SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_26psu_4_S16_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_4_S16_L001_R2_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 716.93 s (42 us/read; 1.45 M reads/minute). === Summary === Total reads processed: 17,274,454 Reads with adapters: 13,645,900 (79.0%) Reads written (passing filters): 17,274,454 (100.0%) Total basepairs processed: 2,591,168,100 bp Quality-trimmed: 13,876,099 bp (0.5%) Total written (filtered): 1,990,000,241 bp (76.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 13645900 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 27.8% C: 13.6% G: 24.3% T: 34.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2190701 4318613.5 0 2190701 2 333937 1079653.4 0 333937 3 193297 269913.3 0 193297 4 108228 67478.3 0 108228 5 96340 16869.6 0 96340 6 82360 4217.4 0 82360 7 66626 1054.3 0 66626 8 94895 263.6 0 94895 9 77384 65.9 0 77094 290 10 82708 16.5 1 78572 4136 11 89357 4.1 1 83568 5789 12 89625 1.0 1 83594 6031 13 99746 0.3 1 93650 6096 14 92613 0.3 1 86134 6479 15 76114 0.3 1 71248 4866 16 111173 0.3 1 104156 7017 17 86562 0.3 1 80610 5952 18 85573 0.3 1 80223 5350 19 106850 0.3 1 99751 7099 20 100367 0.3 1 94128 6239 21 90921 0.3 1 85159 5762 22 101235 0.3 1 95178 6057 23 104933 0.3 1 98391 6542 24 104547 0.3 1 97881 6666 25 118815 0.3 1 111628 7187 26 97285 0.3 1 91138 6147 27 109196 0.3 1 101511 7685 28 101869 0.3 1 96609 5260 29 109573 0.3 1 102802 6771 30 108062 0.3 1 102093 5969 31 117609 0.3 1 110646 6963 32 106258 0.3 1 100439 5819 33 117522 0.3 1 110451 7071 34 150731 0.3 1 141819 8912 35 85761 0.3 1 81040 4721 36 120033 0.3 1 112538 7495 37 128229 0.3 1 120721 7508 38 120207 0.3 1 114092 6115 39 117619 0.3 1 111621 5998 40 131723 0.3 1 123921 7802 41 124695 0.3 1 117864 6831 42 129575 0.3 1 122681 6894 43 116234 0.3 1 109884 6350 44 134420 0.3 1 127012 7408 45 140609 0.3 1 133114 7495 46 107286 0.3 1 101613 5673 47 132633 0.3 1 125745 6888 48 129386 0.3 1 122927 6459 49 135218 0.3 1 128159 7059 50 128960 0.3 1 121933 7027 51 158199 0.3 1 150290 7909 52 115635 0.3 1 110127 5508 53 138536 0.3 1 132192 6344 54 107841 0.3 1 102539 5302 55 138155 0.3 1 131891 6264 56 143145 0.3 1 136120 7025 57 134481 0.3 1 128427 6054 58 129238 0.3 1 123474 5764 59 132359 0.3 1 126122 6237 60 136774 0.3 1 130227 6547 61 140635 0.3 1 133777 6858 62 151391 0.3 1 144144 7247 63 203160 0.3 1 194409 8751 64 167385 0.3 1 160989 6396 65 109630 0.3 1 104767 4863 66 118791 0.3 1 113616 5175 67 117636 0.3 1 112066 5570 68 118814 0.3 1 113546 5268 69 118228 0.3 1 112812 5416 70 124633 0.3 1 118945 5688 71 132024 0.3 1 126339 5685 72 125001 0.3 1 119396 5605 73 132138 0.3 1 126543 5595 74 121069 0.3 1 115983 5086 75 115800 0.3 1 110816 4984 76 113271 0.3 1 108471 4800 77 113434 0.3 1 108479 4955 78 108048 0.3 1 103289 4759 79 104688 0.3 1 100095 4593 80 104276 0.3 1 99811 4465 81 103173 0.3 1 98658 4515 82 98745 0.3 1 94559 4186 83 96106 0.3 1 91915 4191 84 93144 0.3 1 88994 4150 85 92176 0.3 1 88129 4047 86 91669 0.3 1 87622 4047 87 92154 0.3 1 88295 3859 88 89148 0.3 1 85288 3860 89 81149 0.3 1 77666 3483 90 78174 0.3 1 74845 3329 91 73485 0.3 1 70395 3090 92 69397 0.3 1 66501 2896 93 66171 0.3 1 63215 2956 94 65063 0.3 1 62271 2792 95 61764 0.3 1 59094 2670 96 58368 0.3 1 55944 2424 97 55755 0.3 1 53423 2332 98 52903 0.3 1 50745 2158 99 53244 0.3 1 51088 2156 100 47728 0.3 1 45793 1935 101 43677 0.3 1 41891 1786 102 42206 0.3 1 40454 1752 103 39193 0.3 1 37641 1552 104 38151 0.3 1 36638 1513 105 33427 0.3 1 32096 1331 106 30687 0.3 1 29498 1189 107 27695 0.3 1 26647 1048 108 24686 0.3 1 23641 1045 109 22730 0.3 1 21817 913 110 20941 0.3 1 20113 828 111 19623 0.3 1 18797 826 112 17030 0.3 1 16327 703 113 14883 0.3 1 14295 588 114 13223 0.3 1 12713 510 115 11548 0.3 1 11042 506 116 9826 0.3 1 9358 468 117 8325 0.3 1 7930 395 118 7266 0.3 1 6933 333 119 6187 0.3 1 5890 297 120 5282 0.3 1 5029 253 121 4888 0.3 1 4641 247 122 4001 0.3 1 3828 173 123 3492 0.3 1 3320 172 124 2873 0.3 1 2729 144 125 2466 0.3 1 2331 135 126 2028 0.3 1 1925 103 127 1732 0.3 1 1662 70 128 1274 0.3 1 1214 60 129 1089 0.3 1 1028 61 130 827 0.3 1 782 45 131 699 0.3 1 652 47 132 657 0.3 1 618 39 133 790 0.3 1 750 40 134 1089 0.3 1 1048 41 135 486 0.3 1 468 18 136 232 0.3 1 220 12 137 137 0.3 1 130 7 138 117 0.3 1 101 16 139 79 0.3 1 72 7 140 58 0.3 1 53 5 141 42 0.3 1 40 2 142 42 0.3 1 37 5 143 28 0.3 1 25 3 144 19 0.3 1 18 1 145 43 0.3 1 41 2 146 41 0.3 1 36 5 147 80 0.3 1 71 9 148 57 0.3 1 57 149 45 0.3 1 41 4 150 372 0.3 1 355 17 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_26psu_4_S16_L001_R2_001.fastq.gz ============================================= 17274454 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 28578 (0.2%)