SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/CTRL_8C_26psu_1_S17_L002_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: 487093). 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_L002_R1_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 54.39 s (4 us/read; 15.03 M reads/minute). === Summary === Total reads processed: 13,627,098 Reads with adapters: 10,357,003 (76.0%) Reads written (passing filters): 13,627,098 (100.0%) Total basepairs processed: 2,044,064,700 bp Quality-trimmed: 4,208,565 bp (0.2%) Total written (filtered): 1,627,255,744 bp (79.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10357003 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 31.3% C: 15.7% G: 18.6% T: 34.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2086122 3406774.5 0 2086122 2 266568 851693.6 0 266568 3 152542 212923.4 0 152542 4 89399 53230.9 0 89399 5 70209 13307.7 0 70209 6 66787 3326.9 0 66787 7 53852 831.7 0 53852 8 67948 207.9 0 67948 9 69323 52.0 0 68200 1123 10 63939 13.0 1 59604 4335 11 71265 3.2 1 64858 6407 12 68721 0.8 1 63494 5227 13 67596 0.2 1 62302 5294 14 70216 0.2 1 64057 6159 15 71638 0.2 1 65898 5740 16 71622 0.2 1 65051 6571 17 87796 0.2 1 79687 8109 18 71999 0.2 1 66604 5395 19 63344 0.2 1 58390 4954 20 75324 0.2 1 69407 5917 21 84178 0.2 1 77194 6984 22 70154 0.2 1 65038 5116 23 81908 0.2 1 75394 6514 24 75905 0.2 1 68761 7144 25 81978 0.2 1 75339 6639 26 74054 0.2 1 68713 5341 27 83694 0.2 1 76279 7415 28 82366 0.2 1 75736 6630 29 86579 0.2 1 78687 7892 30 91938 0.2 1 85372 6566 31 70649 0.2 1 65160 5489 32 86162 0.2 1 79280 6882 33 82680 0.2 1 75408 7272 34 100154 0.2 1 90695 9459 35 94358 0.2 1 85860 8498 36 148458 0.2 1 139524 8934 37 35889 0.2 1 31244 4645 38 78400 0.2 1 72661 5739 39 96881 0.2 1 88590 8291 40 92469 0.2 1 85322 7147 41 105619 0.2 1 96453 9166 42 87195 0.2 1 78548 8647 43 141743 0.2 1 132343 9400 44 53443 0.2 1 48101 5342 45 80210 0.2 1 73892 6318 46 94587 0.2 1 87548 7039 47 98921 0.2 1 91675 7246 48 85740 0.2 1 78755 6985 49 103381 0.2 1 94837 8544 50 84900 0.2 1 78738 6162 51 91291 0.2 1 84483 6808 52 97726 0.2 1 89264 8462 53 111539 0.2 1 103945 7594 54 78508 0.2 1 72278 6230 55 97750 0.2 1 90509 7241 56 115622 0.2 1 107685 7937 57 89129 0.2 1 81822 7307 58 92584 0.2 1 86772 5812 59 73435 0.2 1 67515 5920 60 100185 0.2 1 92834 7351 61 93396 0.2 1 86891 6505 62 93505 0.2 1 86821 6684 63 85463 0.2 1 78881 6582 64 86705 0.2 1 80704 6001 65 94221 0.2 1 87522 6699 66 100565 0.2 1 93273 7292 67 109840 0.2 1 100139 9701 68 202049 0.2 1 190563 11486 69 52634 0.2 1 48583 4051 70 17146 0.2 1 14429 2717 71 47197 0.2 1 43653 3544 72 76160 0.2 1 71164 4996 73 81740 0.2 1 76081 5659 74 82050 0.2 1 76332 5718 75 80287 0.2 1 74463 5824 76 79839 0.2 1 73807 6032 77 80016 0.2 1 74278 5738 78 74795 0.2 1 69265 5530 79 74038 0.2 1 68576 5462 80 73576 0.2 1 68130 5446 81 72243 0.2 1 66987 5256 82 69871 0.2 1 64751 5120 83 67762 0.2 1 62929 4833 84 65749 0.2 1 60930 4819 85 64210 0.2 1 59436 4774 86 62228 0.2 1 57683 4545 87 59511 0.2 1 55197 4314 88 59103 0.2 1 54779 4324 89 57029 0.2 1 52911 4118 90 56111 0.2 1 51929 4182 91 53588 0.2 1 49754 3834 92 50869 0.2 1 47115 3754 93 47789 0.2 1 44363 3426 94 47204 0.2 1 43712 3492 95 44549 0.2 1 41263 3286 96 41699 0.2 1 38638 3061 97 39043 0.2 1 36086 2957 98 35735 0.2 1 32882 2853 99 35123 0.2 1 32338 2785 100 32434 0.2 1 30000 2434 101 30205 0.2 1 27895 2310 102 28238 0.2 1 26075 2163 103 26099 0.2 1 24128 1971 104 24785 0.2 1 22897 1888 105 21850 0.2 1 20176 1674 106 20336 0.2 1 18803 1533 107 18435 0.2 1 16991 1444 108 17298 0.2 1 15900 1398 109 15693 0.2 1 14418 1275 110 13857 0.2 1 12707 1150 111 12767 0.2 1 11710 1057 112 11323 0.2 1 10411 912 113 9639 0.2 1 8850 789 114 8830 0.2 1 8052 778 115 7781 0.2 1 7105 676 116 6721 0.2 1 6151 570 117 5849 0.2 1 5270 579 118 5202 0.2 1 4706 496 119 4310 0.2 1 3919 391 120 3867 0.2 1 3492 375 121 3291 0.2 1 2960 331 122 2743 0.2 1 2485 258 123 2310 0.2 1 2091 219 124 2101 0.2 1 1881 220 125 1771 0.2 1 1559 212 126 1539 0.2 1 1390 149 127 1290 0.2 1 1141 149 128 1070 0.2 1 950 120 129 924 0.2 1 833 91 130 685 0.2 1 617 68 131 612 0.2 1 545 67 132 539 0.2 1 487 52 133 666 0.2 1 596 70 134 1493 0.2 1 1414 79 135 574 0.2 1 548 26 136 201 0.2 1 183 18 137 159 0.2 1 145 14 138 108 0.2 1 98 10 139 49 0.2 1 44 5 140 42 0.2 1 38 4 141 43 0.2 1 37 6 142 35 0.2 1 31 4 143 45 0.2 1 39 6 144 56 0.2 1 49 7 145 155 0.2 1 139 16 146 240 0.2 1 219 21 147 1341 0.2 1 1228 113 148 773 0.2 1 707 66 149 433 0.2 1 399 34 150 2986 0.2 1 2547 439 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/CTRL_8C_26psu_1_S17_L002_R1_001.fastq.gz ============================================= 13627098 sequences processed in total