Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/36/3f7857cf3631691670402b25e041e8/.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/36/3f7857cf3631691670402b25e041e8/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_LT1-N1-BDNA-1_B2377KTLT3_2/869_LT1-N1-BDNA-1_B2377KTLT3_2.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_LT1-N1-BDNA-1_B2377KTLT3_2/869_LT1-N1-BDNA-1_B2377KTLT3_2.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] [W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 869_LT1-N1-BDNA-1_B2377KTLT3_2.recalibrated.bam.baiThe index file is older than the data file: 869_LT1-N1-BDNA-1_B2377KTLT3_2.recalibrated.bam.baiThe index file is older than the data file: 869_LT1-N1-BDNA-1_B2377KTLT3_2.recalibrated.bam.bai
The index file is older than the data file: 869_LT1-N1-BDNA-1_B2377KTLT3_2.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: 82343578 total, 76351 skipped (flags/unmapped)
Fragments: 41329948 total (40885896 tlen-paired, 21605 hash-paired, 6611 singletons, 8114 discordant, 407722 orphans, 10832 too large [>5000 bp], 9263206 duplicates)
Reads: 82966822 total, 62439 skipped (flags/unmapped)
Fragments: 41662244 total (41186272 tlen-paired, 21172 hash-paired, 6439 singletons, 7569 discordant, 440792 orphans, 13563 too large [>5000 bp], 9297308 duplicates)
Reads: 91802211 total, 63542 skipped (flags/unmapped)
Fragments: 46098502 total (45593566 tlen-paired, 20965 hash-paired, 7113 singletons, 6392 discordant, 470466 orphans, 9622 too large [>5000 bp], 10291021 duplicates)
Reads: 93002804 total, 115431 skipped (flags/unmapped)
Fragments: 46920574 total (45418901 tlen-paired, 23132 hash-paired, 7370 singletons, 293128 discordant, 1178043 orphans, 115819 too large [>5000 bp], 10371646 duplicates)