SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/CTRL_16C_26psu_1_S19_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: 545015). 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_16C_26psu_1_S19_L001_R2_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 74.67 s (4 us/read; 14.93 M reads/minute). === Summary === Total reads processed: 18,576,202 Reads with adapters: 14,527,088 (78.2%) Reads written (passing filters): 18,576,202 (100.0%) Total basepairs processed: 2,786,430,300 bp Quality-trimmed: 12,297,720 bp (0.4%) Total written (filtered): 2,186,026,388 bp (78.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14527088 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.0% C: 12.4% G: 24.5% T: 35.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2397075 4644050.5 0 2397075 2 377772 1161012.6 0 377772 3 209931 290253.2 0 209931 4 123717 72563.3 0 123717 5 112624 18140.8 0 112624 6 97477 4535.2 0 97477 7 81404 1133.8 0 81404 8 114796 283.5 0 114796 9 89736 70.9 0 89386 350 10 100021 17.7 1 95112 4909 11 103726 4.4 1 97357 6369 12 104603 1.1 1 97938 6665 13 116572 0.3 1 109738 6834 14 110440 0.3 1 102780 7660 15 91038 0.3 1 85192 5846 16 129548 0.3 1 121431 8117 17 105093 0.3 1 97969 7124 18 99076 0.3 1 93067 6009 19 126890 0.3 1 118635 8255 20 118457 0.3 1 111491 6966 21 103736 0.3 1 97365 6371 22 118151 0.3 1 110881 7270 23 121946 0.3 1 114464 7482 24 121962 0.3 1 114186 7776 25 136854 0.3 1 128708 8146 26 113321 0.3 1 106068 7253 27 126381 0.3 1 117798 8583 28 118846 0.3 1 112727 6119 29 125505 0.3 1 117793 7712 30 125215 0.3 1 118459 6756 31 135187 0.3 1 127291 7896 32 121491 0.3 1 114900 6591 33 135254 0.3 1 127041 8213 34 169655 0.3 1 159717 9938 35 101342 0.3 1 95776 5566 36 136505 0.3 1 128363 8142 37 143293 0.3 1 134875 8418 38 134051 0.3 1 127357 6694 39 131563 0.3 1 124738 6825 40 145300 0.3 1 136735 8565 41 138947 0.3 1 131652 7295 42 144334 0.3 1 136660 7674 43 131871 0.3 1 124782 7089 44 149402 0.3 1 141199 8203 45 161283 0.3 1 152880 8403 46 115740 0.3 1 109551 6189 47 146650 0.3 1 139277 7373 48 144979 0.3 1 137763 7216 49 149370 0.3 1 141741 7629 50 140556 0.3 1 132993 7563 51 176763 0.3 1 167628 9135 52 125327 0.3 1 119270 6057 53 150468 0.3 1 143751 6717 54 114488 0.3 1 108938 5550 55 150264 0.3 1 143436 6828 56 154642 0.3 1 147075 7567 57 145698 0.3 1 138895 6803 58 139003 0.3 1 132772 6231 59 141639 0.3 1 135020 6619 60 145216 0.3 1 138147 7069 61 149173 0.3 1 141978 7195 62 161580 0.3 1 153777 7803 63 211777 0.3 1 202721 9056 64 166013 0.3 1 159545 6468 65 115072 0.3 1 109927 5145 66 124032 0.3 1 118392 5640 67 121997 0.3 1 116256 5741 68 123305 0.3 1 117689 5616 69 119979 0.3 1 114424 5555 70 126522 0.3 1 120645 5877 71 131428 0.3 1 125503 5925 72 124583 0.3 1 118750 5833 73 129753 0.3 1 124066 5687 74 119016 0.3 1 113726 5290 75 113191 0.3 1 108419 4772 76 111393 0.3 1 106547 4846 77 111470 0.3 1 106513 4957 78 104799 0.3 1 100049 4750 79 100883 0.3 1 96421 4462 80 100236 0.3 1 95706 4530 81 98928 0.3 1 94651 4277 82 94279 0.3 1 90155 4124 83 90115 0.3 1 86173 3942 84 87249 0.3 1 83373 3876 85 85689 0.3 1 81793 3896 86 84888 0.3 1 81207 3681 87 84171 0.3 1 80558 3613 88 82226 0.3 1 78630 3596 89 73279 0.3 1 70084 3195 90 71368 0.3 1 68189 3179 91 66468 0.3 1 63502 2966 92 61869 0.3 1 59204 2665 93 59677 0.3 1 57086 2591 94 57840 0.3 1 55318 2522 95 54875 0.3 1 52595 2280 96 51698 0.3 1 49449 2249 97 47519 0.3 1 45519 2000 98 43527 0.3 1 41676 1851 99 42094 0.3 1 40263 1831 100 37940 0.3 1 36384 1556 101 34646 0.3 1 33175 1471 102 32213 0.3 1 30921 1292 103 29202 0.3 1 27960 1242 104 28501 0.3 1 27313 1188 105 25308 0.3 1 24224 1084 106 22773 0.3 1 21858 915 107 20894 0.3 1 20051 843 108 18912 0.3 1 18081 831 109 17072 0.3 1 16336 736 110 15374 0.3 1 14700 674 111 14518 0.3 1 13895 623 112 12456 0.3 1 11891 565 113 10771 0.3 1 10329 442 114 9374 0.3 1 8976 398 115 7920 0.3 1 7555 365 116 6787 0.3 1 6458 329 117 5803 0.3 1 5538 265 118 4857 0.3 1 4636 221 119 4060 0.3 1 3861 199 120 3400 0.3 1 3228 172 121 3132 0.3 1 2976 156 122 2609 0.3 1 2493 116 123 2165 0.3 1 2072 93 124 1770 0.3 1 1676 94 125 1516 0.3 1 1432 84 126 1213 0.3 1 1153 60 127 1001 0.3 1 941 60 128 776 0.3 1 728 48 129 744 0.3 1 699 45 130 486 0.3 1 463 23 131 460 0.3 1 438 22 132 343 0.3 1 315 28 133 355 0.3 1 338 17 134 428 0.3 1 403 25 135 226 0.3 1 216 10 136 133 0.3 1 120 13 137 125 0.3 1 117 8 138 70 0.3 1 62 8 139 38 0.3 1 35 3 140 38 0.3 1 31 7 141 35 0.3 1 33 2 142 27 0.3 1 26 1 143 32 0.3 1 30 2 144 14 0.3 1 13 1 145 17 0.3 1 16 1 146 23 0.3 1 23 147 69 0.3 1 65 4 148 40 0.3 1 38 2 149 38 0.3 1 34 4 150 229 0.3 1 219 10 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/CTRL_16C_26psu_1_S19_L001_R2_001.fastq.gz ============================================= 18576202 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 18576202 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 138540 (0.75%)