SUMMARISING RUN PARAMETERS ========================== Input filename: /Users/strigg/Desktop/Salmo_Calig/CTRL_16C_26psu_2_S21_L001_R1_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.6.0 Cutadapt version: 2.4 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 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 5 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 5 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /Users/strigg/Desktop/Salmo_Calig/TRIM/FASTQC Output file will be GZIP compressed This is cutadapt 2.4 with Python 3.6.8 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /Users/strigg/Desktop/Salmo_Calig/CTRL_16C_26psu_2_S21_L001_R1_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 478.70 s (36 us/read; 1.68 M reads/minute). === Summary === Total reads processed: 13,433,110 Reads with adapters: 11,700,096 (87.1%) Reads written (passing filters): 13,433,110 (100.0%) Total basepairs processed: 2,014,966,500 bp Quality-trimmed: 3,988,642 bp (0.2%) Total written (filtered): 1,426,352,975 bp (70.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11700096 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.8% C: 12.5% G: 23.6% T: 35.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 952009 3358277.5 0 952009 2 175701 839569.4 0 175701 3 106315 209892.3 0 106315 4 68924 52473.1 0 68924 5 62282 13118.3 0 62282 6 61633 3279.6 0 61633 7 52554 819.9 0 52554 8 65132 205.0 0 65132 9 65306 51.2 0 64521 785 10 61900 12.8 1 58796 3104 11 68989 3.2 1 63880 5109 12 67245 0.8 1 63248 3997 13 69213 0.2 1 64859 4354 14 71768 0.2 1 66846 4922 15 75062 0.2 1 70553 4509 16 74514 0.2 1 69133 5381 17 90491 0.2 1 83695 6796 18 77417 0.2 1 72980 4437 19 68949 0.2 1 64670 4279 20 81015 0.2 1 76032 4983 21 89626 0.2 1 83646 5980 22 77941 0.2 1 73613 4328 23 90688 0.2 1 84959 5729 24 86332 0.2 1 79509 6823 25 91755 0.2 1 85888 5867 26 86085 0.2 1 81297 4788 27 95329 0.2 1 88851 6478 28 95528 0.2 1 89551 5977 29 99349 0.2 1 92034 7315 30 106567 0.2 1 101023 5544 31 85587 0.2 1 80666 4921 32 103697 0.2 1 97691 6006 33 99669 0.2 1 93324 6345 34 119451 0.2 1 111551 7900 35 94360 0.2 1 88955 5405 36 108596 0.2 1 102097 6499 37 113594 0.2 1 106631 6963 38 108790 0.2 1 101383 7407 39 126706 0.2 1 119375 7331 40 103711 0.2 1 97817 5894 41 130432 0.2 1 122153 8279 42 110139 0.2 1 101991 8148 43 183261 0.2 1 174857 8404 44 57830 0.2 1 53254 4576 45 123796 0.2 1 116975 6821 46 119988 0.2 1 113024 6964 47 130141 0.2 1 122976 7165 48 120988 0.2 1 113912 7076 49 138463 0.2 1 129394 9069 50 122247 0.2 1 115770 6477 51 132587 0.2 1 124814 7773 52 139338 0.2 1 129873 9465 53 153954 0.2 1 145822 8132 54 118275 0.2 1 111358 6917 55 139368 0.2 1 131390 7978 56 164199 0.2 1 155690 8509 57 126552 0.2 1 118427 8125 58 144214 0.2 1 137457 6757 59 116278 0.2 1 109533 6745 60 144971 0.2 1 136747 8224 61 139800 0.2 1 132274 7526 62 147932 0.2 1 140286 7646 63 129438 0.2 1 121520 7918 64 136148 0.2 1 129121 7027 65 148136 0.2 1 139981 8155 66 158867 0.2 1 150035 8832 67 172296 0.2 1 160373 11923 68 325502 0.2 1 311428 14074 69 62909 0.2 1 58208 4701 70 23526 0.2 1 20186 3340 71 82740 0.2 1 78158 4582 72 124178 0.2 1 117785 6393 73 132921 0.2 1 125940 6981 74 131071 0.2 1 124071 7000 75 128974 0.2 1 122028 6946 76 128069 0.2 1 121139 6930 77 126522 0.2 1 119822 6700 78 120502 0.2 1 113788 6714 79 118821 0.2 1 112166 6655 80 115866 0.2 1 109547 6319 81 115264 0.2 1 108988 6276 82 110755 0.2 1 104576 6179 83 107566 0.2 1 101669 5897 84 105597 0.2 1 99846 5751 85 102751 0.2 1 97220 5531 86 97615 0.2 1 92219 5396 87 92989 0.2 1 87786 5203 88 92437 0.2 1 87288 5149 89 88099 0.2 1 83258 4841 90 86764 0.2 1 81847 4917 91 81829 0.2 1 77279 4550 92 77590 0.2 1 73265 4325 93 73175 0.2 1 69095 4080 94 69476 0.2 1 65477 3999 95 65431 0.2 1 61622 3809 96 61527 0.2 1 57946 3581 97 57358 0.2 1 54065 3293 98 53633 0.2 1 50498 3135 99 51351 0.2 1 48285 3066 100 46130 0.2 1 43457 2673 101 43563 0.2 1 40904 2659 102 39390 0.2 1 37016 2374 103 35867 0.2 1 33682 2185 104 32606 0.2 1 30634 1972 105 28646 0.2 1 26808 1838 106 26227 0.2 1 24640 1587 107 23172 0.2 1 21743 1429 108 21298 0.2 1 19891 1407 109 18913 0.2 1 17580 1333 110 16998 0.2 1 15871 1127 111 15038 0.2 1 14044 994 112 12635 0.2 1 11815 820 113 11352 0.2 1 10604 748 114 9838 0.2 1 9171 667 115 8151 0.2 1 7529 622 116 7025 0.2 1 6508 517 117 5831 0.2 1 5406 425 118 5154 0.2 1 4783 371 119 4064 0.2 1 3743 321 120 3640 0.2 1 3365 275 121 2769 0.2 1 2540 229 122 2341 0.2 1 2118 223 123 2056 0.2 1 1883 173 124 1687 0.2 1 1543 144 125 1340 0.2 1 1233 107 126 1317 0.2 1 1201 116 127 1059 0.2 1 975 84 128 810 0.2 1 740 70 129 681 0.2 1 600 81 130 748 0.2 1 679 69 131 837 0.2 1 795 42 132 954 0.2 1 903 51 133 1339 0.2 1 1266 73 134 1750 0.2 1 1667 83 135 759 0.2 1 718 41 136 229 0.2 1 209 20 137 121 0.2 1 104 17 138 84 0.2 1 73 11 139 75 0.2 1 63 12 140 73 0.2 1 58 15 141 35 0.2 1 32 3 142 38 0.2 1 35 3 143 19 0.2 1 15 4 144 19 0.2 1 11 8 145 22 0.2 1 21 1 146 64 0.2 1 59 5 147 278 0.2 1 250 28 148 168 0.2 1 142 26 149 83 0.2 1 70 13 150 577 0.2 1 506 71 RUN STATISTICS FOR INPUT FILE: /Users/strigg/Desktop/Salmo_Calig/CTRL_16C_26psu_2_S21_L001_R1_001.fastq.gz ============================================= 13433110 sequences processed in total