SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_32psu_1_S5_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: 749024). 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/8C_32psu_1_S5_L001_R1_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 43.57 s (3 us/read; 19.28 M reads/minute). === Summary === Total reads processed: 14,000,021 Reads with adapters: 12,585,652 (89.9%) Reads written (passing filters): 14,000,021 (100.0%) Total basepairs processed: 2,100,003,150 bp Quality-trimmed: 3,933,676 bp (0.2%) Total written (filtered): 1,383,592,146 bp (65.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 12585652 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.5% C: 15.4% G: 21.7% T: 34.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 794832 3500005.2 0 794832 2 137499 875001.3 0 137499 3 88574 218750.3 0 88574 4 55463 54687.6 0 55463 5 52467 13671.9 0 52467 6 51009 3418.0 0 51009 7 43440 854.5 0 43440 8 53882 213.6 0 53882 9 54563 53.4 0 53971 592 10 51819 13.4 1 49209 2610 11 57911 3.3 1 53768 4143 12 56442 0.8 1 53088 3354 13 57081 0.2 1 53583 3498 14 60408 0.2 1 56320 4088 15 62034 0.2 1 58378 3656 16 63250 0.2 1 58624 4626 17 76887 0.2 1 70864 6023 18 66288 0.2 1 62429 3859 19 56979 0.2 1 53412 3567 20 69709 0.2 1 65411 4298 21 77411 0.2 1 72341 5070 22 66479 0.2 1 62829 3650 23 78177 0.2 1 73134 5043 24 74482 0.2 1 68678 5804 25 80818 0.2 1 75690 5128 26 74228 0.2 1 70119 4109 27 83394 0.2 1 77679 5715 28 82403 0.2 1 76936 5467 29 90670 0.2 1 83444 7226 30 98605 0.2 1 93586 5019 31 72678 0.2 1 68276 4402 32 92171 0.2 1 86613 5558 33 90475 0.2 1 84682 5793 34 99774 0.2 1 93593 6181 35 93327 0.2 1 87313 6014 36 107093 0.2 1 100026 7067 37 103597 0.2 1 96127 7470 38 104511 0.2 1 98484 6027 39 106907 0.2 1 100401 6506 40 106662 0.2 1 100220 6442 41 122253 0.2 1 114028 8225 42 104346 0.2 1 96706 7640 43 169940 0.2 1 161783 8157 44 58164 0.2 1 53449 4715 45 118320 0.2 1 111612 6708 46 116293 0.2 1 109496 6797 47 124205 0.2 1 117076 7129 48 123424 0.2 1 116139 7285 49 135448 0.2 1 126575 8873 50 119092 0.2 1 112535 6557 51 128971 0.2 1 121071 7900 52 136415 0.2 1 127168 9247 53 146369 0.2 1 138214 8155 54 119815 0.2 1 112779 7036 55 143900 0.2 1 135212 8688 56 174050 0.2 1 164777 9273 57 117416 0.2 1 109615 7801 58 150456 0.2 1 142969 7487 59 132324 0.2 1 124478 7846 60 149629 0.2 1 140649 8980 61 147926 0.2 1 139679 8247 62 163513 0.2 1 154547 8966 63 134239 0.2 1 125798 8441 64 148604 0.2 1 140497 8107 65 167908 0.2 1 158298 9610 66 177387 0.2 1 167350 10037 67 194374 0.2 1 180373 14001 68 370239 0.2 1 354139 16100 69 62415 0.2 1 57251 5164 70 26365 0.2 1 22180 4185 71 101894 0.2 1 96350 5544 72 143779 0.2 1 135850 7929 73 154356 0.2 1 145962 8394 74 154436 0.2 1 145829 8607 75 155208 0.2 1 146440 8768 76 154614 0.2 1 146122 8492 77 156184 0.2 1 147502 8682 78 149615 0.2 1 141324 8291 79 149903 0.2 1 141513 8390 80 146761 0.2 1 138705 8056 81 147739 0.2 1 139495 8244 82 146032 0.2 1 137919 8113 83 142429 0.2 1 134446 7983 84 139641 0.2 1 132001 7640 85 137362 0.2 1 129737 7625 86 134899 0.2 1 127375 7524 87 130083 0.2 1 122670 7413 88 129596 0.2 1 122229 7367 89 124621 0.2 1 117492 7129 90 125612 0.2 1 118454 7158 91 119798 0.2 1 113079 6719 92 115717 0.2 1 109150 6567 93 109774 0.2 1 103564 6210 94 107743 0.2 1 101578 6165 95 101804 0.2 1 95988 5816 96 96724 0.2 1 91079 5645 97 92176 0.2 1 86874 5302 98 87424 0.2 1 82235 5189 99 86913 0.2 1 81280 5633 100 78985 0.2 1 74394 4591 101 75410 0.2 1 70955 4455 102 69075 0.2 1 64932 4143 103 64987 0.2 1 61075 3912 104 61751 0.2 1 58031 3720 105 55260 0.2 1 51879 3381 106 50545 0.2 1 47309 3236 107 46617 0.2 1 43701 2916 108 44206 0.2 1 41370 2836 109 39556 0.2 1 36926 2630 110 36531 0.2 1 34163 2368 111 32673 0.2 1 30562 2111 112 28896 0.2 1 26907 1989 113 25292 0.2 1 23480 1812 114 22657 0.2 1 21036 1621 115 19857 0.2 1 18470 1387 116 17394 0.2 1 16192 1202 117 14695 0.2 1 13605 1090 118 12814 0.2 1 11815 999 119 11036 0.2 1 10138 898 120 9387 0.2 1 8609 778 121 8006 0.2 1 7333 673 122 6428 0.2 1 5956 472 123 5508 0.2 1 5035 473 124 4687 0.2 1 4248 439 125 3879 0.2 1 3508 371 126 3097 0.2 1 2779 318 127 2720 0.2 1 2457 263 128 2100 0.2 1 1898 202 129 1767 0.2 1 1595 172 130 1354 0.2 1 1200 154 131 1174 0.2 1 1057 117 132 1133 0.2 1 1029 104 133 1115 0.2 1 1004 111 134 1260 0.2 1 1149 111 135 611 0.2 1 547 64 136 316 0.2 1 271 45 137 241 0.2 1 219 22 138 161 0.2 1 140 21 139 107 0.2 1 93 14 140 137 0.2 1 117 20 141 53 0.2 1 47 6 142 47 0.2 1 41 6 143 37 0.2 1 32 5 144 37 0.2 1 26 11 145 44 0.2 1 34 10 146 50 0.2 1 46 4 147 126 0.2 1 111 15 148 84 0.2 1 69 15 149 71 0.2 1 62 9 150 642 0.2 1 568 74 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_32psu_1_S5_L001_R1_001.fastq.gz ============================================= 14000021 sequences processed in total