SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_26psu_1_S13_L001_R1_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.6.4_dev Cutadapt version: 2.4 Python version: could not detect Number of cores used for trimming: 8 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Using Illumina adapter for trimming (count: 538094). Second best hit was smallRNA (count: 0) Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /gscratch/scrubbed/strigg/analyses/20200427/TG_PE_FASTQS/FastQC --threads 28 Output file will be GZIP compressed This is cutadapt 2.4 with Python 3.7.6 Command line parameters: -j 8 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_26psu_1_S13_L001_R1_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 83.34 s (4 us/read; 15.95 M reads/minute). === Summary === Total reads processed: 22,159,935 Reads with adapters: 17,366,785 (78.4%) Reads written (passing filters): 22,159,935 (100.0%) Total basepairs processed: 3,323,990,250 bp Quality-trimmed: 20,636,466 bp (0.6%) Total written (filtered): 2,599,584,885 bp (78.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 17366785 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.9% C: 14.0% G: 20.5% T: 35.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2904827 5539983.8 0 2904827 2 423079 1384995.9 0 423079 3 231866 346249.0 0 231866 4 143449 86562.2 0 143449 5 117570 21640.6 0 117570 6 115529 5410.1 0 115529 7 96119 1352.5 0 96119 8 119364 338.1 0 119364 9 118406 84.5 0 116886 1520 10 112051 21.1 1 106032 6019 11 122987 5.3 1 113734 9253 12 119477 1.3 1 111842 7635 13 120023 0.3 1 112246 7777 14 122963 0.3 1 114085 8878 15 127528 0.3 1 119209 8319 16 126445 0.3 1 117002 9443 17 152761 0.3 1 140488 12273 18 129037 0.3 1 121213 7824 19 112889 0.3 1 105773 7116 20 133616 0.3 1 125004 8612 21 146516 0.3 1 136291 10225 22 126419 0.3 1 119045 7374 23 145391 0.3 1 135716 9675 24 136894 0.3 1 125670 11224 25 145117 0.3 1 135313 9804 26 134897 0.3 1 126717 8180 27 148757 0.3 1 137734 11023 28 145635 0.3 1 135492 10143 29 153188 0.3 1 140948 12240 30 163373 0.3 1 154030 9343 31 130689 0.3 1 122129 8560 32 157390 0.3 1 147156 10234 33 145226 0.3 1 135269 9957 34 158524 0.3 1 147826 10698 35 161582 0.3 1 148734 12848 36 173098 0.3 1 162838 10260 37 141921 0.3 1 133053 8868 38 164933 0.3 1 154468 10465 39 167185 0.3 1 155913 11272 40 175799 0.3 1 163207 12592 41 197239 0.3 1 176427 20812 42 165247 0.3 1 150517 14730 43 270149 0.3 1 254538 15611 44 85600 0.3 1 76961 8639 45 197628 0.3 1 175697 21931 46 723044 0.3 1 688287 34757 47 254889 0.3 1 240372 14517 48 114855 0.3 1 101708 13147 49 409546 0.3 1 390013 19533 50 125438 0.3 1 116192 9246 51 110069 0.3 1 99667 10402 52 381945 0.3 1 364475 17470 53 196688 0.3 1 188239 8449 54 63003 0.3 1 58174 4829 55 106109 0.3 1 101117 4992 56 55521 0.3 1 50154 5367 57 169184 0.3 1 161794 7390 58 35182 0.3 1 32212 2970 59 44244 0.3 1 39185 5059 60 173147 0.3 1 165425 7722 61 86440 0.3 1 82402 4038 62 40559 0.3 1 36479 4080 63 130914 0.3 1 123404 7510 64 122315 0.3 1 116337 5978 65 65805 0.3 1 60428 5377 66 148115 0.3 1 139100 9015 67 175930 0.3 1 163369 12561 68 293688 0.3 1 278052 15636 69 189726 0.3 1 179114 10612 70 75474 0.3 1 69457 6017 71 27345 0.3 1 23952 3393 72 97969 0.3 1 91968 6001 73 138145 0.3 1 130111 8034 74 143624 0.3 1 135279 8345 75 142674 0.3 1 134066 8608 76 141682 0.3 1 133308 8374 77 141205 0.3 1 132947 8258 78 133036 0.3 1 124966 8070 79 131630 0.3 1 123633 7997 80 128859 0.3 1 121116 7743 81 126119 0.3 1 118667 7452 82 123492 0.3 1 116262 7230 83 118847 0.3 1 111615 7232 84 115583 0.3 1 108642 6941 85 111409 0.3 1 104817 6592 86 107099 0.3 1 100545 6554 87 102731 0.3 1 96477 6254 88 101527 0.3 1 95245 6282 89 95383 0.3 1 89600 5783 90 95037 0.3 1 89230 5807 91 89836 0.3 1 84395 5441 92 84977 0.3 1 79865 5112 93 79479 0.3 1 74762 4717 94 76672 0.3 1 72010 4662 95 70676 0.3 1 66313 4363 96 66886 0.3 1 62766 4120 97 63105 0.3 1 59150 3955 98 58813 0.3 1 55101 3712 99 56801 0.3 1 52921 3880 100 51251 0.3 1 47973 3278 101 48131 0.3 1 44969 3162 102 43975 0.3 1 41134 2841 103 40749 0.3 1 38132 2617 104 37602 0.3 1 35059 2543 105 33601 0.3 1 31318 2283 106 30687 0.3 1 28622 2065 107 27550 0.3 1 25698 1852 108 25919 0.3 1 24135 1784 109 23271 0.3 1 21584 1687 110 20524 0.3 1 19077 1447 111 18563 0.3 1 17263 1300 112 16204 0.3 1 15036 1168 113 14110 0.3 1 13017 1093 114 12321 0.3 1 11394 927 115 10629 0.3 1 9884 745 116 9483 0.3 1 8756 727 117 8057 0.3 1 7440 617 118 7067 0.3 1 6491 576 119 5777 0.3 1 5264 513 120 4917 0.3 1 4511 406 121 4181 0.3 1 3800 381 122 3506 0.3 1 3174 332 123 2912 0.3 1 2640 272 124 2546 0.3 1 2297 249 125 2101 0.3 1 1902 199 126 1717 0.3 1 1548 169 127 1536 0.3 1 1361 175 128 1201 0.3 1 1095 106 129 1012 0.3 1 912 100 130 739 0.3 1 668 71 131 638 0.3 1 572 66 132 553 0.3 1 500 53 133 556 0.3 1 500 56 134 665 0.3 1 607 58 135 362 0.3 1 324 38 136 207 0.3 1 176 31 137 143 0.3 1 128 15 138 99 0.3 1 86 13 139 84 0.3 1 72 12 140 58 0.3 1 50 8 141 42 0.3 1 38 4 142 37 0.3 1 29 8 143 24 0.3 1 22 2 144 25 0.3 1 17 8 145 26 0.3 1 22 4 146 29 0.3 1 21 8 147 85 0.3 1 77 8 148 64 0.3 1 59 5 149 40 0.3 1 35 5 150 355 0.3 1 318 37 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_26psu_1_S13_L001_R1_001.fastq.gz ============================================= 22159935 sequences processed in total