SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_26psu_4_S12_L001_R1_001.fastq.gz Trimming mode: single-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; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length before a sequence gets removed: 20 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /Volumes/web/metacarcinus/Salmo_Calig/analyses/20190722/TRIM_adapt/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 /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_26psu_4_S12_L001_R1_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 507.33 s (40 us/read; 1.49 M reads/minute). === Summary === Total reads processed: 12,592,704 Reads with adapters: 8,958,992 (71.1%) Reads written (passing filters): 12,592,704 (100.0%) Total basepairs processed: 1,888,905,600 bp Quality-trimmed: 4,951,530 bp (0.3%) Total written (filtered): 1,571,128,982 bp (83.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 8958992 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 31.4% C: 15.5% G: 17.3% T: 35.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2360389 3148176.0 0 2360389 2 294874 787044.0 0 294874 3 161693 196761.0 0 161693 4 87416 49190.2 0 87416 5 59722 12297.6 0 59722 6 57196 3074.4 0 57196 7 45727 768.6 0 45727 8 58159 192.1 0 58159 9 58762 48.0 0 57759 1003 10 54824 12.0 1 51199 3625 11 61143 3.0 1 55667 5476 12 58318 0.8 1 53717 4601 13 56920 0.2 1 52502 4418 14 60297 0.2 1 55050 5247 15 60573 0.2 1 55708 4865 16 61479 0.2 1 55954 5525 17 74409 0.2 1 67438 6971 18 61009 0.2 1 56681 4328 19 53089 0.2 1 48849 4240 20 63972 0.2 1 58870 5102 21 70043 0.2 1 64287 5756 22 58590 0.2 1 54441 4149 23 68150 0.2 1 62728 5422 24 64229 0.2 1 58023 6206 25 68130 0.2 1 62567 5563 26 62420 0.2 1 57820 4600 27 69993 0.2 1 63874 6119 28 67875 0.2 1 62387 5488 29 71196 0.2 1 64376 6820 30 75799 0.2 1 70433 5366 31 59056 0.2 1 54472 4584 32 73671 0.2 1 68075 5596 33 63947 0.2 1 58700 5247 34 74583 0.2 1 67925 6658 35 70104 0.2 1 64152 5952 36 77250 0.2 1 71393 5857 37 68309 0.2 1 62839 5470 38 72505 0.2 1 67371 5134 39 75409 0.2 1 69866 5543 40 72478 0.2 1 66543 5935 41 78235 0.2 1 70876 7359 42 73557 0.2 1 66866 6691 43 105788 0.2 1 99220 6568 44 39203 0.2 1 34910 4293 45 75980 0.2 1 70161 5819 46 74377 0.2 1 68346 6031 47 78776 0.2 1 72951 5825 48 70677 0.2 1 64756 5921 49 81336 0.2 1 74410 6926 50 66909 0.2 1 62092 4817 51 72737 0.2 1 67212 5525 52 78934 0.2 1 71865 7069 53 86579 0.2 1 80550 6029 54 62022 0.2 1 57173 4849 55 75974 0.2 1 70348 5626 56 85877 0.2 1 79807 6070 57 71505 0.2 1 65936 5569 58 69856 0.2 1 65606 4250 59 57167 0.2 1 52447 4720 60 78076 0.2 1 72356 5720 61 73472 0.2 1 68201 5271 62 71844 0.2 1 66745 5099 63 67131 0.2 1 62070 5061 64 65598 0.2 1 60901 4697 65 70779 0.2 1 65435 5344 66 77405 0.2 1 71580 5825 67 84608 0.2 1 76761 7847 68 150617 0.2 1 142058 8559 69 37132 0.2 1 33982 3150 70 13103 0.2 1 10914 2189 71 35026 0.2 1 32099 2927 72 57779 0.2 1 53691 4088 73 61230 0.2 1 56931 4299 74 61166 0.2 1 56777 4389 75 60302 0.2 1 55958 4344 76 59928 0.2 1 55484 4444 77 59440 0.2 1 54970 4470 78 56149 0.2 1 51928 4221 79 55286 0.2 1 51002 4284 80 53792 0.2 1 49846 3946 81 52637 0.2 1 48756 3881 82 51226 0.2 1 47353 3873 83 49579 0.2 1 45690 3889 84 48468 0.2 1 44896 3572 85 45867 0.2 1 42408 3459 86 44887 0.2 1 41555 3332 87 42251 0.2 1 38964 3287 88 42216 0.2 1 39029 3187 89 40149 0.2 1 37066 3083 90 40387 0.2 1 37102 3285 91 37214 0.2 1 34343 2871 92 35614 0.2 1 32860 2754 93 33363 0.2 1 30676 2687 94 32052 0.2 1 29598 2454 95 29858 0.2 1 27450 2408 96 28594 0.2 1 26301 2293 97 26730 0.2 1 24584 2146 98 25261 0.2 1 23132 2129 99 24232 0.2 1 22120 2112 100 22159 0.2 1 20358 1801 101 20488 0.2 1 18713 1775 102 19117 0.2 1 17450 1667 103 17468 0.2 1 15984 1484 104 16181 0.2 1 14728 1453 105 14521 0.2 1 13231 1290 106 13349 0.2 1 12105 1244 107 12159 0.2 1 11005 1154 108 11376 0.2 1 10302 1074 109 10099 0.2 1 9151 948 110 9379 0.2 1 8450 929 111 8577 0.2 1 7720 857 112 7623 0.2 1 6797 826 113 6486 0.2 1 5771 715 114 5676 0.2 1 5112 564 115 5089 0.2 1 4501 588 116 4254 0.2 1 3781 473 117 3599 0.2 1 3183 416 118 3110 0.2 1 2758 352 119 2723 0.2 1 2363 360 120 2307 0.2 1 1995 312 121 2051 0.2 1 1780 271 122 1835 0.2 1 1588 247 123 1508 0.2 1 1291 217 124 1263 0.2 1 1083 180 125 1119 0.2 1 966 153 126 1055 0.2 1 916 139 127 900 0.2 1 780 120 128 681 0.2 1 568 113 129 550 0.2 1 468 82 130 520 0.2 1 423 97 131 523 0.2 1 467 56 132 590 0.2 1 526 64 133 974 0.2 1 878 96 134 2631 0.2 1 2466 165 135 822 0.2 1 768 54 136 169 0.2 1 154 15 137 111 0.2 1 90 21 138 83 0.2 1 75 8 139 53 0.2 1 41 12 140 56 0.2 1 43 13 141 26 0.2 1 20 6 142 15 0.2 1 12 3 143 20 0.2 1 16 4 144 56 0.2 1 47 9 145 231 0.2 1 197 34 146 229 0.2 1 199 30 147 1212 0.2 1 1078 134 148 767 0.2 1 701 66 149 472 0.2 1 430 42 150 3085 0.2 1 2595 490 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_26psu_4_S12_L001_R1_001.fastq.gz ============================================= 12592704 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 12180 (0.1%)