SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_26psu_3_S11_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: 684443). Second best hit was Nextera (count: 1) 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_26psu_3_S11_L001_R1_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 59.94 s (3 us/read; 17.24 M reads/minute). === Summary === Total reads processed: 17,221,011 Reads with adapters: 14,907,348 (86.6%) Reads written (passing filters): 17,221,011 (100.0%) Total basepairs processed: 2,583,151,650 bp Quality-trimmed: 4,970,961 bp (0.2%) Total written (filtered): 1,823,787,303 bp (70.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14907348 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.8% C: 14.0% G: 22.2% T: 35.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1339401 4305252.8 0 1339401 2 221513 1076313.2 0 221513 3 135887 269078.3 0 135887 4 86877 67269.6 0 86877 5 77129 16817.4 0 77129 6 76711 4204.3 0 76711 7 64192 1051.1 0 64192 8 80722 262.8 0 80722 9 81072 65.7 0 80149 923 10 77051 16.4 1 73224 3827 11 85961 4.1 1 79699 6262 12 83198 1.0 1 78237 4961 13 86825 0.3 1 81365 5460 14 84806 0.3 1 79388 5418 15 92317 0.3 1 86654 5663 16 89335 0.3 1 83153 6182 17 108017 0.3 1 99755 8262 18 99925 0.3 1 94377 5548 19 81101 0.3 1 76294 4807 20 100416 0.3 1 94250 6166 21 108388 0.3 1 101446 6942 22 94203 0.3 1 89329 4874 23 109171 0.3 1 102371 6800 24 104496 0.3 1 96618 7878 25 111703 0.3 1 104639 7064 26 103882 0.3 1 98042 5840 27 115801 0.3 1 107736 8065 28 113315 0.3 1 105981 7334 29 122732 0.3 1 113578 9154 30 129896 0.3 1 123034 6862 31 104938 0.3 1 98897 6041 32 124822 0.3 1 117479 7343 33 120235 0.3 1 112658 7577 34 135691 0.3 1 125410 10281 35 143924 0.3 1 135732 8192 36 114731 0.3 1 107772 6959 37 138113 0.3 1 128706 9407 38 183834 0.3 1 174741 9093 39 91269 0.3 1 83934 7335 40 144200 0.3 1 135345 8855 41 167039 0.3 1 155843 11196 42 124510 0.3 1 116014 8496 43 229902 0.3 1 218995 10907 44 61751 0.3 1 56507 5244 45 153093 0.3 1 144067 9026 46 145804 0.3 1 137245 8559 47 154404 0.3 1 145632 8772 48 154492 0.3 1 145156 9336 49 169124 0.3 1 158402 10722 50 144085 0.3 1 136047 8038 51 159010 0.3 1 149344 9666 52 165606 0.3 1 154687 10919 53 178026 0.3 1 167943 10083 54 145073 0.3 1 136817 8256 55 172012 0.3 1 161558 10454 56 210944 0.3 1 199588 11356 57 131803 0.3 1 123033 8770 58 178194 0.3 1 169188 9006 59 157761 0.3 1 148537 9224 60 170653 0.3 1 160454 10199 61 170629 0.3 1 161244 9385 62 190264 0.3 1 180168 10096 63 148311 0.3 1 139056 9255 64 170495 0.3 1 161109 9386 65 191349 0.3 1 180352 10997 66 199623 0.3 1 188220 11403 67 212270 0.3 1 197036 15234 68 412894 0.3 1 394953 17941 69 59319 0.3 1 54157 5162 70 23953 0.3 1 19703 4250 71 116809 0.3 1 110410 6399 72 157277 0.3 1 148914 8363 73 165912 0.3 1 156892 9020 74 164518 0.3 1 155310 9208 75 163178 0.3 1 154082 9096 76 162323 0.3 1 153580 8743 77 162174 0.3 1 153149 9025 78 154081 0.3 1 145262 8819 79 153448 0.3 1 144767 8681 80 149998 0.3 1 141770 8228 81 150056 0.3 1 141671 8385 82 147165 0.3 1 139005 8160 83 142399 0.3 1 134518 7881 84 137532 0.3 1 129880 7652 85 134287 0.3 1 126887 7400 86 129443 0.3 1 122227 7216 87 125510 0.3 1 118421 7089 88 124525 0.3 1 117462 7063 89 118345 0.3 1 111665 6680 90 118308 0.3 1 111670 6638 91 111912 0.3 1 105689 6223 92 106445 0.3 1 100472 5973 93 100557 0.3 1 94827 5730 94 97750 0.3 1 92088 5662 95 91346 0.3 1 86041 5305 96 86885 0.3 1 81735 5150 97 81399 0.3 1 76644 4755 98 75784 0.3 1 71395 4389 99 72904 0.3 1 68310 4594 100 67617 0.3 1 63610 4007 101 63261 0.3 1 59615 3646 102 58086 0.3 1 54536 3550 103 54397 0.3 1 51127 3270 104 50493 0.3 1 47351 3142 105 44481 0.3 1 41579 2902 106 41013 0.3 1 38506 2507 107 36987 0.3 1 34603 2384 108 34766 0.3 1 32511 2255 109 30744 0.3 1 28764 1980 110 27509 0.3 1 25598 1911 111 24797 0.3 1 23127 1670 112 21804 0.3 1 20294 1510 113 18744 0.3 1 17435 1309 114 16804 0.3 1 15658 1146 115 14315 0.3 1 13251 1064 116 12612 0.3 1 11627 985 117 10473 0.3 1 9684 789 118 8921 0.3 1 8216 705 119 7563 0.3 1 6922 641 120 6332 0.3 1 5781 551 121 5619 0.3 1 5122 497 122 4576 0.3 1 4198 378 123 3737 0.3 1 3370 367 124 3104 0.3 1 2823 281 125 2623 0.3 1 2320 303 126 2119 0.3 1 1927 192 127 1819 0.3 1 1640 179 128 1359 0.3 1 1208 151 129 1165 0.3 1 1033 132 130 852 0.3 1 749 103 131 856 0.3 1 765 91 132 726 0.3 1 633 93 133 874 0.3 1 793 81 134 1491 0.3 1 1401 90 135 611 0.3 1 548 63 136 207 0.3 1 187 20 137 166 0.3 1 155 11 138 132 0.3 1 107 25 139 75 0.3 1 67 8 140 69 0.3 1 60 9 141 42 0.3 1 32 10 142 26 0.3 1 19 7 143 26 0.3 1 15 11 144 18 0.3 1 13 5 145 37 0.3 1 33 4 146 26 0.3 1 20 6 147 73 0.3 1 60 13 148 47 0.3 1 37 10 149 55 0.3 1 48 7 150 636 0.3 1 548 88 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_26psu_3_S11_L001_R1_001.fastq.gz ============================================= 17221011 sequences processed in total