SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/CTRL_8C_26psu_1_S17_L001_R2_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_R2_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 57.44 s (4 us/read; 14.40 M reads/minute). === Summary === Total reads processed: 13,781,290 Reads with adapters: 10,393,178 (75.4%) Reads written (passing filters): 13,781,290 (100.0%) Total basepairs processed: 2,067,193,500 bp Quality-trimmed: 10,332,398 bp (0.5%) Total written (filtered): 1,650,693,153 bp (79.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10393178 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.0% C: 12.4% G: 22.9% T: 34.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2177342 3445322.5 0 2177342 2 279599 861330.6 0 279599 3 156926 215332.7 0 156926 4 90665 53833.2 0 90665 5 76306 13458.3 0 76306 6 64993 3364.6 0 64993 7 53352 841.1 0 53352 8 75967 210.3 0 75967 9 61280 52.6 0 61074 206 10 66110 13.1 1 62970 3140 11 69828 3.3 1 65500 4328 12 69328 0.8 1 64877 4451 13 77454 0.2 1 72977 4477 14 71203 0.2 1 66291 4912 15 59758 0.2 1 55879 3879 16 86601 0.2 1 81117 5484 17 65384 0.2 1 60933 4451 18 67208 0.2 1 63111 4097 19 81178 0.2 1 76029 5149 20 77499 0.2 1 72833 4666 21 68546 0.2 1 64113 4433 22 76276 0.2 1 71754 4522 23 78702 0.2 1 73839 4863 24 78191 0.2 1 73447 4744 25 88316 0.2 1 83190 5126 26 73679 0.2 1 68983 4696 27 82923 0.2 1 77281 5642 28 76296 0.2 1 72446 3850 29 82111 0.2 1 77123 4988 30 79614 0.2 1 75308 4306 31 89456 0.2 1 84223 5233 32 78118 0.2 1 73947 4171 33 86787 0.2 1 81520 5267 34 111454 0.2 1 105036 6418 35 64200 0.2 1 60716 3484 36 89863 0.2 1 84483 5380 37 97027 0.2 1 91271 5756 38 90403 0.2 1 85738 4665 39 89856 0.2 1 85089 4767 40 98244 0.2 1 92516 5728 41 92652 0.2 1 87737 4915 42 94536 0.2 1 89519 5017 43 85154 0.2 1 80486 4668 44 96817 0.2 1 91511 5306 45 102115 0.2 1 96823 5292 46 77381 0.2 1 73350 4031 47 94700 0.2 1 89756 4944 48 92948 0.2 1 88160 4788 49 96945 0.2 1 91985 4960 50 91133 0.2 1 86206 4927 51 111309 0.2 1 105778 5531 52 80724 0.2 1 76802 3922 53 97109 0.2 1 92582 4527 54 75460 0.2 1 71575 3885 55 96939 0.2 1 92436 4503 56 100452 0.2 1 95531 4921 57 93931 0.2 1 89647 4284 58 91630 0.2 1 87584 4046 59 91476 0.2 1 87193 4283 60 94295 0.2 1 89743 4552 61 96075 0.2 1 91458 4617 62 103947 0.2 1 98742 5205 63 139881 0.2 1 133644 6237 64 115738 0.2 1 111196 4542 65 76600 0.2 1 73143 3457 66 81388 0.2 1 77826 3562 67 79784 0.2 1 76063 3721 68 81137 0.2 1 77492 3645 69 80187 0.2 1 76468 3719 70 85090 0.2 1 81074 4016 71 89717 0.2 1 85778 3939 72 84263 0.2 1 80409 3854 73 87216 0.2 1 83465 3751 74 81093 0.2 1 77528 3565 75 77500 0.2 1 74052 3448 76 75266 0.2 1 71946 3320 77 75853 0.2 1 72329 3524 78 72260 0.2 1 68950 3310 79 68908 0.2 1 65817 3091 80 69469 0.2 1 66410 3059 81 68119 0.2 1 65042 3077 82 65495 0.2 1 62627 2868 83 64033 0.2 1 61248 2785 84 61976 0.2 1 59216 2760 85 61317 0.2 1 58515 2802 86 60982 0.2 1 58300 2682 87 61128 0.2 1 58498 2630 88 60002 0.2 1 57306 2696 89 53699 0.2 1 51332 2367 90 51966 0.2 1 49630 2336 91 49026 0.2 1 46908 2118 92 46213 0.2 1 44244 1969 93 44796 0.2 1 42840 1956 94 44237 0.2 1 42309 1928 95 41556 0.2 1 39752 1804 96 39335 0.2 1 37550 1785 97 36382 0.2 1 34875 1507 98 33450 0.2 1 32005 1445 99 32975 0.2 1 31610 1365 100 29764 0.2 1 28510 1254 101 27741 0.2 1 26626 1115 102 25948 0.2 1 24908 1040 103 23781 0.2 1 22799 982 104 22951 0.2 1 22001 950 105 20726 0.2 1 19855 871 106 19269 0.2 1 18460 809 107 17116 0.2 1 16344 772 108 16142 0.2 1 15422 720 109 14186 0.2 1 13581 605 110 13235 0.2 1 12682 553 111 12589 0.2 1 12054 535 112 10912 0.2 1 10466 446 113 9393 0.2 1 8942 451 114 8457 0.2 1 8091 366 115 7197 0.2 1 6874 323 116 6211 0.2 1 5908 303 117 5216 0.2 1 4981 235 118 4612 0.2 1 4406 206 119 3969 0.2 1 3800 169 120 3391 0.2 1 3233 158 121 3136 0.2 1 3000 136 122 2549 0.2 1 2419 130 123 2350 0.2 1 2231 119 124 1891 0.2 1 1802 89 125 1725 0.2 1 1617 108 126 1554 0.2 1 1484 70 127 1178 0.2 1 1121 57 128 930 0.2 1 883 47 129 904 0.2 1 851 53 130 653 0.2 1 624 29 131 560 0.2 1 529 31 132 495 0.2 1 468 27 133 660 0.2 1 626 34 134 1423 0.2 1 1385 38 135 575 0.2 1 556 19 136 211 0.2 1 198 13 137 131 0.2 1 127 4 138 83 0.2 1 76 7 139 59 0.2 1 52 7 140 46 0.2 1 40 6 141 37 0.2 1 35 2 142 28 0.2 1 27 1 143 41 0.2 1 38 3 144 59 0.2 1 58 1 145 179 0.2 1 178 1 146 263 0.2 1 249 14 147 1229 0.2 1 1166 63 148 791 0.2 1 756 35 149 435 0.2 1 415 20 150 2389 0.2 1 2255 134 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/CTRL_8C_26psu_1_S17_L001_R2_001.fastq.gz ============================================= 13781290 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 13781290 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 136880 (0.99%)