Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_66U-N1-BDNA-1_A23NMNVLT4_1/1136_66U-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/1fa50057ff96527393fd30ac62ce83/.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/32/1fa50057ff96527393fd30ac62ce83/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_66U-N1-BDNA-1_A23NMNVLT4_1/1136_66U-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_66U-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_66U-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_66U-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_66U-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: 67337292 total, 62412 skipped (flags/unmapped)
Fragments: 33802544 total (33450297 tlen-paired, 2487 hash-paired, 309 singletons, 7410 discordant, 342041 orphans, 6071 too large [>5000 bp], 11068707 duplicates)
Reads: 71972733 total, 53120 skipped (flags/unmapped)
Fragments: 36143022 total (35754220 tlen-paired, 2090 hash-paired, 379 singletons, 5247 discordant, 381086 orphans, 7517 too large [>5000 bp], 11677678 duplicates)
Reads: 79854046 total, 59586 skipped (flags/unmapped)
Fragments: 40093514 total (39644304 tlen-paired, 3940 hash-paired, 303 singletons, 7406 discordant, 437561 orphans, 22648 too large [>5000 bp], 13466888 duplicates)
Reads: 81470729 total, 114331 skipped (flags/unmapped)
Fragments: 41088790 total (39802218 tlen-paired, 1971 hash-paired, 498 singletons, 259893 discordant, 1024210 orphans, 101763 too large [>5000 bp], 13675375 duplicates)