.command.out - Workdir - NFCORE_RNAFUSION:DEMUX_FROM_RUNDIR:DEMULTIPLEX:SAMPLESHEET_CHECK (REGRESSION)

File Info

Filename: .command.out
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4c/b3b57b68a8cd47f112a2eaff576b7a/.command.out
Size: 3.1 KB
Task: NFCORE_RNAFUSION:DEMUX_FROM_RUNDIR:DEMULTIPLEX:SAMPLESHEET_CHECK (REGRESSION)
Attempt

Content

Analyzing demux output from: merged
Loading Demultiplex_Stats.csv from: merged/Reports/Demultiplex_Stats.csv
Loaded 12 rows from Demultiplex_Stats.csv

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1. % UNDETERMINED PER LANE
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Undetermined Summary per Lane:
      %_Undetermined  Undetermined_Reads  Total_Reads
Lane                                                 
1                0.0                   0      5000000
2                0.0                   0      5000000
3                0.0                   0      5000000
4                0.0                   0      5000000

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2. SAMPLES WITH <1000000 READS (NON-NTC)
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No samples found with <1000000 reads

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3. NTC SAMPLES WITH >2000000 READS
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No NTC samples found in the data

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4. TOP UNKNOWN BARCODES (>0.05% OF LANE READS)
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Loading Top_Unknown_Barcodes.csv from: merged/Reports/Top_Unknown_Barcodes.csv

No barcodes found with >0.05% of lane reads in any lane

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5. BARCODES WITH HIGH MISMATCH RATES
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No barcodes found with >20.0% mismatch rate

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FINAL STATUS CHECK
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Overall % Undetermined: 0.00%
Status: 🟢 PASS
Thresholds: <5.0% = PASS, 5.0-10.0% = WARNING, >10.0% = FAIL
NTC gate: >2,000,000 reads = FAIL

=== Creating reports in . ===
QC summary saved to: ./qc_report.csv
Detailed QC report saved to: ./qc_report_detailed.txt
Pass file created: ./samplesheet_status.pass

================================================================================
QC SUMMARY
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                        Metric    Value
                   Total_Reads 20000000
        Total_Samples_Analyzed        3
               Number_of_Lanes        4
   Global_Percent_Undetermined    0.00%
Lanes_Exceeding_Fail_Threshold     None
        Samples_with_Low_Reads        0
   NTC_Samples_with_High_Reads        0
  Significant_Unknown_Barcodes        0
        High_Mismatch_Barcodes        0
                  Final_Status     PASS

================================================================================
QC Analysis completed successfully!
Flowcell Status: PASS
Reports generated:
  - ./qc_report.csv
  - ./qc_report_detailed.txt
  - ./samplesheet_status.pass
================================================================================