SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_32psu_4_S8_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: 498122). 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_4_S8_L001_R1_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 59.38 s (4 us/read; 14.84 M reads/minute). === Summary === Total reads processed: 14,686,084 Reads with adapters: 11,112,819 (75.7%) Reads written (passing filters): 14,686,084 (100.0%) Total basepairs processed: 2,202,912,600 bp Quality-trimmed: 9,079,514 bp (0.4%) Total written (filtered): 1,783,990,340 bp (81.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11112819 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.7% C: 11.7% G: 21.0% T: 36.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2196567 3671521.0 0 2196567 2 292186 917880.2 0 292186 3 157941 229470.1 0 157941 4 100753 57367.5 0 100753 5 83202 14341.9 0 83202 6 81280 3585.5 0 81280 7 68619 896.4 0 68619 8 84673 224.1 0 84673 9 83412 56.0 0 82605 807 10 77900 14.0 1 74163 3737 11 86076 3.5 1 80161 5915 12 82933 0.9 1 78087 4846 13 83856 0.2 1 78977 4879 14 84709 0.2 1 79208 5501 15 88097 0.2 1 82938 5159 16 88174 0.2 1 82008 6166 17 105389 0.2 1 97630 7759 18 89620 0.2 1 84611 5009 19 77413 0.2 1 72875 4538 20 91427 0.2 1 86037 5390 21 101267 0.2 1 94618 6649 22 86534 0.2 1 82143 4391 23 99603 0.2 1 93638 5965 24 92844 0.2 1 85594 7250 25 98567 0.2 1 92532 6035 26 89487 0.2 1 84719 4768 27 100312 0.2 1 93524 6788 28 97676 0.2 1 91379 6297 29 103869 0.2 1 95980 7889 30 115073 0.2 1 109144 5929 31 81679 0.2 1 76971 4708 32 104832 0.2 1 98556 6276 33 97135 0.2 1 91030 6105 34 104303 0.2 1 98156 6147 35 102079 0.2 1 95269 6810 36 105105 0.2 1 98314 6791 37 106489 0.2 1 100050 6439 38 111587 0.2 1 104304 7283 39 98240 0.2 1 93162 5078 40 110224 0.2 1 103236 6988 41 119138 0.2 1 109010 10128 42 107751 0.2 1 99258 8493 43 167048 0.2 1 157990 9058 44 54792 0.2 1 50043 4749 45 116148 0.2 1 107107 9041 46 253343 0.2 1 239166 14177 47 141220 0.2 1 133245 7975 48 70788 0.2 1 63989 6799 49 218187 0.2 1 207304 10883 50 67793 0.2 1 62869 4924 51 84957 0.2 1 78961 5996 52 231141 0.2 1 220209 10932 53 159552 0.2 1 153244 6308 54 57820 0.2 1 54077 3743 55 96525 0.2 1 92498 4027 56 56201 0.2 1 52298 3903 57 134736 0.2 1 129198 5538 58 33322 0.2 1 31241 2081 59 35361 0.2 1 32301 3060 60 121909 0.2 1 116692 5217 61 80368 0.2 1 77075 3293 62 37240 0.2 1 34469 2771 63 91660 0.2 1 86780 4880 64 81468 0.2 1 77877 3591 65 53211 0.2 1 49893 3318 66 93831 0.2 1 88616 5215 67 107034 0.2 1 100335 6699 68 187851 0.2 1 179197 8654 69 100255 0.2 1 94892 5363 70 35399 0.2 1 32342 3057 71 19897 0.2 1 17997 1900 72 63849 0.2 1 60613 3236 73 81267 0.2 1 77051 4216 74 82339 0.2 1 77944 4395 75 80643 0.2 1 76099 4544 76 79016 0.2 1 74790 4226 77 78401 0.2 1 74108 4293 78 73966 0.2 1 69851 4115 79 71627 0.2 1 67584 4043 80 70426 0.2 1 66563 3863 81 69818 0.2 1 65954 3864 82 67366 0.2 1 63575 3791 83 63649 0.2 1 60193 3456 84 61172 0.2 1 57824 3348 85 59276 0.2 1 56040 3236 86 56575 0.2 1 53454 3121 87 53078 0.2 1 50236 2842 88 51788 0.2 1 48829 2959 89 48314 0.2 1 45638 2676 90 48321 0.2 1 45629 2692 91 45543 0.2 1 43073 2470 92 42075 0.2 1 39779 2296 93 38814 0.2 1 36658 2156 94 37722 0.2 1 35616 2106 95 34423 0.2 1 32423 2000 96 32157 0.2 1 30284 1873 97 29965 0.2 1 28206 1759 98 27347 0.2 1 25797 1550 99 26166 0.2 1 24583 1583 100 23354 0.2 1 21969 1385 101 21467 0.2 1 20157 1310 102 19539 0.2 1 18344 1195 103 17855 0.2 1 16735 1120 104 16360 0.2 1 15329 1031 105 14296 0.2 1 13369 927 106 12633 0.2 1 11870 763 107 11358 0.2 1 10612 746 108 10534 0.2 1 9836 698 109 9078 0.2 1 8461 617 110 8053 0.2 1 7464 589 111 6944 0.2 1 6454 490 112 6153 0.2 1 5691 462 113 5306 0.2 1 4906 400 114 4518 0.2 1 4189 329 115 3910 0.2 1 3603 307 116 3193 0.2 1 2951 242 117 2651 0.2 1 2439 212 118 2314 0.2 1 2103 211 119 1875 0.2 1 1673 202 120 1577 0.2 1 1427 150 121 1320 0.2 1 1198 122 122 1105 0.2 1 995 110 123 920 0.2 1 816 104 124 791 0.2 1 709 82 125 642 0.2 1 583 59 126 507 0.2 1 450 57 127 422 0.2 1 367 55 128 333 0.2 1 289 44 129 238 0.2 1 206 32 130 186 0.2 1 162 24 131 174 0.2 1 151 23 132 134 0.2 1 118 16 133 148 0.2 1 129 19 134 197 0.2 1 182 15 135 113 0.2 1 97 16 136 58 0.2 1 50 8 137 58 0.2 1 48 10 138 42 0.2 1 35 7 139 30 0.2 1 28 2 140 22 0.2 1 20 2 141 15 0.2 1 9 6 142 13 0.2 1 11 2 143 11 0.2 1 6 5 144 2 0.2 1 1 1 145 7 0.2 1 6 1 146 5 0.2 1 4 1 147 21 0.2 1 20 1 148 23 0.2 1 19 4 149 14 0.2 1 12 2 150 119 0.2 1 95 24 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_32psu_4_S8_L001_R1_001.fastq.gz ============================================= 14686084 sequences processed in total