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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 6.80 256076560 3764221011
2 6.68 249916067 3743254453
3 6.99 259502348 3713846173
4 7.39 273892746 3706675031
5 7.41 272345315 3676440007
6 6.76 254194919 3761057280
7 6.56 248021330 3778753744
8 6.78 255971636 3774977755
================================================================================
2. SAMPLES WITH <1000000 READS (NON-NTC)
================================================================================
Found 1 samples with <1000000 reads:
SampleID ... Lane(s)
20 1173_FWA_T1_RNA_SLD_01_A23T55JLT4_2 ... 1,2,3,4,5,6,7,8
[1 rows x 4 columns]
================================================================================
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 16 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
0 ACCAGGAATT GGGGGGGGGG 5754910 0.1529 0.0192
1 AGCCTCTGCT GGGGGGGGGG 5445921 0.1447 0.0182
2 GTGACGCACA GGGGGGGGGG 4425130 0.1176 0.0148
3 AGACGACAGA GGGGGGGGGG 4040373 0.1073 0.0135
4 ACTCGTCCAG GGGGGGGGGG 3980549 0.1057 0.0133
5 GAGTAGTGAC GGGGGGGGGG 3951009 0.1050 0.0132
6 TGGCACTGAT GGGGGGGGGG 3799569 0.1009 0.0127
7 TGAGTGTACA GGGGGGGGGG 3752965 0.0997 0.0125
8 GCATTCCTTC GGGGGGGGGG 3283868 0.0872 0.0110
9 CTCTATACTG GGGGGGGGGG 3041321 0.0808 0.0102
10 TCTCCGTACT GGGGGGGGGG 3040129 0.0808 0.0102
11 GCAGAAGTCT GGGGGGGGGG 2817544 0.0749 0.0094
12 GATAGGTGAA GGGGGGGGGG 2737065 0.0727 0.0091
13 TAGCGAGGCT GGGGGGGGGG 2362509 0.0628 0.0079
14 TCACCGTGGT GGGGGGGGGG 2201252 0.0585 0.0074
15 TTGCCGTATC GGGGGGGGGG 2026053 0.0538 0.0068
Lane 2 - Found 15 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
3000 ACCAGGAATT GGGGGGGGGG 5518342 0.1474 0.0184
3001 AGCCTCTGCT GGGGGGGGGG 5198858 0.1389 0.0174
3002 GTGACGCACA GGGGGGGGGG 4256841 0.1137 0.0142
3003 AGACGACAGA GGGGGGGGGG 3913329 0.1045 0.0131
3004 ACTCGTCCAG GGGGGGGGGG 3823855 0.1022 0.0128
3005 GAGTAGTGAC GGGGGGGGGG 3744352 0.1000 0.0125
3006 TGGCACTGAT GGGGGGGGGG 3700076 0.0988 0.0124
3007 TGAGTGTACA GGGGGGGGGG 3651655 0.0976 0.0122
3008 GCATTCCTTC GGGGGGGGGG 3240950 0.0866 0.0108
3009 TCTCCGTACT GGGGGGGGGG 2966452 0.0792 0.0099
3010 CTCTATACTG GGGGGGGGGG 2943543 0.0786 0.0098
3011 GCAGAAGTCT GGGGGGGGGG 2749993 0.0735 0.0092
3012 GATAGGTGAA GGGGGGGGGG 2643038 0.0706 0.0088
3013 TAGCGAGGCT GGGGGGGGGG 2293719 0.0613 0.0077
3014 TCACCGTGGT GGGGGGGGGG 2152967 0.0575 0.0072
Lane 3 - Found 17 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
5000 ACCAGGAATT GGGGGGGGGG 5754547 0.1549 0.0192
5001 AGCCTCTGCT GGGGGGGGGG 4996013 0.1345 0.0167
5002 GTGACGCACA GGGGGGGGGG 4234808 0.1140 0.0142
5003 ACTCGTCCAG GGGGGGGGGG 4047358 0.1090 0.0135
5004 TGGCACTGAT GGGGGGGGGG 3884212 0.1046 0.0130
5005 GAGTAGTGAC GGGGGGGGGG 3867643 0.1041 0.0129
5006 AGACGACAGA GGGGGGGGGG 3734697 0.1006 0.0125
5007 TGAGTGTACA GGGGGGGGGG 3561319 0.0959 0.0119
5008 TCTCCGTACT GGGGGGGGGG 3318618 0.0894 0.0111
5009 GCATTCCTTC GGGGGGGGGG 3040510 0.0819 0.0102
5010 CTCTATACTG GGGGGGGGGG 3035642 0.0817 0.0101
5011 GCAGAAGTCT GGGGGGGGGG 2839537 0.0765 0.0095
5012 TAGCGAGGCT GGGGGGGGGG 2537684 0.0683 0.0085
5013 GATAGGTGAA GGGGGGGGGG 2518457 0.0678 0.0084
5014 TTGCCGTATC GGGGGGGGGG 2328594 0.0627 0.0078
5015 TCACCGTGGT GGGGGGGGGG 2088619 0.0562 0.0070
5016 GCACTACCAG GGGGGGGGGG 1863200 0.0502 0.0062
Lane 4 - Found 19 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
1000 ACCAGGAATT GGGGGGGGGG 5935969 0.1601 0.0198
1001 AGCCTCTGCT GGGGGGGGGG 5005206 0.1350 0.0167
1002 GTGACGCACA GGGGGGGGGG 4314983 0.1164 0.0144
1003 TGGCACTGAT GGGGGGGGGG 4168021 0.1124 0.0139
1004 ACTCGTCCAG GGGGGGGGGG 4116275 0.1111 0.0138
1005 GAGTAGTGAC GGGGGGGGGG 3871275 0.1044 0.0129
1006 AGACGACAGA GGGGGGGGGG 3754763 0.1013 0.0125
1007 TGAGTGTACA GGGGGGGGGG 3578641 0.0965 0.0120
1008 TCTCCGTACT GGGGGGGGGG 3528687 0.0952 0.0118
1009 CTCTATACTG GGGGGGGGGG 3155066 0.0851 0.0105
1010 GCAGAAGTCT GGGGGGGGGG 3056289 0.0825 0.0102
1011 GCATTCCTTC GGGGGGGGGG 2992824 0.0807 0.0100
1012 TAGCGAGGCT GGGGGGGGGG 2672706 0.0721 0.0089
1013 GATAGGTGAA GGGGGGGGGG 2533806 0.0684 0.0085
1014 TTGCCGTATC GGGGGGGGGG 2429398 0.0655 0.0081
1015 GCACTACCAG GGGGGGGGGG 2169800 0.0585 0.0073
1016 GATTGGCGAT GGGGGGGGGG 2137471 0.0577 0.0071
1017 CCACTCAACG GGGGGGGGGG 2091394 0.0564 0.0070
1018 TCACCGTGGT GGGGGGGGGG 2055667 0.0555 0.0069
Lane 5 - Found 20 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
2000 ACCAGGAATT GGGGGGGGGG 5823993 0.1584 0.0195
2001 AGCCTCTGCT GGGGGGGGGG 4820673 0.1311 0.0161
2002 GTGACGCACA GGGGGGGGGG 4228057 0.1150 0.0141
2003 ACTCGTCCAG GGGGGGGGGG 4045505 0.1100 0.0135
2004 TGGCACTGAT GGGGGGGGGG 4005573 0.1090 0.0134
2005 GAGTAGTGAC GGGGGGGGGG 3860216 0.1050 0.0129
2006 AGACGACAGA GGGGGGGGGG 3615673 0.0983 0.0121
2007 TGAGTGTACA GGGGGGGGGG 3582225 0.0974 0.0120
2008 TCTCCGTACT GGGGGGGGGG 3414616 0.0929 0.0114
2009 CTCTATACTG GGGGGGGGGG 3049855 0.0830 0.0102
2010 GCATTCCTTC GGGGGGGGGG 2998867 0.0816 0.0100
2011 GCAGAAGTCT GGGGGGGGGG 2879936 0.0783 0.0096
2012 TAGCGAGGCT GGGGGGGGGG 2639442 0.0718 0.0088
2013 TTGCCGTATC GGGGGGGGGG 2633074 0.0716 0.0088
2014 GATAGGTGAA GGGGGGGGGG 2474170 0.0673 0.0083
2015 TCACCGTGGT GGGGGGGGGG 2083146 0.0567 0.0070
2016 GCACTACCAG GGGGGGGGGG 2012157 0.0547 0.0067
2017 GATTGGCGAT GGGGGGGGGG 1971375 0.0536 0.0066
2018 ATCCAGCATG AGATCTCGGT 1921932 0.0523 0.0064
2019 CCACTCAACG GGGGGGGGGG 1920206 0.0522 0.0064
Lane 6 - Found 16 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
6000 ACCAGGAATT GGGGGGGGGG 5700301 0.1516 0.0191
6001 AGCCTCTGCT GGGGGGGGGG 5081395 0.1351 0.0170
6002 GTGACGCACA GGGGGGGGGG 4214886 0.1121 0.0141
6003 ACTCGTCCAG GGGGGGGGGG 3980604 0.1058 0.0133
6004 GAGTAGTGAC GGGGGGGGGG 3840003 0.1021 0.0128
6005 TGGCACTGAT GGGGGGGGGG 3814600 0.1014 0.0127
6006 AGACGACAGA GGGGGGGGGG 3792318 0.1008 0.0127
6007 TGAGTGTACA GGGGGGGGGG 3575856 0.0951 0.0120
6008 TCTCCGTACT GGGGGGGGGG 3153155 0.0838 0.0105
6009 GCATTCCTTC GGGGGGGGGG 3128472 0.0832 0.0105
6010 CTCTATACTG GGGGGGGGGG 2997077 0.0797 0.0100
6011 GCAGAAGTCT GGGGGGGGGG 2783276 0.0740 0.0093
6012 GATAGGTGAA GGGGGGGGGG 2561031 0.0681 0.0086
6013 TAGCGAGGCT GGGGGGGGGG 2413183 0.0642 0.0081
6014 TCACCGTGGT GGGGGGGGGG 2104264 0.0559 0.0070
6015 TTGCCGTATC GGGGGGGGGG 2068331 0.0550 0.0069
Lane 7 - Found 17 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
7000 ACCAGGAATT GGGGGGGGGG 5604199 0.1483 0.0187
7001 AGCCTCTGCT GGGGGGGGGG 5271769 0.1395 0.0176
7002 GTGACGCACA GGGGGGGGGG 4296770 0.1137 0.0144
7003 AGACGACAGA GGGGGGGGGG 3894373 0.1031 0.0130
7004 ACTCGTCCAG GGGGGGGGGG 3883331 0.1028 0.0130
7005 GAGTAGTGAC GGGGGGGGGG 3841180 0.1017 0.0128
7006 TGGCACTGAT GGGGGGGGGG 3683893 0.0975 0.0123
7007 TGAGTGTACA GGGGGGGGGG 3617051 0.0957 0.0121
7008 GCATTCCTTC GGGGGGGGGG 3155024 0.0835 0.0105
7009 TCTCCGTACT GGGGGGGGGG 2973204 0.0787 0.0099
7010 CTCTATACTG GGGGGGGGGG 2957480 0.0783 0.0099
7011 GCAGAAGTCT GGGGGGGGGG 2715372 0.0719 0.0091
7012 GATAGGTGAA GGGGGGGGGG 2626419 0.0695 0.0088
7013 TAGCGAGGCT GGGGGGGGGG 2293063 0.0607 0.0077
7014 TCACCGTGGT GGGGGGGGGG 2117939 0.0560 0.0071
7015 TTGCCGTATC GGGGGGGGGG 1993122 0.0527 0.0067
7016 ATCCAGCATG AGATCTCGGT 1901800 0.0503 0.0064
Lane 8 - Found 16 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
4000 ACCAGGAATT GGGGGGGGGG 5695957 0.1509 0.0190
4001 AGCCTCTGCT GGGGGGGGGG 5401826 0.1431 0.0181
4002 GTGACGCACA GGGGGGGGGG 4334850 0.1148 0.0145
4003 AGACGACAGA GGGGGGGGGG 4005933 0.1061 0.0134
4004 ACTCGTCCAG GGGGGGGGGG 3993991 0.1058 0.0133
4005 GAGTAGTGAC GGGGGGGGGG 3856942 0.1022 0.0129
4006 TGGCACTGAT GGGGGGGGGG 3766465 0.0998 0.0126
4007 TGAGTGTACA GGGGGGGGGG 3693635 0.0978 0.0123
4008 GCATTCCTTC GGGGGGGGGG 3227519 0.0855 0.0108
4009 TCTCCGTACT GGGGGGGGGG 3060307 0.0811 0.0102
4010 CTCTATACTG GGGGGGGGGG 3024366 0.0801 0.0101
4011 GCAGAAGTCT GGGGGGGGGG 2817806 0.0746 0.0094
4012 GATAGGTGAA GGGGGGGGGG 2667562 0.0707 0.0089
4013 TAGCGAGGCT GGGGGGGGGG 2333333 0.0618 0.0078
4014 TCACCGTGGT GGGGGGGGGG 2168604 0.0574 0.0072
4015 TTGCCGTATC GGGGGGGGGG 1955813 0.0518 0.0065
================================================================================
5. BARCODES WITH HIGH MISMATCH RATES
================================================================================
⚠️ WARNING: 4 sample(s) with >20.0% mismatch rate:
Lane SampleID ... # Reads Mismatch_Rate
273 5 1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2 ... 29720632 21.36
176 4 1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2 ... 29694497 20.36
661 6 1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2 ... 30796012 20.07
564 3 1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2 ... 30230749 20.01
[4 rows x 5 columns]
Mismatch Rate Summary:
Average mismatch rate: 2.55%
Maximum mismatch rate: 21.36%
Samples with >20.0% mismatch: 4
================================================================================
FINAL STATUS CHECK
================================================================================
Overall % Undetermined: 6.92%
Status: 🟡 WARNING
Reason(s):
Overall undetermined 6.92% >= 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 29919225454
Total_Samples_Analyzed 97
Number_of_Lanes 8
Global_Percent_Undetermined 6.92%
Lanes_Exceeding_Fail_Threshold None
Samples_with_Low_Reads 1
NTC_Samples_with_High_Reads 0
Significant_Unknown_Barcodes 136
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
================================================================================