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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 6.38 244051853 3823250855
2 6.42 248061909 3861686106
3 6.60 254304579 3851275165
4 6.80 259655929 3820642153
5 6.51 250131631 3845143934
6 6.49 251922362 3881820429
7 6.31 247868778 3929568091
8 6.32 247513752 3913431892
================================================================================
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 13 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
3000 CCAGTCGTCA GGGGGGGGGG 6962531 0.1821 0.0225
3001 ATGACAGCAC GGGGGGGGGG 6066989 0.1587 0.0196
3002 AGATTAGCGT GGGGGGGGGG 5414319 0.1416 0.0175
3003 GAGCAGCTTG GGGGGGGGGG 4509348 0.1179 0.0146
3004 TATCCGCGTC GGGGGGGGGG 3561076 0.0931 0.0115
3005 TGGAGATCGA GGGGGGGGGG 3547884 0.0928 0.0115
3006 CCTAAGCTGA GGGGGGGGGG 3378865 0.0884 0.0109
3007 TAACTTGGTC GGGGGGGGGG 3219663 0.0842 0.0104
3008 CCGATAGTAG GGGGGGGGGG 2615803 0.0684 0.0085
3009 CAACTGCGCA GGGGGGGGGG 2422296 0.0634 0.0078
3010 TCCAACTGAA GGGGGGGGGG 2048053 0.0536 0.0066
3011 ACGAGACGTC GGGGGGGGGG 1993788 0.0521 0.0064
3012 GCCACCTAGT GGGGGGGGGG 1934287 0.0506 0.0063
Lane 2 - Found 13 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
2000 CCAGTCGTCA GGGGGGGGGG 7002464 0.1813 0.0226
2001 ATGACAGCAC GGGGGGGGGG 6079630 0.1574 0.0197
2002 AGATTAGCGT GGGGGGGGGG 5403185 0.1399 0.0175
2003 GAGCAGCTTG GGGGGGGGGG 4539477 0.1176 0.0147
2004 TGGAGATCGA GGGGGGGGGG 3565220 0.0923 0.0115
2005 TATCCGCGTC GGGGGGGGGG 3556202 0.0921 0.0115
2006 CCTAAGCTGA GGGGGGGGGG 3379747 0.0875 0.0109
2007 TAACTTGGTC GGGGGGGGGG 3247512 0.0841 0.0105
2008 CCGATAGTAG GGGGGGGGGG 2660223 0.0689 0.0086
2009 CAACTGCGCA GGGGGGGGGG 2448085 0.0634 0.0079
2010 TCCAACTGAA GGGGGGGGGG 2048279 0.0530 0.0066
2011 ACGAGACGTC GGGGGGGGGG 2022141 0.0524 0.0065
2012 GCCACCTAGT GGGGGGGGGG 1945197 0.0504 0.0063
Lane 3 - Found 13 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
5000 CCAGTCGTCA GGGGGGGGGG 7009127 0.1820 0.0227
5001 ATGACAGCAC GGGGGGGGGG 6077048 0.1578 0.0196
5002 AGATTAGCGT GGGGGGGGGG 5396656 0.1401 0.0174
5003 GAGCAGCTTG GGGGGGGGGG 4552837 0.1182 0.0147
5004 TGGAGATCGA GGGGGGGGGG 3605847 0.0936 0.0117
5005 TATCCGCGTC GGGGGGGGGG 3571626 0.0927 0.0115
5006 CCTAAGCTGA GGGGGGGGGG 3367563 0.0874 0.0109
5007 TAACTTGGTC GGGGGGGGGG 3222048 0.0837 0.0104
5008 CCGATAGTAG GGGGGGGGGG 2801355 0.0727 0.0091
5009 CAACTGCGCA GGGGGGGGGG 2502817 0.0650 0.0081
5010 TCCAACTGAA GGGGGGGGGG 2071468 0.0538 0.0067
5011 ACGAGACGTC GGGGGGGGGG 2049373 0.0532 0.0066
5012 GCCACCTAGT GGGGGGGGGG 2015133 0.0523 0.0065
Lane 4 - Found 13 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
6000 CCAGTCGTCA GGGGGGGGGG 6759686 0.1769 0.0219
6001 ATGACAGCAC GGGGGGGGGG 5851328 0.1532 0.0189
6002 AGATTAGCGT GGGGGGGGGG 5216733 0.1365 0.0169
6003 GAGCAGCTTG GGGGGGGGGG 4309555 0.1128 0.0139
6004 TGGAGATCGA GGGGGGGGGG 3611682 0.0945 0.0117
6005 TATCCGCGTC GGGGGGGGGG 3485342 0.0912 0.0113
6006 CCTAAGCTGA GGGGGGGGGG 3120977 0.0817 0.0101
6007 TAACTTGGTC GGGGGGGGGG 3021419 0.0791 0.0098
6008 CCGATAGTAG GGGGGGGGGG 2890807 0.0757 0.0093
6009 CAACTGCGCA GGGGGGGGGG 2547273 0.0667 0.0082
6010 GCCACCTAGT GGGGGGGGGG 2184381 0.0572 0.0071
6011 TCCAACTGAA GGGGGGGGGG 2049099 0.0536 0.0066
6012 ACGAGACGTC GGGGGGGGGG 2006695 0.0525 0.0065
Lane 5 - Found 13 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
0 CCAGTCGTCA GGGGGGGGGG 6619744 0.1722 0.0214
1 ATGACAGCAC GGGGGGGGGG 5783382 0.1504 0.0187
2 AGATTAGCGT GGGGGGGGGG 5159306 0.1342 0.0167
3 GAGCAGCTTG GGGGGGGGGG 4274546 0.1112 0.0138
4 TGGAGATCGA GGGGGGGGGG 3482530 0.0906 0.0113
5 TATCCGCGTC GGGGGGGGGG 3380706 0.0879 0.0109
6 CCTAAGCTGA GGGGGGGGGG 3111228 0.0809 0.0101
7 TAACTTGGTC GGGGGGGGGG 3018179 0.0785 0.0098
8 CCGATAGTAG GGGGGGGGGG 2792883 0.0726 0.0090
9 CAACTGCGCA GGGGGGGGGG 2444129 0.0636 0.0079
10 GCCACCTAGT GGGGGGGGGG 2051625 0.0534 0.0066
11 TCCAACTGAA GGGGGGGGGG 1972323 0.0513 0.0064
12 ACGAGACGTC GGGGGGGGGG 1946441 0.0506 0.0063
Lane 6 - Found 13 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
4000 CCAGTCGTCA GGGGGGGGGG 7005402 0.1805 0.0227
4001 ATGACAGCAC GGGGGGGGGG 6099344 0.1571 0.0197
4002 AGATTAGCGT GGGGGGGGGG 5434523 0.1400 0.0176
4003 GAGCAGCTTG GGGGGGGGGG 4574407 0.1178 0.0148
4004 TGGAGATCGA GGGGGGGGGG 3591340 0.0925 0.0116
4005 TATCCGCGTC GGGGGGGGGG 3577830 0.0922 0.0116
4006 CCTAAGCTGA GGGGGGGGGG 3455802 0.0890 0.0112
4007 TAACTTGGTC GGGGGGGGGG 3298469 0.0850 0.0107
4008 CCGATAGTAG GGGGGGGGGG 2724401 0.0702 0.0088
4009 CAACTGCGCA GGGGGGGGGG 2486138 0.0640 0.0080
4010 ACGAGACGTC GGGGGGGGGG 2066669 0.0532 0.0067
4011 TCCAACTGAA GGGGGGGGGG 2062199 0.0531 0.0067
4012 GCCACCTAGT GGGGGGGGGG 1973703 0.0508 0.0064
Lane 7 - Found 12 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
1000 CCAGTCGTCA GGGGGGGGGG 7173914 0.1826 0.0232
1001 ATGACAGCAC GGGGGGGGGG 6237383 0.1587 0.0202
1002 AGATTAGCGT GGGGGGGGGG 5539174 0.1410 0.0179
1003 GAGCAGCTTG GGGGGGGGGG 4704683 0.1197 0.0152
1004 TGGAGATCGA GGGGGGGGGG 3654695 0.0930 0.0118
1005 TATCCGCGTC GGGGGGGGGG 3615798 0.0920 0.0117
1006 CCTAAGCTGA GGGGGGGGGG 3454689 0.0879 0.0112
1007 TAACTTGGTC GGGGGGGGGG 3351724 0.0853 0.0108
1008 CCGATAGTAG GGGGGGGGGG 2736628 0.0696 0.0088
1009 CAACTGCGCA GGGGGGGGGG 2516660 0.0640 0.0081
1010 ACGAGACGTC GGGGGGGGGG 2098673 0.0534 0.0068
1011 TCCAACTGAA GGGGGGGGGG 2073661 0.0528 0.0067
Lane 8 - Found 12 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
7000 CCAGTCGTCA GGGGGGGGGG 7182417 0.1835 0.0232
7001 ATGACAGCAC GGGGGGGGGG 6238558 0.1594 0.0202
7002 AGATTAGCGT GGGGGGGGGG 5574858 0.1425 0.0180
7003 GAGCAGCTTG GGGGGGGGGG 4673417 0.1194 0.0151
7004 TGGAGATCGA GGGGGGGGGG 3647178 0.0932 0.0118
7005 TATCCGCGTC GGGGGGGGGG 3606572 0.0922 0.0117
7006 CCTAAGCTGA GGGGGGGGGG 3444183 0.0880 0.0111
7007 TAACTTGGTC GGGGGGGGGG 3327404 0.0850 0.0108
7008 CCGATAGTAG GGGGGGGGGG 2679540 0.0685 0.0087
7009 CAACTGCGCA GGGGGGGGGG 2494052 0.0637 0.0081
7010 TCCAACTGAA GGGGGGGGGG 2072877 0.0530 0.0067
7011 ACGAGACGTC GGGGGGGGGG 2061601 0.0527 0.0067
================================================================================
5. BARCODES WITH HIGH MISMATCH RATES
================================================================================
No barcodes found with >20.0% mismatch rate
================================================================================
FINAL STATUS CHECK
================================================================================
Overall % Undetermined: 6.48%
Status: 🟡 WARNING
Reason(s):
Overall undetermined 6.48% >= 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 30926818625
Total_Samples_Analyzed 97
Number_of_Lanes 8
Global_Percent_Undetermined 6.48%
Lanes_Exceeding_Fail_Threshold None
Samples_with_Low_Reads 0
NTC_Samples_with_High_Reads 0
Significant_Unknown_Barcodes 102
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
================================================================================