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==> STAGING COMPLETE (18 inputs)
Analyzing demux output from: merged
Loading Demultiplex_Stats.csv from: merged/Reports/Demultiplex_Stats.csv
Loaded 776 rows from Demultiplex_Stats.csv
================================================================================
1. % UNDETERMINED PER LANE
================================================================================
Undetermined Summary per Lane:
%_Undetermined Undetermined_Reads Total_Reads
Lane
1 5.95 233947699 3931034380
2 6.01 239773877 3991224545
3 5.94 234118434 3942663684
4 5.94 237495583 3997997030
5 5.94 235094038 3958095123
6 6.03 241483687 4003600854
7 5.96 243845442 4093831853
8 5.99 243525848 4067831854
================================================================================
2. SAMPLES WITH <1000000 READS (NON-NTC)
================================================================================
No samples found with <1000000 reads
================================================================================
3. NTC SAMPLES WITH >2000000 READS
================================================================================
No NTC samples found in the data
================================================================================
4. TOP UNKNOWN BARCODES (>0.05% OF LANE READS)
================================================================================
Loading Top_Unknown_Barcodes.csv from: merged/Reports/Top_Unknown_Barcodes.csv
Lane 1 - Found 11 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
1000 AGCCTCTG GGGGGGGG 6186368 0.1574 0.0193
1001 CCAACTGT GGGGGGGG 4883299 0.1242 0.0153
1002 GCATTCCT GGGGGGGG 4044087 0.1029 0.0126
1003 TCACCGTG GGGGGGGG 3098930 0.0788 0.0097
1004 ACTCGTCC GGGGGGGG 2792982 0.0710 0.0087
1005 TGAGTGTA GGGGGGGG 2621482 0.0667 0.0082
1006 ACCAGGAA GGGGGGGG 2456029 0.0625 0.0077
1007 GTGACGCA GGGGGGGG 2449206 0.0623 0.0077
1008 CTCTATAC GGGGGGGG 2434122 0.0619 0.0076
1009 AAGGTGTA GGGGGGGG 2372002 0.0603 0.0074
1010 GATAGGTG GGGGGGGG 2253422 0.0573 0.0070
Lane 2 - Found 11 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
4000 AGCCTCTG GGGGGGGG 6223186 0.1559 0.0195
4001 CCAACTGT GGGGGGGG 4891916 0.1226 0.0153
4002 GCATTCCT GGGGGGGG 4046940 0.1014 0.0127
4003 TCACCGTG GGGGGGGG 3141765 0.0787 0.0098
4004 ACTCGTCC GGGGGGGG 2931881 0.0735 0.0092
4005 TGAGTGTA GGGGGGGG 2634735 0.0660 0.0082
4006 ACCAGGAA GGGGGGGG 2545124 0.0638 0.0080
4007 CTCTATAC GGGGGGGG 2494781 0.0625 0.0078
4008 GTGACGCA GGGGGGGG 2459358 0.0616 0.0077
4009 AAGGTGTA GGGGGGGG 2422623 0.0607 0.0076
4010 GATAGGTG GGGGGGGG 2243379 0.0562 0.0070
Lane 3 - Found 11 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
7000 AGCCTCTG GGGGGGGG 6010276 0.1524 0.0188
7001 CCAACTGT GGGGGGGG 4760228 0.1207 0.0149
7002 GCATTCCT GGGGGGGG 3975836 0.1008 0.0124
7003 TCACCGTG GGGGGGGG 3053128 0.0774 0.0095
7004 ACTCGTCC GGGGGGGG 2714646 0.0689 0.0085
7005 TGAGTGTA GGGGGGGG 2545025 0.0646 0.0080
7006 ACCAGGAA GGGGGGGG 2421871 0.0614 0.0076
7007 GTGACGCA GGGGGGGG 2379014 0.0603 0.0074
7008 CTCTATAC GGGGGGGG 2351723 0.0596 0.0074
7009 AAGGTGTA GGGGGGGG 2300242 0.0583 0.0072
7010 GATAGGTG GGGGGGGG 2169483 0.0550 0.0068
Lane 4 - Found 11 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
5000 AGCCTCTG GGGGGGGG 6002162 0.1501 0.0188
5001 CCAACTGT GGGGGGGG 4767987 0.1193 0.0149
5002 GCATTCCT GGGGGGGG 4038799 0.1010 0.0126
5003 TCACCGTG GGGGGGGG 3108752 0.0778 0.0097
5004 ACTCGTCC GGGGGGGG 2732827 0.0684 0.0085
5005 TGAGTGTA GGGGGGGG 2587951 0.0647 0.0081
5006 ACCAGGAA GGGGGGGG 2415882 0.0604 0.0076
5007 GTGACGCA GGGGGGGG 2405180 0.0602 0.0075
5008 CTCTATAC GGGGGGGG 2386615 0.0597 0.0075
5009 AAGGTGTA GGGGGGGG 2303808 0.0576 0.0072
5010 GATAGGTG GGGGGGGG 2189738 0.0548 0.0068
Lane 5 - Found 11 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
3000 AGCCTCTG GGGGGGGG 5909062 0.1493 0.0185
3001 CCAACTGT GGGGGGGG 4687902 0.1184 0.0147
3002 GCATTCCT GGGGGGGG 3911811 0.0988 0.0122
3003 TCACCGTG GGGGGGGG 3026715 0.0765 0.0095
3004 ACTCGTCC GGGGGGGG 2760081 0.0697 0.0086
3005 TGAGTGTA GGGGGGGG 2540606 0.0642 0.0079
3006 ACCAGGAA GGGGGGGG 2432108 0.0614 0.0076
3007 CTCTATAC GGGGGGGG 2399358 0.0606 0.0075
3008 GTGACGCA GGGGGGGG 2368860 0.0598 0.0074
3009 AAGGTGTA GGGGGGGG 2313750 0.0585 0.0072
3010 GATAGGTG GGGGGGGG 2140217 0.0541 0.0067
Lane 6 - Found 11 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
6000 AGCCTCTG GGGGGGGG 6264392 0.1565 0.0196
6001 CCAACTGT GGGGGGGG 4944016 0.1235 0.0155
6002 GCATTCCT GGGGGGGG 4092382 0.1022 0.0128
6003 TCACCGTG GGGGGGGG 3189094 0.0797 0.0100
6004 ACTCGTCC GGGGGGGG 2883040 0.0720 0.0090
6005 TGAGTGTA GGGGGGGG 2666490 0.0666 0.0083
6006 ACCAGGAA GGGGGGGG 2550150 0.0637 0.0080
6007 CTCTATAC GGGGGGGG 2495753 0.0623 0.0078
6008 GTGACGCA GGGGGGGG 2480628 0.0620 0.0078
6009 AAGGTGTA GGGGGGGG 2425351 0.0606 0.0076
6010 GATAGGTG GGGGGGGG 2269104 0.0567 0.0071
Lane 7 - Found 11 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
0 AGCCTCTG GGGGGGGG 6451874 0.1576 0.0202
1 CCAACTGT GGGGGGGG 5026343 0.1228 0.0157
2 GCATTCCT GGGGGGGG 4071976 0.0995 0.0127
3 TCACCGTG GGGGGGGG 3220917 0.0787 0.0101
4 ACTCGTCC GGGGGGGG 3027481 0.0740 0.0095
5 TGAGTGTA GGGGGGGG 2697968 0.0659 0.0084
6 ACCAGGAA GGGGGGGG 2593802 0.0634 0.0081
7 CTCTATAC GGGGGGGG 2557332 0.0625 0.0080
8 GTGACGCA GGGGGGGG 2484353 0.0607 0.0078
9 AAGGTGTA GGGGGGGG 2459352 0.0601 0.0077
10 GATAGGTG GGGGGGGG 2278527 0.0557 0.0071
Lane 8 - Found 11 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
2000 AGCCTCTG GGGGGGGG 6437485 0.1583 0.0201
2001 CCAACTGT GGGGGGGG 5045382 0.1240 0.0158
2002 GCATTCCT GGGGGGGG 4069146 0.1000 0.0127
2003 TCACCGTG GGGGGGGG 3215445 0.0790 0.0101
2004 ACTCGTCC GGGGGGGG 2928813 0.0720 0.0092
2005 TGAGTGTA GGGGGGGG 2717767 0.0668 0.0085
2006 GTGACGCA GGGGGGGG 2552214 0.0627 0.0080
2007 CTCTATAC GGGGGGGG 2546810 0.0626 0.0080
2008 ACCAGGAA GGGGGGGG 2507773 0.0616 0.0078
2009 AAGGTGTA GGGGGGGG 2441541 0.0600 0.0076
2010 GATAGGTG GGGGGGGG 2288292 0.0563 0.0072
================================================================================
5. BARCODES WITH HIGH MISMATCH RATES
================================================================================
No barcodes found with >20.0% mismatch rate
================================================================================
FINAL STATUS CHECK
================================================================================
Overall % Undetermined: 5.97%
Status: 🟡 WARNING
Reason(s):
Overall undetermined 5.97% >= 5.0%
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
Warning file created: ./samplesheet_status.warning
================================================================================
QC SUMMARY
================================================================================
Metric Value
Total_Reads 31986279323
Total_Samples_Analyzed 97
Number_of_Lanes 8
Global_Percent_Undetermined 5.97%
Lanes_Exceeding_Fail_Threshold None
Samples_with_Low_Reads 0
NTC_Samples_with_High_Reads 0
Significant_Unknown_Barcodes 88
High_Mismatch_Barcodes 0
Final_Status WARNING
================================================================================
QC Analysis completed successfully!
Flowcell Status: WARNING
Reports generated:
- ./qc_report.csv
- ./qc_report_detailed.txt
- ./samplesheet_status.warning
================================================================================