, 388 singletons, 132833 discordant, 564094 orphans, 55482 too large [>5000 bp], 14143994 duplicates)
Reads: 92513431 total, 56400 skipped (flags/unmapped)
Fragments: 46357624 total (46040546 tlen-paired, 6492 hash-paired, 308 singletons, 13103 discordant, 297175 orphans, 19633 too large [>5000 bp], 14017033 duplicates)