Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/83/b2d28e749086010a4dc82b6ba75b21/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1136_4EL-N1-BDNA-1_B23MHTGLT4_1/1136_4EL-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam
  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/83/b2d28e749086010a4dc82b6ba75b21/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1136_4EL-N1-BDNA-1_B23MHTGLT4_1/1136_4EL-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_4EL-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4EL-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4EL-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_4EL-N1-BDNA-1_B23MHTGLT4_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: 88228543 total, 56652 skipped (flags/unmapped)
Fragments: 44286700 total (43845086 tlen-paired, 3454 hash-paired, 551 singletons, 10591 discordant, 427018 orphans, 13030 too large [>5000 bp], 14398480 duplicates)
Reads: 83768593 total, 64779 skipped (flags/unmapped)
Fragments: 42049058 total (41614358 tlen-paired, 2740 hash-paired, 445 singletons, 15348 discordant, 416167 orphans, 11155 too large [>5000 bp], 13969555 duplicates)
Reads: 96733011 total, 60361 skipped (flags/unmapped)
Fragments: 48561257 total (48037634 tlen-paired, 3083 hash-paired, 500 singletons, 16240 discordant, 503800 orphans, 27218 too large [>5000 bp], 16211348 duplicates)
Reads: 97907605 total, 102997 skipped (flags/unmapped)
Fragments: 49334269 total (47992075 tlen-paired, 3446 hash-paired, 547 singletons, 258272 discordant, 1079929 orphans, 108273 too large [>5000 bp], 16442873 duplicates)