SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_26psu_3_S15_L001_R2_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/16C_26psu_3_S15_L001_R2_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 625.12 s (43 us/read; 1.41 M reads/minute). === Summary === Total reads processed: 14,705,097 Reads with adapters: 10,980,117 (74.7%) Reads written (passing filters): 14,705,097 (100.0%) Total basepairs processed: 2,205,764,550 bp Quality-trimmed: 13,510,954 bp (0.6%) Total written (filtered): 1,769,417,806 bp (80.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10980117 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.1% C: 14.1% G: 23.8% T: 33.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2264307 3676274.2 0 2264307 2 373214 919068.6 0 373214 3 218063 229767.1 0 218063 4 104965 57441.8 0 104965 5 83066 14360.4 0 83066 6 70406 3590.1 0 70406 7 54672 897.5 0 54672 8 80609 224.4 0 80609 9 63967 56.1 0 63675 292 10 69384 14.0 1 65411 3973 11 74885 3.5 1 69453 5432 12 74890 0.9 1 69291 5599 13 82476 0.2 1 76999 5477 14 78491 0.2 1 72263 6228 15 61874 0.2 1 57566 4308 16 91303 0.2 1 84745 6558 17 72220 0.2 1 66746 5474 18 69582 0.2 1 64867 4715 19 88040 0.2 1 81744 6296 20 81620 0.2 1 76073 5547 21 72843 0.2 1 67713 5130 22 82391 0.2 1 76741 5650 23 83759 0.2 1 77887 5872 24 82590 0.2 1 76725 5865 25 94974 0.2 1 88688 6286 26 78108 0.2 1 72602 5506 27 87345 0.2 1 80708 6637 28 80301 0.2 1 75686 4615 29 86749 0.2 1 80805 5944 30 84969 0.2 1 79761 5208 31 91560 0.2 1 85496 6064 32 82472 0.2 1 77608 4864 33 91075 0.2 1 85011 6064 34 115701 0.2 1 108310 7391 35 65587 0.2 1 61631 3956 36 92396 0.2 1 86112 6284 37 97880 0.2 1 91450 6430 38 93812 0.2 1 88555 5257 39 89857 0.2 1 84658 5199 40 100686 0.2 1 94165 6521 41 95917 0.2 1 90320 5597 42 99426 0.2 1 93710 5716 43 89895 0.2 1 84632 5263 44 101978 0.2 1 95733 6245 45 107145 0.2 1 100731 6414 46 78559 0.2 1 74098 4461 47 99270 0.2 1 93634 5636 48 97566 0.2 1 92156 5410 49 101230 0.2 1 95394 5836 50 95465 0.2 1 89881 5584 51 119107 0.2 1 112449 6658 52 84719 0.2 1 80119 4600 53 101734 0.2 1 96544 5190 54 78783 0.2 1 74521 4262 55 102169 0.2 1 97154 5015 56 104926 0.2 1 99510 5416 57 97330 0.2 1 92599 4731 58 94743 0.2 1 90360 4383 59 96773 0.2 1 91767 5006 60 98229 0.2 1 93172 5057 61 101518 0.2 1 96208 5310 62 108759 0.2 1 103148 5611 63 145227 0.2 1 138420 6807 64 118502 0.2 1 113544 4958 65 77875 0.2 1 74180 3695 66 85279 0.2 1 81158 4121 67 82906 0.2 1 78696 4210 68 83568 0.2 1 79559 4009 69 83055 0.2 1 79009 4046 70 85605 0.2 1 81510 4095 71 91438 0.2 1 87015 4423 72 86608 0.2 1 82445 4163 73 91905 0.2 1 87632 4273 74 84442 0.2 1 80649 3793 75 80482 0.2 1 76627 3855 76 78424 0.2 1 74783 3641 77 78513 0.2 1 74716 3797 78 74066 0.2 1 70442 3624 79 70946 0.2 1 67597 3349 80 70802 0.2 1 67560 3242 81 69586 0.2 1 66414 3172 82 67330 0.2 1 64176 3154 83 64772 0.2 1 61853 2919 84 63911 0.2 1 60972 2939 85 62434 0.2 1 59365 3069 86 62539 0.2 1 59521 3018 87 61465 0.2 1 58594 2871 88 60482 0.2 1 57646 2836 89 54895 0.2 1 52333 2562 90 52052 0.2 1 49599 2453 91 49106 0.2 1 46822 2284 92 45843 0.2 1 43672 2171 93 44679 0.2 1 42566 2113 94 43439 0.2 1 41408 2031 95 41369 0.2 1 39446 1923 96 39301 0.2 1 37521 1780 97 36285 0.2 1 34613 1672 98 34034 0.2 1 32424 1610 99 33720 0.2 1 32265 1455 100 30495 0.2 1 29039 1456 101 27811 0.2 1 26487 1324 102 25647 0.2 1 24471 1176 103 23848 0.2 1 22756 1092 104 23030 0.2 1 22018 1012 105 20481 0.2 1 19504 977 106 19291 0.2 1 18417 874 107 17027 0.2 1 16232 795 108 15744 0.2 1 15015 729 109 13986 0.2 1 13295 691 110 13128 0.2 1 12523 605 111 12855 0.2 1 12274 581 112 11119 0.2 1 10542 577 113 9437 0.2 1 8968 469 114 8605 0.2 1 8220 385 115 7442 0.2 1 7067 375 116 6235 0.2 1 5927 308 117 5342 0.2 1 5066 276 118 4634 0.2 1 4366 268 119 4041 0.2 1 3836 205 120 3372 0.2 1 3167 205 121 3329 0.2 1 3149 180 122 2717 0.2 1 2578 139 123 2317 0.2 1 2172 145 124 2087 0.2 1 1969 118 125 1757 0.2 1 1630 127 126 1582 0.2 1 1504 78 127 1368 0.2 1 1287 81 128 1019 0.2 1 960 59 129 887 0.2 1 843 44 130 669 0.2 1 637 32 131 775 0.2 1 731 44 132 814 0.2 1 771 43 133 1245 0.2 1 1202 43 134 1982 0.2 1 1926 56 135 810 0.2 1 778 32 136 281 0.2 1 260 21 137 198 0.2 1 181 17 138 183 0.2 1 171 12 139 135 0.2 1 124 11 140 85 0.2 1 83 2 141 71 0.2 1 66 5 142 55 0.2 1 52 3 143 87 0.2 1 84 3 144 82 0.2 1 77 5 145 214 0.2 1 204 10 146 799 0.2 1 768 31 147 4799 0.2 1 4649 150 148 3222 0.2 1 3110 112 149 1903 0.2 1 1826 77 150 15860 0.2 1 15305 555 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_26psu_3_S15_L001_R2_001.fastq.gz ============================================= 14705097 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 55347 (0.4%)