Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c2/f3b6065cac37cf1dc8943c7270a58c/output/Reports/Demultiplex_Stats.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f8/10af8c782695e52ce4344e42745f74/output/Reports/Demultiplex_Stats.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1a/02c90b191cce101f96625fd648cb2a/output/Reports/Top_Unknown_Barcodes.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/72/c8ff5af4ddd605d3b26679c068c7c4/output/Reports/Top_Unknown_Barcodes.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d0/7d534cbd3ad369b7dafd0d517f0c73/output/Reports/Demultiplex_Stats.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/a7d21c1f9883c0aed2ffeacf4c8229/output/Reports/Top_Unknown_Barcodes.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1a/02c90b191cce101f96625fd648cb2a/output/Reports/Demultiplex_Stats.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bc/cb1850e3a16ff6caa1f0a70f672684/output/Reports/Demultiplex_Stats.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c2/f3b6065cac37cf1dc8943c7270a58c/output/Reports/Top_Unknown_Barcodes.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3c/e3f060ef91ab35c837366c007d09a1/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7b/4d3ca8d8defb338de5c0c615fb26a7/output/Reports/Demultiplex_Stats.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7b/4d3ca8d8defb338de5c0c615fb26a7/output/Reports/Top_Unknown_Barcodes.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d0/7d534cbd3ad369b7dafd0d517f0c73/output/Reports/Top_Unknown_Barcodes.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3c/e3f060ef91ab35c837366c007d09a1/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/72/c8ff5af4ddd605d3b26679c068c7c4/output/Reports/Demultiplex_Stats.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/a7d21c1f9883c0aed2ffeacf4c8229/output/Reports/Demultiplex_Stats.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f8/10af8c782695e52ce4344e42745f74/output/Reports/Top_Unknown_Barcodes.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bc/cb1850e3a16ff6caa1f0a70f672684/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 388 rows from Demultiplex_Stats.csv ================================================================================ 1. % UNDETERMINED PER LANE ================================================================================ Undetermined Summary per Lane: %_Undetermined Undetermined_Reads Total_Reads Lane 1 5.22 211346066 4046804284 2 5.33 213604774 4005741146 3 5.18 210105409 4055602240 4 4.90 196957742 4015754163 5 3.56 144447804 4059237853 6 3.75 152658631 4075260777 7 3.85 158180325 4111566941 8 3.87 157368459 4070182884 ================================================================================ 2. SAMPLES WITH <1000000 READS (NON-NTC) ================================================================================ No samples found with <1000000 reads ================================================================================ 3. NTC SAMPLES WITH >2000000 READS ================================================================================ Found 1 NTC samples with >2000000 reads: SampleID Index # Reads 0 NTC_0001_0001_23LGNLLT4_1 AATTGGCACA-CAGTCGGAGT 3344443 ================================================================================ 4. TOP UNKNOWN BARCODES (>0.05% OF LANE READS) ================================================================================ Loading Top_Unknown_Barcodes.csv from: merged/Reports/Top_Unknown_Barcodes.csv Lane 1 - Found 14 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 1001 CCAACTGTAT GGGGGGGGGG 16512354 0.4080 0.0509 1002 GTGACGCACA GGGGGGGGGG 6109919 0.1510 0.0188 1003 GAGTAGTGAC GGGGGGGGGG 5095319 0.1259 0.0157 1004 GATAGGTGAA GGGGGGGGGG 4626452 0.1143 0.0143 1005 AGACGACAGA GGGGGGGGGG 4425791 0.1094 0.0136 1006 TGAGTGTACA GGGGGGGGGG 3787896 0.0936 0.0117 1007 TAGCGAGGCT GGGGGGGGGG 3727400 0.0921 0.0115 1008 AAGGTGTACT GGGGGGGGGG 3677456 0.0909 0.0113 1009 CTCTATACTG GGGGGGGGGG 3616335 0.0894 0.0111 1010 TGTGACGTAT GGGGGGGGGG 3000754 0.0742 0.0093 1011 ACCAGGAATT GGGGGGGGGG 2549661 0.0630 0.0079 1012 TAAGGCTCAC GGGGGGGGGG 2174868 0.0537 0.0067 1013 ATCATACCGC GGGGGGGGGG 2147851 0.0531 0.0066 1014 TCTCCGTACT GGGGGGGGGG 2053900 0.0508 0.0063 Lane 2 - Found 14 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 2001 CCAACTGTAT GGGGGGGGGG 15161678 0.3785 0.0467 2002 GTGACGCACA GGGGGGGGGG 5669869 0.1415 0.0175 2003 GAGTAGTGAC GGGGGGGGGG 5064184 0.1264 0.0156 2004 GATAGGTGAA GGGGGGGGGG 4188170 0.1046 0.0129 2005 AGACGACAGA GGGGGGGGGG 4035783 0.1007 0.0124 2006 TAGCGAGGCT GGGGGGGGGG 3606840 0.0900 0.0111 2007 TGAGTGTACA GGGGGGGGGG 3514278 0.0877 0.0108 2008 AAGGTGTACT GGGGGGGGGG 3471119 0.0867 0.0107 2009 CTCTATACTG GGGGGGGGGG 3427535 0.0856 0.0106 2010 ATCCAGCATG AGATCTCGGT 3346817 0.0836 0.0103 2011 TGTGACGTAT GGGGGGGGGG 2561274 0.0639 0.0079 2012 ACCAGGAATT GGGGGGGGGG 2473783 0.0618 0.0076 2013 ATCATACCGC GGGGGGGGGG 2088118 0.0521 0.0064 2014 TAAGGCTCAC GGGGGGGGGG 2028720 0.0506 0.0063 Lane 3 - Found 12 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 4001 CCAACTGTAT GGGGGGGGGG 15100371 0.3723 0.0465 4002 GTGACGCACA GGGGGGGGGG 5596458 0.1380 0.0173 4003 GAGTAGTGAC GGGGGGGGGG 4917015 0.1212 0.0152 4004 GATAGGTGAA GGGGGGGGGG 4171417 0.1029 0.0129 4005 AGACGACAGA GGGGGGGGGG 3959603 0.0976 0.0122 4006 TGAGTGTACA GGGGGGGGGG 3470378 0.0856 0.0107 4007 TAGCGAGGCT GGGGGGGGGG 3457160 0.0852 0.0107 4008 AAGGTGTACT GGGGGGGGGG 3367739 0.0830 0.0104 4009 CTCTATACTG GGGGGGGGGG 3290240 0.0811 0.0101 4010 ATCCAGCATG AGATCTCGGT 3113478 0.0768 0.0096 4011 TGTGACGTAT GGGGGGGGGG 2514623 0.0620 0.0078 4012 ACCAGGAATT GGGGGGGGGG 2425246 0.0598 0.0075 Lane 4 - Found 12 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 5001 CCAACTGTAT GGGGGGGGGG 14837857 0.3695 0.0457 5002 GTGACGCACA GGGGGGGGGG 5492973 0.1368 0.0169 5003 GAGTAGTGAC GGGGGGGGGG 4397564 0.1095 0.0136 5004 GATAGGTGAA GGGGGGGGGG 4211227 0.1049 0.0130 5005 AGACGACAGA GGGGGGGGGG 3868534 0.0963 0.0119 5006 TGAGTGTACA GGGGGGGGGG 3474004 0.0865 0.0107 5007 TAGCGAGGCT GGGGGGGGGG 3315912 0.0826 0.0102 5008 AAGGTGTACT GGGGGGGGGG 3173047 0.0790 0.0098 5009 CTCTATACTG GGGGGGGGGG 3114019 0.0775 0.0096 5010 TGTGACGTAT GGGGGGGGGG 2835605 0.0706 0.0087 5011 ACCAGGAATT GGGGGGGGGG 2230348 0.0555 0.0069 5012 TAAGGCTCAC GGGGGGGGGG 2041112 0.0508 0.0063 Lane 5 - Found 6 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 6001 TTGGATTGTC GGGGGGGGGG 6386285 0.1573 0.0197 6002 TGCAACACTA GGGGGGGGGG 3653641 0.0900 0.0113 6003 TCGCATGACA GGGGGGGGGG 3506075 0.0864 0.0108 6004 CATCAGGCGT GGGGGGGGGG 3140590 0.0774 0.0097 6005 CCACCTGCTT GGGGGGGGGG 3040546 0.0749 0.0094 6006 CCAGTGCACT GGGGGGGGGG 2445200 0.0602 0.0075 Lane 6 - Found 6 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 7001 TTGGATTGTC GGGGGGGGGG 6897136 0.1692 0.0213 7002 TGCAACACTA GGGGGGGGGG 3977480 0.0976 0.0123 7003 TCGCATGACA GGGGGGGGGG 3856686 0.0946 0.0119 7004 CATCAGGCGT GGGGGGGGGG 3410098 0.0837 0.0105 7005 CCACCTGCTT GGGGGGGGGG 3267007 0.0802 0.0101 7006 CCAGTGCACT GGGGGGGGGG 2652819 0.0651 0.0082 Lane 7 - Found 8 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 3001 TTGGATTGTC GGGGGGGGGG 7196004 0.1750 0.0222 3002 TGCAACACTA GGGGGGGGGG 4140080 0.1007 0.0128 3003 TCGCATGACA GGGGGGGGGG 4133143 0.1005 0.0127 3004 CATCAGGCGT GGGGGGGGGG 3609071 0.0878 0.0111 3005 CCACCTGCTT GGGGGGGGGG 3599203 0.0875 0.0111 3006 CCAGTGCACT GGGGGGGGGG 2744600 0.0668 0.0085 3007 GAAGCAAGCG GGGGGGGGGG 2170074 0.0528 0.0067 3008 ACAATAGCAC GGGGGGGGGG 2116078 0.0515 0.0065 Lane 8 - Found 9 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 0 TTGGATTGTC GGGGGGGGGG 7535038 0.1851 0.0232 1 TGCAACACTA GGGGGGGGGG 4232194 0.1040 0.0130 2 TCGCATGACA GGGGGGGGGG 4042491 0.0993 0.0125 3 CATCAGGCGT GGGGGGGGGG 3662512 0.0900 0.0113 4 CCACCTGCTT GGGGGGGGGG 3431616 0.0843 0.0106 5 CCAGTGCACT GGGGGGGGGG 2926417 0.0719 0.0090 6 GAAGCAAGCG GGGGGGGGGG 2275317 0.0559 0.0070 7 ACAATAGCAC GGGGGGGGGG 2140678 0.0526 0.0066 8 CGTACTTAGA GGGGGGGGGG 2057009 0.0505 0.0063 ================================================================================ 5. BARCODES WITH HIGH MISMATCH RATES ================================================================================ No barcodes found with >20.0% mismatch rate ================================================================================ FINAL STATUS CHECK ================================================================================ Overall % Undetermined: 4.45% Status: 🔴 FAIL Reason(s): NTC sample NTC_0001_0001_23LGNLLT4_1 has 3,344,443 reads > 2,000,000 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 Fail file created: ./samplesheet_status.fail ================================================================================ QC SUMMARY ================================================================================ Metric Value Total_Reads 32440150288 Total_Samples_Analyzed 96 Number_of_Lanes 8 Global_Percent_Undetermined 4.45% Lanes_Exceeding_Fail_Threshold None Samples_with_Low_Reads 0 NTC_Samples_with_High_Reads 1 Significant_Unknown_Barcodes 81 High_Mismatch_Barcodes 0 Final_Status FAIL ================================================================================ QC Analysis completed successfully! Flowcell Status: FAIL Reports generated: - ./qc_report.csv - ./qc_report_detailed.txt - ./samplesheet_status.fail ================================================================================