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==> STAGING COMPLETE (18 inputs)
Analyzing demux output from: merged
Loading Demultiplex_Stats.csv from: merged/Reports/Demultiplex_Stats.csv
Loaded 392 rows from Demultiplex_Stats.csv
================================================================================
1. % UNDETERMINED PER LANE
================================================================================
Undetermined Summary per Lane:
%_Undetermined Undetermined_Reads Total_Reads
Lane
1 6.12 250334217 4090325735
2 7.00 285165933 4074910534
3 6.21 253916096 4088175087
4 6.11 248089917 4059169203
5 6.55 268356261 4095544764
6 6.47 265289440 4099623814
7 6.78 278776905 4109400122
8 6.76 279032115 4129288043
================================================================================
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 17 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
0 AGCCTCTGCT GGGGGGGGGG 15462051 0.3780 0.0472
1 GCATTCCTTC GGGGGGGGGG 6799376 0.1662 0.0208
2 GCAGAAGTCT GGGGGGGGGG 6410016 0.1567 0.0196
3 GATAGATCAG GGGGGGGGGG 6303578 0.1541 0.0192
4 TCACCGTGGT GGGGGGGGGG 5979060 0.1462 0.0183
5 CGGATCATTA GGGGGGGGGG 4890689 0.1196 0.0149
6 TGTGATCGCG GGGGGGGGGG 4725038 0.1155 0.0144
7 GATTCTTAGC GGGGGGGGGG 4442279 0.1086 0.0136
8 AGCACCAGTC GGGGGGGGGG 3933604 0.0962 0.0120
9 GCGACAATAT GGGGGGGGGG 3606282 0.0882 0.0110
10 ATCGAGAGAC GGGGGGGGGG 3575489 0.0874 0.0109
11 CTAGACGAGC GGGGGGGGGG 3425352 0.0837 0.0105
12 CCACTCAACG GGGGGGGGGG 2883641 0.0705 0.0088
13 GCGAAGAATT GGGGGGGGGG 2872728 0.0702 0.0088
14 GTGTTCCTTC GAGCCTGCTT 2779782 0.0680 0.0085
15 ATCTAACCTG GGGGGGGGGG 2283440 0.0558 0.0070
16 CAACTACCGC GGGGGGGGGG 2195123 0.0537 0.0067
Lane 2 - Found 16 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
6000 AGCCTCTGCT GGGGGGGGGG 13801734 0.3387 0.0421
6001 GCATTCCTTC GGGGGGGGGG 6088094 0.1494 0.0186
6002 GATAGATCAG GGGGGGGGGG 5722551 0.1404 0.0175
6003 GCAGAAGTCT GGGGGGGGGG 5716443 0.1403 0.0175
6004 TCACCGTGGT GGGGGGGGGG 5433855 0.1333 0.0166
6005 CGGATCATTA GGGGGGGGGG 4351064 0.1068 0.0133
6006 TGTGATCGCG GGGGGGGGGG 4190213 0.1028 0.0128
6007 GATTCTTAGC GGGGGGGGGG 4160605 0.1021 0.0127
6008 GCGACAATAT GGGGGGGGGG 3629263 0.0891 0.0111
6009 AGCACCAGTC GGGGGGGGGG 3615647 0.0887 0.0110
6010 ATCGAGAGAC GGGGGGGGGG 3338464 0.0819 0.0102
6011 CTAGACGAGC GGGGGGGGGG 3281278 0.0805 0.0100
6012 GCGAAGAATT GGGGGGGGGG 2703105 0.0663 0.0083
6013 CCACTCAACG GGGGGGGGGG 2671012 0.0655 0.0082
6014 GTGTTCCTTC GAGCCTGCTT 2654142 0.0651 0.0081
6015 ATCTAACCTG GGGGGGGGGG 2143704 0.0526 0.0065
Lane 3 - Found 20 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
1000 AGCCTCTGCT GGGGGGGGGG 13354033 0.3267 0.0408
1001 GCATTCCTTC GGGGGGGGGG 5879199 0.1438 0.0180
1002 GCAGAAGTCT GGGGGGGGGG 5775924 0.1413 0.0176
1003 GATAGATCAG GGGGGGGGGG 5684881 0.1391 0.0174
1004 TCACCGTGGT GGGGGGGGGG 5241177 0.1282 0.0160
1005 CGGATCATTA GGGGGGGGGG 4394200 0.1075 0.0134
1006 GATTCTTAGC GGGGGGGGGG 4241888 0.1038 0.0130
1007 TGTGATCGCG GGGGGGGGGG 4086498 0.1000 0.0125
1008 GCGACAATAT GGGGGGGGGG 3959008 0.0968 0.0121
1009 AGCACCAGTC GGGGGGGGGG 3720865 0.0910 0.0114
1010 CTAGACGAGC GGGGGGGGGG 3542724 0.0867 0.0108
1011 ATCGAGAGAC GGGGGGGGGG 3431575 0.0839 0.0105
1012 GCGAAGAATT GGGGGGGGGG 3037634 0.0743 0.0093
1013 CCACTCAACG GGGGGGGGGG 2940399 0.0719 0.0090
1014 GTGTTCCTTC GAGCCTGCTT 2835712 0.0694 0.0087
1015 ATCTAACCTG GGGGGGGGGG 2392837 0.0585 0.0073
1016 CGCACATTAC GGGGGGGGGG 2224352 0.0544 0.0068
1017 CAACTACCGC GGGGGGGGGG 2171869 0.0531 0.0066
1018 GATTGGCGAT GGGGGGGGGG 2155948 0.0527 0.0066
1019 GTAATACTCG GGGGGGGGGG 2052798 0.0502 0.0063
Lane 4 - Found 19 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
3000 AGCCTCTGCT GGGGGGGGGG 13111254 0.3230 0.0400
3001 GCATTCCTTC GGGGGGGGGG 5785178 0.1425 0.0177
3002 GCAGAAGTCT GGGGGGGGGG 5613130 0.1383 0.0171
3003 GATAGATCAG GGGGGGGGGG 5466637 0.1347 0.0167
3004 TCACCGTGGT GGGGGGGGGG 5065498 0.1248 0.0155
3005 CGGATCATTA GGGGGGGGGG 4308240 0.1061 0.0132
3006 TGTGATCGCG GGGGGGGGGG 4150257 0.1022 0.0127
3007 GATTCTTAGC GGGGGGGGGG 3893699 0.0959 0.0119
3008 AGCACCAGTC GGGGGGGGGG 3702627 0.0912 0.0113
3009 GCGACAATAT GGGGGGGGGG 3452816 0.0851 0.0105
3010 CTAGACGAGC GGGGGGGGGG 3401747 0.0838 0.0104
3011 ATCGAGAGAC GGGGGGGGGG 3169982 0.0781 0.0097
3012 GCGAAGAATT GGGGGGGGGG 3151401 0.0776 0.0096
3013 CCACTCAACG GGGGGGGGGG 2927500 0.0721 0.0089
3014 GTGTTCCTTC GAGCCTGCTT 2871127 0.0707 0.0088
3015 ATCTAACCTG GGGGGGGGGG 2388460 0.0588 0.0073
3016 GATTGGCGAT GGGGGGGGGG 2243153 0.0553 0.0069
3017 CAACTACCGC GGGGGGGGGG 2233873 0.0550 0.0068
3018 CGCACATTAC GGGGGGGGGG 2145749 0.0529 0.0066
Lane 5 - Found 14 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
2000 GTCGACTCCT GGGGGGGGGG 28213535 0.6889 0.0862
2001 CCTCTGTCAT GGGGGGGGGG 21211324 0.5179 0.0648
2002 TTGTGAAGGC GGGGGGGGGG 17124222 0.4181 0.0523
2003 CTTCGGAATC GGGGGGGGGG 9047527 0.2209 0.0276
2004 GCAGATGTAA GGGGGGGGGG 6508182 0.1589 0.0199
2005 CAACCATACA GGGGGGGGGG 6450505 0.1575 0.0197
2006 TTGCAATGCG GGGGGGGGGG 5469904 0.1336 0.0167
2007 CATTATCGCT GGGGGGGGGG 5383290 0.1314 0.0164
2008 AACATAAGGC GGGGGGGGGG 3805274 0.0929 0.0116
2009 CGGATTGATC GGGGGGGGGG 3792311 0.0926 0.0116
2010 ACTTAGATCG GGGGGGGGGG 2963370 0.0724 0.0090
2011 AACCGGCCTT GGGGGGGGGG 2671844 0.0652 0.0082
2012 AGGTATTCGG AGATCTCGGT 2576643 0.0629 0.0079
2013 AAGAGTACGA GGGGGGGGGG 2185456 0.0534 0.0067
Lane 6 - Found 13 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
7000 GTCGACTCCT GGGGGGGGGG 31161329 0.7601 0.0952
7001 CCTCTGTCAT GGGGGGGGGG 20161615 0.4918 0.0616
7002 TTGTGAAGGC GGGGGGGGGG 18902057 0.4611 0.0577
7003 CTTCGGAATC GGGGGGGGGG 9912851 0.2418 0.0303
7004 CAACCATACA GGGGGGGGGG 5813006 0.1418 0.0178
7005 TTGCAATGCG GGGGGGGGGG 5404782 0.1318 0.0165
7006 CATTATCGCT GGGGGGGGGG 5307486 0.1295 0.0162
7007 GCAGATGTAA GGGGGGGGGG 5050759 0.1232 0.0154
7008 AACATAAGGC GGGGGGGGGG 3620816 0.0883 0.0111
7009 CGGATTGATC GGGGGGGGGG 3458507 0.0844 0.0106
7010 ACTTAGATCG GGGGGGGGGG 3057781 0.0746 0.0093
7011 AACCGGCCTT GGGGGGGGGG 2391704 0.0583 0.0073
7012 AGGTATTCGG AGATCTCGGT 2384264 0.0582 0.0073
Lane 7 - Found 14 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
5000 GTCGACTCCT GGGGGGGGGG 33418063 0.8132 0.1021
5001 CCTCTGTCAT GGGGGGGGGG 22375267 0.5445 0.0683
5002 TTGTGAAGGC GGGGGGGGGG 20975773 0.5104 0.0641
5003 CTTCGGAATC GGGGGGGGGG 10655032 0.2593 0.0325
5004 CAACCATACA GGGGGGGGGG 6528282 0.1589 0.0199
5005 TTGCAATGCG GGGGGGGGGG 6130695 0.1492 0.0187
5006 GCAGATGTAA GGGGGGGGGG 5931573 0.1443 0.0181
5007 CATTATCGCT GGGGGGGGGG 5737349 0.1396 0.0175
5008 AACATAAGGC GGGGGGGGGG 4069480 0.0990 0.0124
5009 CGGATTGATC GGGGGGGGGG 3947189 0.0961 0.0121
5010 ACTTAGATCG GGGGGGGGGG 3385918 0.0824 0.0103
5011 AACCGGCCTT GGGGGGGGGG 2644753 0.0644 0.0081
5012 AGGTATTCGG AGATCTCGGT 2070736 0.0504 0.0063
5013 AAGAGTACGA GGGGGGGGGG 2058586 0.0501 0.0063
Lane 8 - Found 13 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
4000 GTCGACTCCT GGGGGGGGGG 34256889 0.8296 0.1046
4001 CCTCTGTCAT GGGGGGGGGG 22855710 0.5535 0.0698
4002 TTGTGAAGGC GGGGGGGGGG 21380948 0.5178 0.0653
4003 CTTCGGAATC GGGGGGGGGG 11044249 0.2675 0.0337
4004 TTGCAATGCG GGGGGGGGGG 6330099 0.1533 0.0193
4005 CAACCATACA GGGGGGGGGG 6312569 0.1529 0.0193
4006 GCAGATGTAA GGGGGGGGGG 5877037 0.1423 0.0179
4007 CATTATCGCT GGGGGGGGGG 5828140 0.1411 0.0178
4008 AACATAAGGC GGGGGGGGGG 4069191 0.0985 0.0124
4009 CGGATTGATC GGGGGGGGGG 3901058 0.0945 0.0119
4010 ACTTAGATCG GGGGGGGGGG 3521385 0.0853 0.0108
4011 AACCGGCCTT GGGGGGGGGG 2574437 0.0623 0.0079
4012 AAGAGTACGA GGGGGGGGGG 2103096 0.0509 0.0064
================================================================================
5. BARCODES WITH HIGH MISMATCH RATES
================================================================================
⚠️ WARNING: 4 sample(s) with >20.0% mismatch rate:
Lane SampleID ... # Reads Mismatch_Rate
325 2 FFPE_V4_0001_RNA_0001_B23LG7FLT4_1 ... 69597426 27.97
80 3 FFPE_V4_0001_RNA_0001_B23LG7FLT4_1 ... 70368438 26.90
178 4 FFPE_V4_0001_RNA_0001_B23LG7FLT4_1 ... 69620090 26.32
31 1 FFPE_V4_0001_RNA_0001_B23LG7FLT4_1 ... 70409954 25.77
[4 rows x 5 columns]
Mismatch Rate Summary:
Average mismatch rate: 3.21%
Maximum mismatch rate: 27.97%
Samples with >20.0% mismatch: 4
================================================================================
FINAL STATUS CHECK
================================================================================
Overall % Undetermined: 6.50%
Status: 🟡 WARNING
Reason(s):
Overall undetermined 6.50% >= 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 32746437302
Total_Samples_Analyzed 97
Number_of_Lanes 8
Global_Percent_Undetermined 6.50%
Lanes_Exceeding_Fail_Threshold None
Samples_with_Low_Reads 0
NTC_Samples_with_High_Reads 0
Significant_Unknown_Barcodes 126
High_Mismatch_Barcodes 4
Final_Status WARNING
================================================================================
QC Analysis completed successfully!
Flowcell Status: WARNING
Reports generated:
- ./qc_report.csv
- ./qc_report_detailed.txt
- ./samplesheet_status.warning
================================================================================