File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9f/a170a252acf0a5da38a00761612b1e/.command.log
Size
1.8 KB
Task
NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:SOMATIC_CNV_CALLING:SOMA_CNV_PROBE_COUNTS (1029_11H-T1-TDNA-1_B23KFCWLT4_1)
Attempt

Content

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  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9f/a170a252acf0a5da38a00761612b1e/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9f/a170a252acf0a5da38a00761612b1e/.command.run
  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-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260318_LH00519_0070_B23KFCWLT4__d7a6b981--20260320-092016/alignments/recalibrated/1029_11H-T1-TDNA-1_B23KFCWLT4_1/1029_11H-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260318_LH00519_0070_B23KFCWLT4__d7a6b981--20260320-092016/alignments/recalibrated/1029_11H-T1-TDNA-1_B23KFCWLT4_1/1029_11H-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam
==> 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: 1029_11H-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] Count mode: frac
The index file is older than the data file: 1029_11H-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_11H-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_11H-T1-TDNA-1_B23KFCWLT4_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