Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5a/e5779c2458f3bc08498954e7f04787/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1173_CRL-N1-BDNA-01_A23MHW3LT4_1/1173_CRL-N1-BDNA-01_A23MHW3LT4_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/5a/e5779c2458f3bc08498954e7f04787/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1173_CRL-N1-BDNA-01_A23MHW3LT4_1/1173_CRL-N1-BDNA-01_A23MHW3LT4_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: 1173_CRL-N1-BDNA-01_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CRL-N1-BDNA-01_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CRL-N1-BDNA-01_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CRL-N1-BDNA-01_A23MHW3LT4_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: 70288141 total, 54455 skipped (flags/unmapped)
Fragments: 35352749 total (34848550 tlen-paired, 2953 hash-paired, 392 singletons, 12308 discordant, 488546 orphans, 8563 too large [>5000 bp], 12510357 duplicates)
Reads: 73322942 total, 48320 skipped (flags/unmapped)
Fragments: 36880793 total (36365438 tlen-paired, 2443 hash-paired, 431 singletons, 8030 discordant, 504451 orphans, 8959 too large [>5000 bp], 12701196 duplicates)
Reads: 80598351 total, 53221 skipped (flags/unmapped)
Fragments: 40543572 total (39939332 tlen-paired, 4174 hash-paired, 379 singletons, 13206 discordant, 586481 orphans, 22423 too large [>5000 bp], 14315014 duplicates)
Reads: 82414840 total, 84314 skipped (flags/unmapped)
Fragments: 41708523 total (40003453 tlen-paired, 2658 hash-paired, 410 singletons, 334866 discordant, 1367136 orphans, 140513 too large [>5000 bp], 14628015 duplicates)