Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a2/92c56398ec2202e7ef9d9796e3be24/output/Reports/Demultiplex_Stats.csv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/44/9458faf140bed424a38d67cf7943e9/output/Reports/Demultiplex_Stats.csv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/73de145827dbbd349c3aba9dd001dc/output/Reports/Top_Unknown_Barcodes.csv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/70/ea53bc901de2a111244d585d63dc3f/output/Reports/Top_Unknown_Barcodes.csv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/97/5c5ef481cfd8b05501dd97953b8790/output/Reports/Demultiplex_Stats.csv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/36/24ff362521a76e2899e0b5d941e75c/output/Reports/Top_Unknown_Barcodes.csv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/70/ea53bc901de2a111244d585d63dc3f/output/Reports/Demultiplex_Stats.csv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6e/de2681e4ef37de7e2c3759dc583c4b/output/Reports/Demultiplex_Stats.csv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a2/92c56398ec2202e7ef9d9796e3be24/output/Reports/Top_Unknown_Barcodes.csv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/43/c313691edf3c121d8eee0d4124cfeb/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ec/22f4d689d90589a81c34653078a0af/output/Reports/Demultiplex_Stats.csv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ec/22f4d689d90589a81c34653078a0af/output/Reports/Top_Unknown_Barcodes.csv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/97/5c5ef481cfd8b05501dd97953b8790/output/Reports/Top_Unknown_Barcodes.csv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/43/c313691edf3c121d8eee0d4124cfeb/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/73de145827dbbd349c3aba9dd001dc/output/Reports/Demultiplex_Stats.csv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/36/24ff362521a76e2899e0b5d941e75c/output/Reports/Demultiplex_Stats.csv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/44/9458faf140bed424a38d67cf7943e9/output/Reports/Top_Unknown_Barcodes.csv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6e/de2681e4ef37de7e2c3759dc583c4b/output/Reports/Top_Unknown_Barcodes.csv
==> 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 5.53 219191823 3964832817
2 5.68 226380649 3988663548
3 5.35 214021849 3997011677
4 5.16 205129324 3978308167
5 6.07 241714586 3979714145
6 6.20 247189192 3987606939
7 6.19 250759187 4049269221
8 6.60 268476578 4065832453
================================================================================
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 16 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
7000 GAGCAGTA GGGGGGGG 5982235 0.1509 0.0187
7001 CAGTCCAA GGGGGGGG 5499165 0.1387 0.0172
7002 TGCTTCCA GGGGGGGG 5274755 0.1330 0.0165
7003 GAACATCG GGGGGGGG 5031239 0.1269 0.0157
7004 GATGTGTG GGGGGGGG 4522407 0.1141 0.0141
7005 ATCACACG GGGGGGGG 4268044 0.1076 0.0133
7006 ATCGCCAT GGGGGGGG 3552554 0.0896 0.0111
7007 AGAACGAG GGGGGGGG 3338749 0.0842 0.0104
7008 TGGTAGCT GGGGGGGG 3177342 0.0801 0.0099
7009 TGGTACAG GGGGGGGG 3136301 0.0791 0.0098
7010 CGCTCTAT GGGGGGGG 2943005 0.0742 0.0092
7011 GAAGTTGG GGGGGGGG 2378934 0.0600 0.0074
7012 GTTCTCGT GGGGGGGG 2360630 0.0595 0.0074
7013 TCAGGCTT GGGGGGGG 2299139 0.0580 0.0072
7014 AGTGGATC GGGGGGGG 2250457 0.0568 0.0070
7015 CACTAGCT GGGGGGGG 2211125 0.0558 0.0069
Lane 2 - Found 15 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
4000 GAGCAGTA GGGGGGGG 5513099 0.1382 0.0172
4001 CAGTCCAA GGGGGGGG 5104065 0.1280 0.0159
4002 TGCTTCCA GGGGGGGG 4776222 0.1197 0.0149
4003 GAACATCG GGGGGGGG 4592942 0.1151 0.0143
4004 GATGTGTG GGGGGGGG 4260080 0.1068 0.0133
4005 ATCACACG GGGGGGGG 4122619 0.1034 0.0129
4006 AGAACGAG GGGGGGGG 3344144 0.0838 0.0104
4007 ATCGCCAT GGGGGGGG 3343801 0.0838 0.0104
4008 TGGTAGCT GGGGGGGG 3038490 0.0762 0.0095
4009 CGCTCTAT GGGGGGGG 2942485 0.0738 0.0092
4010 TGGTACAG GGGGGGGG 2873995 0.0721 0.0090
4011 TCAGGCTT GGGGGGGG 2611551 0.0655 0.0082
4012 GTTCTCGT GGGGGGGG 2244897 0.0563 0.0070
4013 GAAGTTGG GGGGGGGG 2165585 0.0543 0.0068
4014 CACTAGCT GGGGGGGG 2035444 0.0510 0.0064
Lane 3 - Found 14 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
0 GAGCAGTA GGGGGGGG 5311402 0.1329 0.0166
1 CAGTCCAA GGGGGGGG 4915169 0.1230 0.0154
2 TGCTTCCA GGGGGGGG 4577195 0.1145 0.0143
3 GAACATCG GGGGGGGG 4413744 0.1104 0.0138
4 GATGTGTG GGGGGGGG 4072772 0.1019 0.0127
5 ATCACACG GGGGGGGG 3927139 0.0983 0.0123
6 ATCGCCAT GGGGGGGG 3192924 0.0799 0.0100
7 AGAACGAG GGGGGGGG 3129215 0.0783 0.0098
8 TGGTAGCT GGGGGGGG 2914023 0.0729 0.0091
9 CGCTCTAT GGGGGGGG 2802636 0.0701 0.0088
10 TGGTACAG GGGGGGGG 2748192 0.0688 0.0086
11 TCAGGCTT GGGGGGGG 2415965 0.0604 0.0075
12 GTTCTCGT GGGGGGGG 2153867 0.0539 0.0067
13 GAAGTTGG GGGGGGGG 2063310 0.0516 0.0064
Lane 4 - Found 14 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
5000 GAGCAGTA GGGGGGGG 5160747 0.1297 0.0161
5001 CAGTCCAA GGGGGGGG 4780548 0.1202 0.0149
5002 TGCTTCCA GGGGGGGG 4448777 0.1118 0.0139
5003 GAACATCG GGGGGGGG 4302038 0.1081 0.0134
5004 GATGTGTG GGGGGGGG 3973106 0.0999 0.0124
5005 ATCACACG GGGGGGGG 3810899 0.0958 0.0119
5006 ATCGCCAT GGGGGGGG 3089021 0.0776 0.0096
5007 AGAACGAG GGGGGGGG 3025031 0.0760 0.0094
5008 TGGTAGCT GGGGGGGG 2824498 0.0710 0.0088
5009 CGCTCTAT GGGGGGGG 2704721 0.0680 0.0084
5010 TGGTACAG GGGGGGGG 2649484 0.0666 0.0083
5011 TCAGGCTT GGGGGGGG 2311320 0.0581 0.0072
5012 GTTCTCGT GGGGGGGG 2064572 0.0519 0.0064
5013 GAAGTTGG GGGGGGGG 1990342 0.0500 0.0062
Lane 5 - Found 14 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
1000 CGCATGAT GGGGGGGG 8801522 0.2212 0.0275
1001 TACGCTAC GGGGGGGG 6451405 0.1621 0.0202
1002 ACCACGAT GGGGGGGG 5928531 0.1490 0.0185
1003 CTGATCGT GGGGGGGG 5834677 0.1466 0.0182
1004 TGTGACTG GGGGGGGG 5328828 0.1339 0.0166
1005 CTTGTCGA GGGGGGGG 5233395 0.1315 0.0163
1006 GTGAAGTG GGGGGGGG 5156735 0.1296 0.0161
1007 TCGCTGTT GGGGGGGG 4476660 0.1125 0.0140
1008 ACTGAGGT GGGGGGGG 4111430 0.1033 0.0128
1009 CAACACCT GGGGGGGG 4098179 0.1030 0.0128
1010 GACGATCT GGGGGGGG 3311987 0.0832 0.0103
1011 GCGTCATT GGGGGGGG 2971871 0.0747 0.0093
1012 GCAAGATC GGGGGGGG 2552718 0.0641 0.0080
1013 AGCACTTC GGGGGGGG 2035712 0.0512 0.0064
Lane 6 - Found 15 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
6000 CGCATGAT GGGGGGGG 9502631 0.2383 0.0297
6001 TACGCTAC GGGGGGGG 7016175 0.1759 0.0219
6002 ACCACGAT GGGGGGGG 6288471 0.1577 0.0196
6003 CTGATCGT GGGGGGGG 6264162 0.1571 0.0196
6004 TGTGACTG GGGGGGGG 5825516 0.1461 0.0182
6005 GTGAAGTG GGGGGGGG 5649857 0.1417 0.0176
6006 CTTGTCGA GGGGGGGG 5549900 0.1392 0.0173
6007 TCGCTGTT GGGGGGGG 4793311 0.1202 0.0150
6008 ACTGAGGT GGGGGGGG 4439327 0.1113 0.0139
6009 CAACACCT GGGGGGGG 4289838 0.1076 0.0134
6010 GACGATCT GGGGGGGG 3539798 0.0888 0.0111
6011 GCGTCATT GGGGGGGG 3164066 0.0793 0.0099
6012 GCAAGATC GGGGGGGG 2752115 0.0690 0.0086
6013 AGCACTTC GGGGGGGG 2143644 0.0538 0.0067
6014 ATCGATCG GGGGGGGG 2030207 0.0509 0.0063
Lane 7 - Found 15 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
2000 CGCATGAT GGGGGGGG 9863571 0.2436 0.0308
2001 TACGCTAC GGGGGGGG 7415184 0.1831 0.0232
2002 ACCACGAT GGGGGGGG 6549750 0.1618 0.0205
2003 CTGATCGT GGGGGGGG 6523851 0.1611 0.0204
2004 TGTGACTG GGGGGGGG 6146532 0.1518 0.0192
2005 GTGAAGTG GGGGGGGG 5959502 0.1472 0.0186
2006 CTTGTCGA GGGGGGGG 5679512 0.1403 0.0177
2007 TCGCTGTT GGGGGGGG 5025259 0.1241 0.0157
2008 ACTGAGGT GGGGGGGG 4682954 0.1156 0.0146
2009 CAACACCT GGGGGGGG 4356898 0.1076 0.0136
2010 GACGATCT GGGGGGGG 3654107 0.0902 0.0114
2011 GCGTCATT GGGGGGGG 3285389 0.0811 0.0103
2012 GCAAGATC GGGGGGGG 2864276 0.0707 0.0089
2013 AGCACTTC GGGGGGGG 2205234 0.0545 0.0069
2014 ATCGATCG GGGGGGGG 2169143 0.0536 0.0068
Lane 8 - Found 17 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
3000 CGCATGAT GGGGGGGG 10889753 0.2678 0.0340
3001 TACGCTAC GGGGGGGG 7971544 0.1961 0.0249
3002 ACCACGAT GGGGGGGG 7225335 0.1777 0.0226
3003 CTGATCGT GGGGGGGG 7126735 0.1753 0.0223
3004 TGTGACTG GGGGGGGG 6808121 0.1674 0.0213
3005 GTGAAGTG GGGGGGGG 6571214 0.1616 0.0205
3006 CTTGTCGA GGGGGGGG 6351498 0.1562 0.0198
3007 TCGCTGTT GGGGGGGG 5562058 0.1368 0.0174
3008 ACTGAGGT GGGGGGGG 5093887 0.1253 0.0159
3009 CAACACCT GGGGGGGG 4906339 0.1207 0.0153
3010 GACGATCT GGGGGGGG 4010868 0.0986 0.0125
3011 GCGTCATT GGGGGGGG 3677385 0.0904 0.0115
3012 GCAAGATC GGGGGGGG 3128980 0.0770 0.0098
3013 AGCACTTC GGGGGGGG 2421012 0.0595 0.0076
3014 ATCGATCG GGGGGGGG 2367361 0.0582 0.0074
3015 CGGTTGTT GGGGGGGG 2132731 0.0525 0.0067
3016 GAGACGAT GGGGGGGG 2090156 0.0514 0.0065
================================================================================
5. BARCODES WITH HIGH MISMATCH RATES
================================================================================
No barcodes found with >20.0% mismatch rate
================================================================================
FINAL STATUS CHECK
================================================================================
Overall % Undetermined: 5.85%
Status: 🟡 WARNING
Reason(s):
Overall undetermined 5.85% >= 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 32011238967
Total_Samples_Analyzed 97
Number_of_Lanes 8
Global_Percent_Undetermined 5.85%
Lanes_Exceeding_Fail_Threshold None
Samples_with_Low_Reads 0
NTC_Samples_with_High_Reads 0
Significant_Unknown_Barcodes 120
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
================================================================================