SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_26psu_1_S9_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: 519755). 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_26psu_1_S9_L001_R2_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 71.70 s (4 us/read; 15.21 M reads/minute). === Summary === Total reads processed: 18,172,174 Reads with adapters: 13,925,142 (76.6%) Reads written (passing filters): 18,172,174 (100.0%) Total basepairs processed: 2,725,826,100 bp Quality-trimmed: 12,772,261 bp (0.5%) Total written (filtered): 2,156,656,577 bp (79.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 13925142 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.0% C: 12.4% G: 23.9% T: 34.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2593588 4543043.5 0 2593588 2 376254 1135760.9 0 376254 3 210205 283940.2 0 210205 4 119037 70985.1 0 119037 5 104651 17746.3 0 104651 6 89236 4436.6 0 89236 7 73097 1109.1 0 73097 8 103442 277.3 0 103442 9 83266 69.3 0 82975 291 10 90702 17.3 1 86533 4169 11 96126 4.3 1 90174 5952 12 96465 1.1 1 90519 5946 13 107004 0.3 1 100993 6011 14 100898 0.3 1 93952 6946 15 82733 0.3 1 77655 5078 16 119602 0.3 1 112441 7161 17 94839 0.3 1 88603 6236 18 92099 0.3 1 86695 5404 19 114214 0.3 1 107016 7198 20 107713 0.3 1 101500 6213 21 95562 0.3 1 89784 5778 22 107588 0.3 1 101222 6366 23 111031 0.3 1 104295 6736 24 110341 0.3 1 103677 6664 25 124129 0.3 1 117008 7121 26 103231 0.3 1 96892 6339 27 114476 0.3 1 106707 7769 28 107750 0.3 1 102430 5320 29 114219 0.3 1 107523 6696 30 113089 0.3 1 107416 5673 31 123120 0.3 1 116178 6942 32 110386 0.3 1 104842 5544 33 123147 0.3 1 116091 7056 34 156685 0.3 1 148041 8644 35 89283 0.3 1 84701 4582 36 120443 0.3 1 113382 7061 37 129458 0.3 1 122208 7250 38 122546 0.3 1 116642 5904 39 119280 0.3 1 113530 5750 40 132471 0.3 1 125158 7313 41 126758 0.3 1 120385 6373 42 130992 0.3 1 124472 6520 43 120675 0.3 1 114532 6143 44 136598 0.3 1 129517 7081 45 144732 0.3 1 137448 7284 46 106581 0.3 1 101258 5323 47 132125 0.3 1 125807 6318 48 130489 0.3 1 124465 6024 49 135590 0.3 1 129070 6520 50 128632 0.3 1 122091 6541 51 159357 0.3 1 151626 7731 52 116120 0.3 1 110786 5334 53 139419 0.3 1 133495 5924 54 106851 0.3 1 101979 4872 55 135687 0.3 1 129810 5877 56 138774 0.3 1 132432 6342 57 131848 0.3 1 126296 5552 58 127061 0.3 1 121713 5348 59 129536 0.3 1 124051 5485 60 133143 0.3 1 127312 5831 61 136216 0.3 1 129973 6243 62 147811 0.3 1 140964 6847 63 197994 0.3 1 190073 7921 64 157927 0.3 1 152075 5852 65 105906 0.3 1 101567 4339 66 114677 0.3 1 109835 4842 67 114010 0.3 1 108938 5072 68 114564 0.3 1 109670 4894 69 112505 0.3 1 107761 4744 70 118303 0.3 1 113227 5076 71 123531 0.3 1 118496 5035 72 117539 0.3 1 112405 5134 73 122781 0.3 1 117929 4852 74 113055 0.3 1 108472 4583 75 107896 0.3 1 103502 4394 76 106239 0.3 1 101975 4264 77 105105 0.3 1 100663 4442 78 99929 0.3 1 95794 4135 79 96680 0.3 1 92707 3973 80 95740 0.3 1 91762 3978 81 93945 0.3 1 90030 3915 82 89626 0.3 1 86049 3577 83 87905 0.3 1 84339 3566 84 84781 0.3 1 81246 3535 85 83386 0.3 1 79899 3487 86 83197 0.3 1 79728 3469 87 82660 0.3 1 79311 3349 88 81067 0.3 1 77676 3391 89 73343 0.3 1 70291 3052 90 69973 0.3 1 67072 2901 91 65096 0.3 1 62445 2651 92 61646 0.3 1 59119 2527 93 59393 0.3 1 56935 2458 94 57203 0.3 1 54848 2355 95 53756 0.3 1 51532 2224 96 50956 0.3 1 49026 1930 97 47276 0.3 1 45371 1905 98 44746 0.3 1 43017 1729 99 42641 0.3 1 41013 1628 100 39899 0.3 1 38401 1498 101 36809 0.3 1 35396 1413 102 34264 0.3 1 32958 1306 103 31058 0.3 1 29842 1216 104 30002 0.3 1 28912 1090 105 26784 0.3 1 25668 1116 106 24257 0.3 1 23303 954 107 21941 0.3 1 21141 800 108 20010 0.3 1 19251 759 109 18313 0.3 1 17584 729 110 16702 0.3 1 16007 695 111 15559 0.3 1 14968 591 112 13419 0.3 1 12890 529 113 11631 0.3 1 11113 518 114 10507 0.3 1 10110 397 115 8927 0.3 1 8561 366 116 7354 0.3 1 7008 346 117 6258 0.3 1 5993 265 118 5422 0.3 1 5194 228 119 4575 0.3 1 4365 210 120 3972 0.3 1 3799 173 121 3338 0.3 1 3179 159 122 2723 0.3 1 2578 145 123 2312 0.3 1 2208 104 124 2044 0.3 1 1948 96 125 1725 0.3 1 1623 102 126 1567 0.3 1 1498 69 127 1207 0.3 1 1135 72 128 957 0.3 1 886 71 129 782 0.3 1 739 43 130 614 0.3 1 575 39 131 601 0.3 1 565 36 132 573 0.3 1 543 30 133 862 0.3 1 829 33 134 1185 0.3 1 1148 37 135 434 0.3 1 412 22 136 191 0.3 1 179 12 137 150 0.3 1 137 13 138 67 0.3 1 59 8 139 66 0.3 1 55 11 140 41 0.3 1 35 6 141 28 0.3 1 25 3 142 18 0.3 1 17 1 143 17 0.3 1 17 144 10 0.3 1 7 3 145 31 0.3 1 30 1 146 24 0.3 1 21 3 147 69 0.3 1 63 6 148 53 0.3 1 49 4 149 41 0.3 1 39 2 150 371 0.3 1 357 14 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_26psu_1_S9_L001_R2_001.fastq.gz ============================================= 18172174 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 18172174 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 154574 (0.85%)