SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/CTRL_8C_26psu_1_S17_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: 497913). Second best hit was Nextera (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/CTRL_8C_26psu_1_S17_L001_R1_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 54.64 s (4 us/read; 15.13 M reads/minute). === Summary === Total reads processed: 13,781,290 Reads with adapters: 10,464,679 (75.9%) Reads written (passing filters): 13,781,290 (100.0%) Total basepairs processed: 2,067,193,500 bp Quality-trimmed: 4,066,824 bp (0.2%) Total written (filtered): 1,647,743,968 bp (79.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10464679 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 31.2% C: 15.6% G: 18.6% T: 34.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2115194 3445322.5 0 2115194 2 272894 861330.6 0 272894 3 153504 215332.7 0 153504 4 91420 53833.2 0 91420 5 70039 13458.3 0 70039 6 67409 3364.6 0 67409 7 55787 841.1 0 55787 8 69144 210.3 0 69144 9 70298 52.6 0 69211 1087 10 65479 13.1 1 61710 3769 11 71864 3.3 1 66237 5627 12 69709 0.8 1 65113 4596 13 68649 0.2 1 64099 4550 14 71371 0.2 1 66030 5341 15 72335 0.2 1 67349 4986 16 73096 0.2 1 67373 5723 17 87823 0.2 1 80650 7173 18 73513 0.2 1 68795 4718 19 64905 0.2 1 60375 4530 20 76453 0.2 1 71101 5352 21 83756 0.2 1 77496 6260 22 71860 0.2 1 67380 4480 23 82380 0.2 1 76793 5587 24 76931 0.2 1 70531 6400 25 82900 0.2 1 77013 5887 26 75729 0.2 1 70800 4929 27 84549 0.2 1 78103 6446 28 82744 0.2 1 76781 5963 29 87966 0.2 1 80505 7461 30 92743 0.2 1 87256 5487 31 72956 0.2 1 68033 4923 32 86797 0.2 1 81028 5769 33 84425 0.2 1 77963 6462 34 100255 0.2 1 92044 8211 35 94925 0.2 1 87424 7501 36 151403 0.2 1 144008 7395 37 34431 0.2 1 30234 4197 38 81160 0.2 1 76071 5089 39 98494 0.2 1 91430 7064 40 94229 0.2 1 88176 6053 41 105491 0.2 1 97539 7952 42 89350 0.2 1 81822 7528 43 144554 0.2 1 136557 7997 44 52667 0.2 1 48059 4608 45 80312 0.2 1 74870 5442 46 96347 0.2 1 89778 6569 47 100619 0.2 1 94323 6296 48 87690 0.2 1 81510 6180 49 103414 0.2 1 95838 7576 50 86689 0.2 1 81209 5480 51 92177 0.2 1 85927 6250 52 98128 0.2 1 90537 7591 53 111470 0.2 1 104728 6742 54 79643 0.2 1 74106 5537 55 98690 0.2 1 92247 6443 56 114543 0.2 1 107715 6828 57 91001 0.2 1 84632 6369 58 94668 0.2 1 89637 5031 59 73433 0.2 1 68107 5326 60 100893 0.2 1 94469 6424 61 94258 0.2 1 88482 5776 62 93437 0.2 1 87751 5686 63 86189 0.2 1 80341 5848 64 87860 0.2 1 82577 5283 65 95579 0.2 1 89442 6137 66 102630 0.2 1 95991 6639 67 110068 0.2 1 101200 8868 68 211731 0.2 1 201178 10553 69 44241 0.2 1 40907 3334 70 13519 0.2 1 11187 2332 71 49103 0.2 1 45715 3388 72 77796 0.2 1 73169 4627 73 81869 0.2 1 76719 5150 74 82069 0.2 1 76896 5173 75 80967 0.2 1 75833 5134 76 79680 0.2 1 74662 5018 77 80336 0.2 1 75241 5095 78 75811 0.2 1 70973 4838 79 74367 0.2 1 69524 4843 80 73534 0.2 1 69012 4522 81 72214 0.2 1 67540 4674 82 70474 0.2 1 66112 4362 83 68507 0.2 1 64201 4306 84 66184 0.2 1 61986 4198 85 64533 0.2 1 60445 4088 86 62422 0.2 1 58352 4070 87 59642 0.2 1 55842 3800 88 59336 0.2 1 55541 3795 89 56406 0.2 1 52805 3601 90 56172 0.2 1 52495 3677 91 53832 0.2 1 50312 3520 92 51101 0.2 1 47868 3233 93 48168 0.2 1 45095 3073 94 47770 0.2 1 44644 3126 95 44085 0.2 1 41250 2835 96 41623 0.2 1 38858 2765 97 39066 0.2 1 36394 2672 98 35943 0.2 1 33581 2362 99 35291 0.2 1 32748 2543 100 32499 0.2 1 30308 2191 101 30357 0.2 1 28386 1971 102 28530 0.2 1 26552 1978 103 26074 0.2 1 24341 1733 104 24528 0.2 1 22773 1755 105 21898 0.2 1 20353 1545 106 20241 0.2 1 18793 1448 107 18328 0.2 1 16963 1365 108 17608 0.2 1 16339 1269 109 15247 0.2 1 14123 1124 110 14054 0.2 1 12990 1064 111 12816 0.2 1 11851 965 112 11319 0.2 1 10448 871 113 9601 0.2 1 8829 772 114 8785 0.2 1 8065 720 115 7727 0.2 1 7075 652 116 6667 0.2 1 6137 530 117 5842 0.2 1 5341 501 118 5116 0.2 1 4650 466 119 4257 0.2 1 3896 361 120 3744 0.2 1 3400 344 121 3378 0.2 1 3078 300 122 2708 0.2 1 2469 239 123 2529 0.2 1 2246 283 124 2015 0.2 1 1814 201 125 1810 0.2 1 1626 184 126 1647 0.2 1 1490 157 127 1294 0.2 1 1150 144 128 1010 0.2 1 909 101 129 964 0.2 1 860 104 130 736 0.2 1 664 72 131 614 0.2 1 553 61 132 536 0.2 1 487 49 133 628 0.2 1 563 65 134 1415 0.2 1 1342 73 135 608 0.2 1 567 41 136 207 0.2 1 188 19 137 132 0.2 1 118 14 138 84 0.2 1 75 9 139 56 0.2 1 44 12 140 46 0.2 1 36 10 141 40 0.2 1 35 5 142 28 0.2 1 23 5 143 39 0.2 1 32 7 144 49 0.2 1 44 5 145 178 0.2 1 162 16 146 250 0.2 1 233 17 147 1272 0.2 1 1190 82 148 812 0.2 1 771 41 149 417 0.2 1 393 24 150 2828 0.2 1 2398 430 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/CTRL_8C_26psu_1_S17_L001_R1_001.fastq.gz ============================================= 13781290 sequences processed in total