SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_32psu_4_S4_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/16C_32psu_4_S4_L001_R1_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 672.52 s (43 us/read; 1.40 M reads/minute). === Summary === Total reads processed: 15,706,000 Reads with adapters: 11,318,033 (72.1%) Reads written (passing filters): 15,706,000 (100.0%) Total basepairs processed: 2,355,900,000 bp Quality-trimmed: 7,618,669 bp (0.3%) Total written (filtered): 1,966,841,132 bp (83.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11318033 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 31.8% C: 13.1% G: 19.5% T: 35.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2758722 3926500.0 0 2758722 2 358574 981625.0 0 358574 3 190965 245406.2 0 190965 4 113114 61351.6 0 113114 5 86888 15337.9 0 86888 6 85123 3834.5 0 85123 7 70336 958.6 0 70336 8 85928 239.7 0 85928 9 87066 59.9 0 86195 871 10 79602 15.0 1 75862 3740 11 88089 3.7 1 81938 6151 12 85321 0.9 1 80325 4996 13 84763 0.2 1 79667 5096 14 88305 0.2 1 82326 5979 15 88981 0.2 1 83685 5296 16 88786 0.2 1 82621 6165 17 106554 0.2 1 98505 8049 18 89122 0.2 1 84209 4913 19 77746 0.2 1 73215 4531 20 92038 0.2 1 86658 5380 21 99609 0.2 1 93006 6603 22 85867 0.2 1 81408 4459 23 100095 0.2 1 93955 6140 24 90779 0.2 1 83874 6905 25 97845 0.2 1 91593 6252 26 88800 0.2 1 83917 4883 27 97906 0.2 1 90971 6935 28 105510 0.2 1 98167 7343 29 95263 0.2 1 88170 7093 30 108904 0.2 1 103370 5534 31 79085 0.2 1 74523 4562 32 103105 0.2 1 96799 6306 33 92937 0.2 1 86945 5992 34 100117 0.2 1 93522 6595 35 106537 0.2 1 100062 6475 36 91203 0.2 1 86381 4822 37 99865 0.2 1 93587 6278 38 105531 0.2 1 98508 7023 39 105906 0.2 1 99469 6437 40 104183 0.2 1 97213 6970 41 116528 0.2 1 106559 9969 42 93606 0.2 1 87149 6457 43 153884 0.2 1 145422 8462 44 48528 0.2 1 44473 4055 45 107110 0.2 1 99279 7831 46 172499 0.2 1 161736 10763 47 116179 0.2 1 109492 6687 48 80709 0.2 1 73983 6726 49 159482 0.2 1 150516 8966 50 64228 0.2 1 59915 4313 51 90888 0.2 1 84987 5901 52 193279 0.2 1 183371 9908 53 141743 0.2 1 135721 6022 54 59956 0.2 1 56077 3879 55 102925 0.2 1 98274 4651 56 66784 0.2 1 62498 4286 57 123279 0.2 1 118108 5171 58 43777 0.2 1 41446 2331 59 39827 0.2 1 36676 3151 60 113430 0.2 1 108052 5378 61 89200 0.2 1 85501 3699 62 44869 0.2 1 41907 2962 63 85974 0.2 1 81524 4450 64 74880 0.2 1 71341 3539 65 59793 0.2 1 56240 3553 66 87755 0.2 1 82874 4881 67 100481 0.2 1 94117 6364 68 167488 0.2 1 159452 8036 69 79463 0.2 1 74811 4652 70 27878 0.2 1 25310 2568 71 23051 0.2 1 21160 1891 72 60528 0.2 1 57268 3260 73 72149 0.2 1 68285 3864 74 73360 0.2 1 69333 4027 75 71612 0.2 1 67692 3920 76 70649 0.2 1 66797 3852 77 70150 0.2 1 66254 3896 78 65804 0.2 1 62003 3801 79 64610 0.2 1 60969 3641 80 63497 0.2 1 60035 3462 81 61317 0.2 1 58042 3275 82 58860 0.2 1 55659 3201 83 57047 0.2 1 53828 3219 84 54423 0.2 1 51371 3052 85 52481 0.2 1 49574 2907 86 50571 0.2 1 47688 2883 87 48288 0.2 1 45567 2721 88 45981 0.2 1 43442 2539 89 43761 0.2 1 41217 2544 90 42661 0.2 1 40245 2416 91 40737 0.2 1 38345 2392 92 38688 0.2 1 36453 2235 93 34947 0.2 1 32894 2053 94 34299 0.2 1 32291 2008 95 31760 0.2 1 29854 1906 96 29525 0.2 1 27743 1782 97 27419 0.2 1 25829 1590 98 24938 0.2 1 23465 1473 99 24209 0.2 1 22665 1544 100 21792 0.2 1 20438 1354 101 20393 0.2 1 19119 1274 102 18597 0.2 1 17433 1164 103 16893 0.2 1 15821 1072 104 15643 0.2 1 14642 1001 105 14032 0.2 1 13104 928 106 12725 0.2 1 11896 829 107 11164 0.2 1 10388 776 108 10327 0.2 1 9611 716 109 9052 0.2 1 8399 653 110 8194 0.2 1 7576 618 111 7205 0.2 1 6690 515 112 6374 0.2 1 5898 476 113 5432 0.2 1 5054 378 114 4742 0.2 1 4349 393 115 4031 0.2 1 3736 295 116 3440 0.2 1 3126 314 117 3047 0.2 1 2793 254 118 2620 0.2 1 2385 235 119 2131 0.2 1 1953 178 120 1732 0.2 1 1592 140 121 1562 0.2 1 1390 172 122 1210 0.2 1 1094 116 123 1050 0.2 1 947 103 124 965 0.2 1 849 116 125 722 0.2 1 635 87 126 663 0.2 1 591 72 127 539 0.2 1 460 79 128 435 0.2 1 362 73 129 406 0.2 1 358 48 130 274 0.2 1 240 34 131 291 0.2 1 261 30 132 213 0.2 1 190 23 133 259 0.2 1 233 26 134 361 0.2 1 342 19 135 151 0.2 1 128 23 136 85 0.2 1 68 17 137 53 0.2 1 45 8 138 43 0.2 1 37 6 139 17 0.2 1 15 2 140 21 0.2 1 18 3 141 17 0.2 1 15 2 142 9 0.2 1 8 1 143 9 0.2 1 7 2 144 15 0.2 1 10 5 145 12 0.2 1 10 2 146 12 0.2 1 10 2 147 49 0.2 1 45 4 148 35 0.2 1 30 5 149 12 0.2 1 11 1 150 163 0.2 1 152 11 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_32psu_4_S4_L001_R1_001.fastq.gz ============================================= 15706000 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 1881 (0.0%)