SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/CTRL_16C_26psu_1_S19_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: 537596). 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_L002_R1_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 73.33 s (4 us/read; 15.13 M reads/minute). === Summary === Total reads processed: 18,490,322 Reads with adapters: 14,542,227 (78.6%) Reads written (passing filters): 18,490,322 (100.0%) Total basepairs processed: 2,773,548,300 bp Quality-trimmed: 5,682,539 bp (0.2%) Total written (filtered): 2,170,540,982 bp (78.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14542227 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.9% C: 14.1% G: 20.7% T: 35.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2352565 4622580.5 0 2352565 2 355744 1155645.1 0 355744 3 197435 288911.3 0 197435 4 119803 72227.8 0 119803 5 101491 18057.0 0 101491 6 98683 4514.2 0 98683 7 82227 1128.6 0 82227 8 107087 282.1 0 107087 9 96108 70.5 0 94984 1124 10 95916 17.6 1 89656 6260 11 105518 4.4 1 96331 9187 12 101326 1.1 1 93731 7595 13 105529 0.3 1 97295 8234 14 104207 0.3 1 95707 8500 15 110166 0.3 1 101496 8670 16 108369 0.3 1 98900 9469 17 132137 0.3 1 119869 12268 18 111785 0.3 1 103776 8009 19 94978 0.3 1 88024 6954 20 115852 0.3 1 107171 8681 21 128602 0.3 1 118248 10354 22 106928 0.3 1 99662 7266 23 130246 0.3 1 120393 9853 24 113598 0.3 1 103348 10250 25 127529 0.3 1 117557 9972 26 114329 0.3 1 106365 7964 27 127671 0.3 1 117117 10554 28 133545 0.3 1 122886 10659 29 127218 0.3 1 116368 10850 30 145807 0.3 1 136218 9589 31 104710 0.3 1 97327 7383 32 136712 0.3 1 126029 10683 33 125051 0.3 1 114983 10068 34 151172 0.3 1 138255 12917 35 121506 0.3 1 112294 9212 36 142450 0.3 1 131732 10718 37 131704 0.3 1 122359 9345 38 144055 0.3 1 132700 11355 39 140259 0.3 1 129402 10857 40 145119 0.3 1 132998 12121 41 151317 0.3 1 136837 14480 42 135755 0.3 1 124185 11570 43 206150 0.3 1 193096 13054 44 75981 0.3 1 68776 7205 45 147101 0.3 1 136563 10538 46 140010 0.3 1 129569 10441 47 150202 0.3 1 139726 10476 48 137985 0.3 1 127406 10579 49 157361 0.3 1 144848 12513 50 132126 0.3 1 123324 8802 51 143254 0.3 1 133169 10085 52 152534 0.3 1 140225 12309 53 166653 0.3 1 155543 11110 54 122896 0.3 1 113877 9019 55 150505 0.3 1 139851 10654 56 178712 0.3 1 166946 11766 57 130999 0.3 1 120759 10240 58 145047 0.3 1 136344 8703 59 119684 0.3 1 110878 8806 60 151206 0.3 1 140682 10524 61 142715 0.3 1 133251 9464 62 148943 0.3 1 139114 9829 63 129912 0.3 1 120416 9496 64 134038 0.3 1 125474 8564 65 146595 0.3 1 136655 9940 66 153978 0.3 1 143441 10537 67 168100 0.3 1 155171 12929 68 298170 0.3 1 281868 16302 69 74393 0.3 1 68405 5988 70 26909 0.3 1 22880 4029 71 75109 0.3 1 70102 5007 72 114931 0.3 1 107946 6985 73 122734 0.3 1 114818 7916 74 120820 0.3 1 112962 7858 75 119099 0.3 1 111010 8089 76 117029 0.3 1 108855 8174 77 117800 0.3 1 109726 8074 78 109388 0.3 1 101815 7573 79 108107 0.3 1 100589 7518 80 105715 0.3 1 98229 7486 81 104556 0.3 1 97305 7251 82 101011 0.3 1 93996 7015 83 97159 0.3 1 90577 6582 84 92283 0.3 1 85890 6393 85 90035 0.3 1 83799 6236 86 86319 0.3 1 80378 5941 87 82376 0.3 1 76893 5483 88 81375 0.3 1 75753 5622 89 77211 0.3 1 71720 5491 90 76508 0.3 1 71173 5335 91 72845 0.3 1 67788 5057 92 67776 0.3 1 63180 4596 93 63675 0.3 1 59371 4304 94 61289 0.3 1 57047 4242 95 57075 0.3 1 53036 4039 96 54087 0.3 1 50327 3760 97 51019 0.3 1 47507 3512 98 46423 0.3 1 43108 3315 99 45164 0.3 1 41742 3422 100 40910 0.3 1 38024 2886 101 38601 0.3 1 35925 2676 102 35185 0.3 1 32582 2603 103 32331 0.3 1 30034 2297 104 30306 0.3 1 28179 2127 105 26497 0.3 1 24651 1846 106 24125 0.3 1 22458 1667 107 22000 0.3 1 20417 1583 108 20719 0.3 1 19189 1530 109 18051 0.3 1 16712 1339 110 16439 0.3 1 15194 1245 111 14466 0.3 1 13407 1059 112 12793 0.3 1 11768 1025 113 11344 0.3 1 10481 863 114 9637 0.3 1 8889 748 115 8596 0.3 1 7840 756 116 7497 0.3 1 6926 571 117 6216 0.3 1 5692 524 118 5413 0.3 1 4943 470 119 4488 0.3 1 4121 367 120 3934 0.3 1 3598 336 121 3277 0.3 1 2991 286 122 2701 0.3 1 2461 240 123 2240 0.3 1 2028 212 124 1944 0.3 1 1730 214 125 1578 0.3 1 1422 156 126 1320 0.3 1 1199 121 127 1172 0.3 1 1056 116 128 861 0.3 1 773 88 129 759 0.3 1 683 76 130 595 0.3 1 520 75 131 487 0.3 1 426 61 132 384 0.3 1 352 32 133 353 0.3 1 318 35 134 434 0.3 1 399 35 135 273 0.3 1 245 28 136 156 0.3 1 137 19 137 94 0.3 1 83 11 138 77 0.3 1 69 8 139 51 0.3 1 44 7 140 30 0.3 1 25 5 141 33 0.3 1 24 9 142 30 0.3 1 24 6 143 35 0.3 1 27 8 144 18 0.3 1 17 1 145 11 0.3 1 9 2 146 25 0.3 1 21 4 147 75 0.3 1 73 2 148 42 0.3 1 37 5 149 44 0.3 1 41 3 150 294 0.3 1 257 37 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/CTRL_16C_26psu_1_S19_L002_R1_001.fastq.gz ============================================= 18490322 sequences processed in total