Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_7ZP-N1-BDNA-1_A23NMNVLT4_1/1136_7ZP-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e4/14a7ac398224c7427df531ae382e5c/.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/e4/14a7ac398224c7427df531ae382e5c/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_7ZP-N1-BDNA-1_A23NMNVLT4_1/1136_7ZP-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_7ZP-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7ZP-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1136_7ZP-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.baiThe index file is older than the data file: 1136_7ZP-N1-BDNA-1_A23NMNVLT4_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: 69777520 total, 55179 skipped (flags/unmapped)
Fragments: 34954655 total (34736516 tlen-paired, 2579 hash-paired, 307 singletons, 12435 discordant, 202818 orphans, 8078 too large [>5000 bp], 10067487 duplicates)
Reads: 75724904 total, 43968 skipped (flags/unmapped)
Fragments: 37936062 total (37719147 tlen-paired, 1907 hash-paired, 334 singletons, 8582 discordant, 206092 orphans, 7619 too large [>5000 bp], 10750935 duplicates)
Reads: 75416507 total, 47573 skipped (flags/unmapped)
Fragments: 37788890 total (37532818 tlen-paired, 2933 hash-paired, 281 singletons, 10675 discordant, 242183 orphans, 16809 too large [>5000 bp], 11042300 duplicates)
Reads: 82904171 total, 78684 skipped (flags/unmapped)
Fragments: 41594104 total (41033584 tlen-paired, 1521 hash-paired, 339 singletons, 106770 discordant, 451890 orphans, 44754 too large [>5000 bp], 12187350 duplicates)