Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/95/faa0feb09cb7941a48b8cd80e0ddd8/output/Reports/Demultiplex_Stats.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/7875453b49a6f58cba1e528557901b/output/Reports/Demultiplex_Stats.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f3/6b39d38e51eaa183a71bbbb736a0dd/output/Reports/Top_Unknown_Barcodes.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/d8cdb55fd4ff39fc82a9f84477f95e/output/Reports/Top_Unknown_Barcodes.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/51597337c883ab424e3a1195e4eccd/output/Reports/Demultiplex_Stats.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ce/e4bb95ca6ba44172cfa6fd6381a60c/output/Reports/Top_Unknown_Barcodes.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f3/6b39d38e51eaa183a71bbbb736a0dd/output/Reports/Demultiplex_Stats.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/70/6c706660dcb07c0b2d5224f8cc6fd9/output/Reports/Demultiplex_Stats.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/95/faa0feb09cb7941a48b8cd80e0ddd8/output/Reports/Top_Unknown_Barcodes.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c6/8b6aed353f754778cf8b7078bf0349/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/20/6bf310d549629dcc3fc4915dbde0d2/output/Reports/Demultiplex_Stats.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/20/6bf310d549629dcc3fc4915dbde0d2/output/Reports/Top_Unknown_Barcodes.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/51597337c883ab424e3a1195e4eccd/output/Reports/Top_Unknown_Barcodes.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c6/8b6aed353f754778cf8b7078bf0349/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/d8cdb55fd4ff39fc82a9f84477f95e/output/Reports/Demultiplex_Stats.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ce/e4bb95ca6ba44172cfa6fd6381a60c/output/Reports/Demultiplex_Stats.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/7875453b49a6f58cba1e528557901b/output/Reports/Top_Unknown_Barcodes.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/70/6c706660dcb07c0b2d5224f8cc6fd9/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 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 ================================================================================