Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/a3c6795e729f73bba0b023af0e6322/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/a3c6795e729f73bba0b023af0e6322/.command.run
  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-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_ZEN-N1-BDNA-1_B2377KTLT3_1/869_ZEN-N1-BDNA-1_B2377KTLT3_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_ZEN-N1-BDNA-1_B2377KTLT3_1/869_ZEN-N1-BDNA-1_B2377KTLT3_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: 869_ZEN-N1-BDNA-1_B2377KTLT3_1.recalibrated.bam.baiThe index file is older than the data file: 869_ZEN-N1-BDNA-1_B2377KTLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] 
The index file is older than the data file: 869_ZEN-N1-BDNA-1_B2377KTLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_ZEN-N1-BDNA-1_B2377KTLT3_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: 98704725 total, 73539 skipped (flags/unmapped)
Fragments: 49508083 total (49037330 tlen-paired, 45160 hash-paired, 6550 singletons, 9319 discordant, 409724 orphans, 15647 too large [>5000 bp], 10598419 duplicates)
Reads: 110433228 total, 132256 skipped (flags/unmapped)
Fragments: 55583465 total (54192469 tlen-paired, 45076 hash-paired, 7467 singletons, 265190 discordant, 1073263 orphans, 107386 too large [>5000 bp], 11865787 duplicates)
Reads: 98034539 total, 82059 skipped (flags/unmapped)
Fragments: 49166792 total (48718338 tlen-paired, 43638 hash-paired, 6557 singletons, 10368 discordant, 387891 orphans, 6672 too large [>5000 bp], 10554654 duplicates)
Reads: 108859745 total, 72758 skipped (flags/unmapped)
Fragments: 54606755 total (54106616 tlen-paired, 43541 hash-paired, 7446 singletons, 7977 discordant, 441175 orphans, 11049 too large [>5000 bp], 11700205 duplicates)