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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 7.73 309611837 4003982799
2 7.63 308632215 4042524069
3 7.72 310603780 4021848294
4 7.58 306145030 4038106205
5 7.42 302305448 4075270033
6 7.75 312709069 4033267142
7 7.55 309485428 4100159606
8 7.62 309533554 4060257736
================================================================================
2. SAMPLES WITH <1000000 READS (NON-NTC)
================================================================================
No samples found with <1000000 reads
================================================================================
3. NTC SAMPLES WITH >2000000 READS
================================================================================
No NTC samples found with >2000000 reads
================================================================================
4. TOP UNKNOWN BARCODES (>0.05% OF LANE READS)
================================================================================
Loading Top_Unknown_Barcodes.csv from: merged/Reports/Top_Unknown_Barcodes.csv
Lane 1 - Found 15 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
3000 CCAGTCGTCA GGGGGGGGGG 8337867 0.2082 0.0258
3001 GCAATCTGCT TATTGCGCTA 6626387 0.1655 0.0205
3002 GAGCAGCTTG GGGGGGGGGG 6216276 0.1553 0.0192
3003 CCTAAGCTGA GGGGGGGGGG 5736898 0.1433 0.0177
3004 AGATTAGCGT GGGGGGGGGG 5584967 0.1395 0.0173
3005 AGTATCCGAT ACGAACCAAG 4857676 0.1213 0.0150
3006 TATCCGCGTC GGGGGGGGGG 4626144 0.1155 0.0143
3007 ATGACAGCAC GGGGGGGGGG 3892670 0.0972 0.0120
3008 TGGAGATCGA GGGGGGGGGG 3572485 0.0892 0.0110
3009 TAACTTGGTC GGGGGGGGGG 3513300 0.0877 0.0109
3010 GCCACCTAGT GGGGGGGGGG 2871254 0.0717 0.0089
3011 ACGAGACGTC GGGGGGGGGG 2825204 0.0706 0.0087
3012 TCCAACTGAA GGGGGGGGGG 2751699 0.0687 0.0085
3013 CGCACTGGTA GGGGGGGGGG 2128660 0.0532 0.0066
3014 CGATGTCTTG GGGGGGGGGG 2081455 0.0520 0.0064
Lane 2 - Found 14 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
5000 CCAGTCGTCA GGGGGGGGGG 8218795 0.2033 0.0254
5001 GCAATCTGCT TATTGCGCTA 6685650 0.1654 0.0207
5002 GAGCAGCTTG GGGGGGGGGG 6219202 0.1538 0.0192
5003 CCTAAGCTGA GGGGGGGGGG 5685542 0.1406 0.0176
5004 AGATTAGCGT GGGGGGGGGG 5515228 0.1364 0.0170
5005 AGTATCCGAT ACGAACCAAG 4894697 0.1211 0.0151
5006 TATCCGCGTC GGGGGGGGGG 4584972 0.1134 0.0142
5007 ATGACAGCAC GGGGGGGGGG 3836934 0.0949 0.0119
5008 TGGAGATCGA GGGGGGGGGG 3524373 0.0872 0.0109
5009 TAACTTGGTC GGGGGGGGGG 3476291 0.0860 0.0107
5010 GCCACCTAGT GGGGGGGGGG 2825582 0.0699 0.0087
5011 ACGAGACGTC GGGGGGGGGG 2777107 0.0687 0.0086
5012 TCCAACTGAA GGGGGGGGGG 2720706 0.0673 0.0084
5013 CGCACTGGTA GGGGGGGGGG 2106267 0.0521 0.0065
Lane 3 - Found 15 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
6000 CCAGTCGTCA GGGGGGGGGG 8197804 0.2038 0.0253
6001 GCAATCTGCT TATTGCGCTA 6667662 0.1658 0.0206
6002 GAGCAGCTTG GGGGGGGGGG 6111079 0.1519 0.0189
6003 CCTAAGCTGA GGGGGGGGGG 5706798 0.1419 0.0176
6004 AGATTAGCGT GGGGGGGGGG 5480667 0.1363 0.0169
6005 AGTATCCGAT ACGAACCAAG 4881117 0.1214 0.0151
6006 TATCCGCGTC GGGGGGGGGG 4538491 0.1128 0.0140
6007 ATGACAGCAC GGGGGGGGGG 3831730 0.0953 0.0118
6008 TAACTTGGTC GGGGGGGGGG 3470353 0.0863 0.0107
6009 TGGAGATCGA GGGGGGGGGG 3452974 0.0859 0.0107
6010 GCCACCTAGT GGGGGGGGGG 2778043 0.0691 0.0086
6011 ACGAGACGTC GGGGGGGGGG 2759015 0.0686 0.0085
6012 TCCAACTGAA GGGGGGGGGG 2666072 0.0663 0.0082
6013 CGCACTGGTA GGGGGGGGGG 2101461 0.0523 0.0065
6014 AACGAAGATC GGGGGGGGGG 2013499 0.0501 0.0062
Lane 4 - Found 14 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
2000 CCAGTCGTCA GGGGGGGGGG 7981195 0.1976 0.0247
2001 GCAATCTGCT TATTGCGCTA 6706390 0.1661 0.0207
2002 GAGCAGCTTG GGGGGGGGGG 5969234 0.1478 0.0184
2003 CCTAAGCTGA GGGGGGGGGG 5551000 0.1375 0.0171
2004 AGATTAGCGT GGGGGGGGGG 5319979 0.1317 0.0164
2005 AGTATCCGAT ACGAACCAAG 4893989 0.1212 0.0151
2006 TATCCGCGTC GGGGGGGGGG 4440834 0.1100 0.0137
2007 ATGACAGCAC GGGGGGGGGG 3730100 0.0924 0.0115
2008 TAACTTGGTC GGGGGGGGGG 3412453 0.0845 0.0105
2009 TGGAGATCGA GGGGGGGGGG 3396409 0.0841 0.0105
2010 GCCACCTAGT GGGGGGGGGG 2762012 0.0684 0.0085
2011 ACGAGACGTC GGGGGGGGGG 2720072 0.0674 0.0084
2012 TCCAACTGAA GGGGGGGGGG 2631882 0.0652 0.0081
2013 CGCACTGGTA GGGGGGGGGG 2072402 0.0513 0.0064
Lane 5 - Found 13 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
4000 CCAGTCGTCA GGGGGGGGGG 7779615 0.1909 0.0240
4001 GCAATCTGCT TATTGCGCTA 6742168 0.1654 0.0208
4002 GAGCAGCTTG GGGGGGGGGG 5978995 0.1467 0.0185
4003 CCTAAGCTGA GGGGGGGGGG 5440028 0.1335 0.0168
4004 AGATTAGCGT GGGGGGGGGG 5247951 0.1288 0.0162
4005 AGTATCCGAT ACGAACCAAG 4934511 0.1211 0.0152
4006 TATCCGCGTC GGGGGGGGGG 4379596 0.1075 0.0135
4007 ATGACAGCAC GGGGGGGGGG 3676119 0.0902 0.0114
4008 TGGAGATCGA GGGGGGGGGG 3336070 0.0819 0.0103
4009 TAACTTGGTC GGGGGGGGGG 3332825 0.0818 0.0103
4010 GCCACCTAGT GGGGGGGGGG 2728834 0.0670 0.0084
4011 ACGAGACGTC GGGGGGGGGG 2609258 0.0640 0.0081
4012 TCCAACTGAA GGGGGGGGGG 2571672 0.0631 0.0079
Lane 6 - Found 16 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
7000 CCAGTCGTCA GGGGGGGGGG 8322877 0.2064 0.0257
7001 GCAATCTGCT TATTGCGCTA 6659067 0.1651 0.0206
7002 GAGCAGCTTG GGGGGGGGGG 6266557 0.1554 0.0194
7003 CCTAAGCTGA GGGGGGGGGG 5774365 0.1432 0.0178
7004 AGATTAGCGT GGGGGGGGGG 5556283 0.1378 0.0172
7005 AGTATCCGAT ACGAACCAAG 4893501 0.1213 0.0151
7006 TATCCGCGTC GGGGGGGGGG 4643234 0.1151 0.0143
7007 ATGACAGCAC GGGGGGGGGG 3892918 0.0965 0.0120
7008 TGGAGATCGA GGGGGGGGGG 3582790 0.0888 0.0111
7009 TAACTTGGTC GGGGGGGGGG 3531914 0.0876 0.0109
7010 GCCACCTAGT GGGGGGGGGG 2900210 0.0719 0.0090
7011 ACGAGACGTC GGGGGGGGGG 2845011 0.0705 0.0088
7012 TCCAACTGAA GGGGGGGGGG 2752254 0.0682 0.0085
7013 CGCACTGGTA GGGGGGGGGG 2164687 0.0537 0.0067
7014 AACGAAGATC GGGGGGGGGG 2057071 0.0510 0.0064
7015 CGATGTCTTG GGGGGGGGGG 2048933 0.0508 0.0063
Lane 7 - Found 15 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
1000 CCAGTCGTCA GGGGGGGGGG 8219668 0.2005 0.0254
1001 GCAATCTGCT TATTGCGCTA 6764398 0.1650 0.0209
1002 GAGCAGCTTG GGGGGGGGGG 6412469 0.1564 0.0198
1003 CCTAAGCTGA GGGGGGGGGG 5712062 0.1393 0.0176
1004 AGATTAGCGT GGGGGGGGGG 5576424 0.1360 0.0172
1005 AGTATCCGAT ACGAACCAAG 4973970 0.1213 0.0154
1006 TATCCGCGTC GGGGGGGGGG 4651953 0.1135 0.0144
1007 ATGACAGCAC GGGGGGGGGG 3874521 0.0945 0.0120
1008 TGGAGATCGA GGGGGGGGGG 3567567 0.0870 0.0110
1009 TAACTTGGTC GGGGGGGGGG 3490969 0.0851 0.0108
1010 GCCACCTAGT GGGGGGGGGG 2897296 0.0707 0.0089
1011 ACGAGACGTC GGGGGGGGGG 2750559 0.0671 0.0085
1012 TCCAACTGAA GGGGGGGGGG 2741406 0.0669 0.0085
1013 CGCACTGGTA GGGGGGGGGG 2076488 0.0506 0.0064
1014 AACGAAGATC GGGGGGGGGG 2068909 0.0505 0.0064
Lane 8 - Found 14 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
0 CCAGTCGTCA GGGGGGGGGG 8497299 0.2093 0.0262
1 GCAATCTGCT TATTGCGCTA 6663183 0.1641 0.0206
2 GAGCAGCTTG GGGGGGGGGG 6512598 0.1604 0.0201
3 CCTAAGCTGA GGGGGGGGGG 5756659 0.1418 0.0178
4 AGATTAGCGT GGGGGGGGGG 5723431 0.1410 0.0177
5 AGTATCCGAT ACGAACCAAG 4918985 0.1211 0.0152
6 TATCCGCGTC GGGGGGGGGG 4749606 0.1170 0.0147
7 ATGACAGCAC GGGGGGGGGG 3950628 0.0973 0.0122
8 TGGAGATCGA GGGGGGGGGG 3656756 0.0901 0.0113
9 TAACTTGGTC GGGGGGGGGG 3521939 0.0867 0.0109
10 GCCACCTAGT GGGGGGGGGG 2896098 0.0713 0.0089
11 ACGAGACGTC GGGGGGGGGG 2825337 0.0696 0.0087
12 TCCAACTGAA GGGGGGGGGG 2825222 0.0696 0.0087
13 CGCACTGGTA GGGGGGGGGG 2093256 0.0516 0.0065
================================================================================
5. BARCODES WITH HIGH MISMATCH RATES
================================================================================
No barcodes found with >20.0% mismatch rate
================================================================================
FINAL STATUS CHECK
================================================================================
Overall % Undetermined: 7.63%
Status: 🟡 WARNING
Reason(s):
Overall undetermined 7.63% >= 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 32375415884
Total_Samples_Analyzed 97
Number_of_Lanes 8
Global_Percent_Undetermined 7.63%
Lanes_Exceeding_Fail_Threshold None
Samples_with_Low_Reads 0
NTC_Samples_with_High_Reads 0
Significant_Unknown_Barcodes 116
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
================================================================================