Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1173_NWE-N1-BDNA-01_A23MHW3LT4_1/1173_NWE-N1-BDNA-01_A23MHW3LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/53/db6515c63ab764a762d4316404838d/.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/53/db6515c63ab764a762d4316404838d/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1173_NWE-N1-BDNA-01_A23MHW3LT4_1/1173_NWE-N1-BDNA-01_A23MHW3LT4_1.recalibrated.bam.bai
==> 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: 1173_NWE-N1-BDNA-01_A23MHW3LT4_1.recalibrated.bam.bai
The index file is older than the data file: 1173_NWE-N1-BDNA-01_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_NWE-N1-BDNA-01_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_NWE-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: 71888078 total, 53663 skipped (flags/unmapped)
Fragments: 36097530 total (35701721 tlen-paired, 3086 hash-paired, 370 singletons, 14808 discordant, 377545 orphans, 8635 too large [>5000 bp], 11338533 duplicates)
Reads: 76317304 total, 45794 skipped (flags/unmapped)
Fragments: 38317436 total (37921583 tlen-paired, 2571 hash-paired, 430 singletons, 9808 discordant, 383044 orphans, 10056 too large [>5000 bp], 11839163 duplicates)
Reads: 83362457 total, 47313 skipped (flags/unmapped)
Fragments: 41864188 total (41394914 tlen-paired, 4514 hash-paired, 396 singletons, 14914 discordant, 449450 orphans, 18307 too large [>5000 bp], 13274331 duplicates)
Reads: 84890555 total, 83800 skipped (flags/unmapped)
Fragments: 42791584 total (41581137 tlen-paired, 3226 hash-paired, 451 singletons, 234796 discordant, 971974 orphans, 98006 too large [>5000 bp], 13529375 duplicates)