File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4a/d0343e3af1cacc5ce4ca32503d478c/.command.log
Size
2.7 KB
Task
NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:SOMATIC_CNV_CALLING:SOMA_CNV_PROBE_COUNTS (1029_11H-N1-BDNA-1_B23KGCJLT4_1)
Attempt

Content

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  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4a/d0343e3af1cacc5ce4ca32503d478c/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1029_11H-N1-BDNA-1_B23KGCJLT4_1/1029_11H-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam
  Downloading: s3://ai-pipelines-experiment/chnobles/ref_data/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/4a/d0343e3af1cacc5ce4ca32503d478c/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1029_11H-N1-BDNA-1_B23KGCJLT4_1/1029_11H-N1-BDNA-1_B23KGCJLT4_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: 1029_11H-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_11H-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_11H-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_11H-N1-BDNA-1_B23KGCJLT4_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: 98213066 total, 72846 skipped (flags/unmapped)
Fragments: 49213881 total (48873647 tlen-paired, 4323 hash-paired, 442 singletons, 22175 discordant, 313294 orphans, 13097 too large [>5000 bp], 19266356 duplicates)
Reads: 105094183 total, 60178 skipped (flags/unmapped)
Fragments: 52659029 total (52326801 tlen-paired, 4125 hash-paired, 508 singletons, 15378 discordant, 312217 orphans, 14336 too large [>5000 bp], 20366016 duplicates)
Reads: 115786846 total, 105104 skipped (flags/unmapped)
Fragments: 58104122 total (57310055 tlen-paired, 3370 hash-paired, 427 singletons, 144527 discordant, 645743 orphans, 59834 too large [>5000 bp], 22937371 duplicates)
Reads: 115144039 total, 67777 skipped (flags/unmapped)
Fragments: 57702021 total (57288685 tlen-paired, 6019 hash-paired, 414 singletons, 22575 discordant, 384328 orphans, 28481 too large [>5000 bp], 22762993 duplicates)