SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_32psu_2_S6_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: 570994). Second best hit was smallRNA (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_2_S6_L001_R1_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 46.46 s (4 us/read; 16.71 M reads/minute). === Summary === Total reads processed: 12,939,154 Reads with adapters: 10,340,662 (79.9%) Reads written (passing filters): 12,939,154 (100.0%) Total basepairs processed: 1,940,873,100 bp Quality-trimmed: 3,580,813 bp (0.2%) Total written (filtered): 1,492,993,480 bp (76.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10340662 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.8% C: 14.7% G: 20.5% T: 35.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1552261 3234788.5 0 1552261 2 232662 808697.1 0 232662 3 131614 202174.3 0 131614 4 79987 50543.6 0 79987 5 67280 12635.9 0 67280 6 66472 3159.0 0 66472 7 55108 789.7 0 55108 8 68928 197.4 0 68928 9 68982 49.4 0 68109 873 10 64214 12.3 1 60894 3320 11 72301 3.1 1 66989 5312 12 69430 0.8 1 65113 4317 13 71580 0.2 1 67020 4560 14 70477 0.2 1 65870 4607 15 75676 0.2 1 70785 4891 16 72936 0.2 1 67871 5065 17 87298 0.2 1 80460 6838 18 79611 0.2 1 74935 4676 19 65534 0.2 1 61501 4033 20 79604 0.2 1 74644 4960 21 85256 0.2 1 79605 5651 22 73838 0.2 1 69798 4040 23 84971 0.2 1 79628 5343 24 80676 0.2 1 74456 6220 25 85904 0.2 1 80404 5500 26 79805 0.2 1 75204 4601 27 88623 0.2 1 82274 6349 28 86173 0.2 1 80506 5667 29 91469 0.2 1 84355 7114 30 95793 0.2 1 90568 5225 31 77688 0.2 1 72851 4837 32 92600 0.2 1 86938 5662 33 87750 0.2 1 82121 5629 34 99316 0.2 1 92291 7025 35 87021 0.2 1 82303 4718 36 99065 0.2 1 92449 6616 37 101447 0.2 1 95128 6319 38 97080 0.2 1 90884 6196 39 103846 0.2 1 96530 7316 40 94829 0.2 1 89475 5354 41 105310 0.2 1 97483 7827 42 95966 0.2 1 89196 6770 43 151686 0.2 1 144208 7478 44 46892 0.2 1 42892 4000 45 105867 0.2 1 99520 6347 46 96566 0.2 1 90512 6054 47 103096 0.2 1 97153 5943 48 102489 0.2 1 96145 6344 49 112243 0.2 1 104909 7334 50 94609 0.2 1 89107 5502 51 103165 0.2 1 96761 6404 52 107310 0.2 1 100073 7237 53 113172 0.2 1 106618 6554 54 92162 0.2 1 86748 5414 55 108541 0.2 1 101655 6886 56 133677 0.2 1 126253 7424 57 81980 0.2 1 76375 5605 58 110163 0.2 1 104385 5778 59 98316 0.2 1 92340 5976 60 104988 0.2 1 98449 6539 61 103910 0.2 1 97861 6049 62 115389 0.2 1 108890 6499 63 89259 0.2 1 83482 5777 64 102584 0.2 1 96877 5707 65 114383 0.2 1 107700 6683 66 118785 0.2 1 111674 7111 67 124927 0.2 1 115790 9137 68 236831 0.2 1 226263 10568 69 32490 0.2 1 29503 2987 70 14743 0.2 1 12126 2617 71 68006 0.2 1 64211 3795 72 89001 0.2 1 84078 4923 73 92459 0.2 1 87195 5264 74 91411 0.2 1 86036 5375 75 90970 0.2 1 85629 5341 76 89709 0.2 1 84538 5171 77 89140 0.2 1 84081 5059 78 83843 0.2 1 78811 5032 79 83141 0.2 1 78204 4937 80 80837 0.2 1 76149 4688 81 79618 0.2 1 74844 4774 82 77902 0.2 1 73376 4526 83 75605 0.2 1 71189 4416 84 73149 0.2 1 68920 4229 85 70442 0.2 1 66393 4049 86 67311 0.2 1 63325 3986 87 65584 0.2 1 61688 3896 88 63773 0.2 1 60070 3703 89 60201 0.2 1 56655 3546 90 59708 0.2 1 56173 3535 91 56748 0.2 1 53363 3385 92 53671 0.2 1 50489 3182 93 50670 0.2 1 47624 3046 94 48704 0.2 1 45782 2922 95 45200 0.2 1 42460 2740 96 42497 0.2 1 39903 2594 97 39947 0.2 1 37451 2496 98 36683 0.2 1 34398 2285 99 36692 0.2 1 34265 2427 100 32868 0.2 1 30853 2015 101 30512 0.2 1 28489 2023 102 27906 0.2 1 26115 1791 103 26175 0.2 1 24518 1657 104 23983 0.2 1 22398 1585 105 21704 0.2 1 20274 1430 106 19667 0.2 1 18358 1309 107 17851 0.2 1 16610 1241 108 16494 0.2 1 15292 1202 109 14962 0.2 1 13856 1106 110 13424 0.2 1 12418 1006 111 12110 0.2 1 11218 892 112 10668 0.2 1 9941 727 113 8879 0.2 1 8200 679 114 7950 0.2 1 7388 562 115 7058 0.2 1 6505 553 116 6198 0.2 1 5702 496 117 5071 0.2 1 4638 433 118 4567 0.2 1 4226 341 119 3829 0.2 1 3494 335 120 3187 0.2 1 2901 286 121 2891 0.2 1 2612 279 122 2303 0.2 1 2110 193 123 1890 0.2 1 1705 185 124 1701 0.2 1 1504 197 125 1363 0.2 1 1208 155 126 1199 0.2 1 1086 113 127 954 0.2 1 859 95 128 812 0.2 1 702 110 129 610 0.2 1 539 71 130 529 0.2 1 472 57 131 405 0.2 1 354 51 132 324 0.2 1 279 45 133 284 0.2 1 248 36 134 306 0.2 1 272 34 135 179 0.2 1 161 18 136 123 0.2 1 97 26 137 92 0.2 1 81 11 138 74 0.2 1 60 14 139 42 0.2 1 38 4 140 25 0.2 1 20 5 141 21 0.2 1 16 5 142 15 0.2 1 14 1 143 11 0.2 1 8 3 144 7 0.2 1 5 2 145 18 0.2 1 14 4 146 10 0.2 1 8 2 147 32 0.2 1 32 148 16 0.2 1 16 149 9 0.2 1 5 4 150 128 0.2 1 105 23 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_32psu_2_S6_L001_R1_001.fastq.gz ============================================= 12939154 sequences processed in total