Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7f/ee24f44c16480c0bb34a265f4d6143/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_2SZ-N1-BDNA-1_A23KFG7LT4_1/1136_2SZ-N1-BDNA-1_A23KFG7LT4_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/7f/ee24f44c16480c0bb34a265f4d6143/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_2SZ-N1-BDNA-1_A23KFG7LT4_1/1136_2SZ-N1-BDNA-1_A23KFG7LT4_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_2SZ-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
The index file is older than the data file: 1136_2SZ-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2SZ-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2SZ-N1-BDNA-1_A23KFG7LT4_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: 65874098 total, 48298 skipped (flags/unmapped)
Fragments: 33144264 total (32649176 tlen-paired, 2820 hash-paired, 329 singletons, 9924 discordant, 482015 orphans, 9808 too large [>5000 bp], 13104355 duplicates)
Reads: 69300809 total, 43078 skipped (flags/unmapped)
Fragments: 34872511 total (34357815 tlen-paired, 2087 hash-paired, 494 singletons, 7054 discordant, 505061 orphans, 9132 too large [>5000 bp], 13319964 duplicates)
Reads: 76478148 total, 46429 skipped (flags/unmapped)
Fragments: 38484009 total (37903647 tlen-paired, 2031 hash-paired, 320 singletons, 10060 discordant, 567951 orphans, 15986 too large [>5000 bp], 15165270 duplicates)
Reads: 78069610 total, 76933 skipped (flags/unmapped)
Fragments: 39549022 total (37807477 tlen-paired, 3029 hash-paired, 394 singletons, 345407 discordant, 1392715 orphans, 143871 too large [>5000 bp], 15449979 duplicates)