SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_26psu_2_S14_L002_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_2_S14_L002_R2_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 765.50 s (45 us/read; 1.35 M reads/minute). === Summary === Total reads processed: 17,174,050 Reads with adapters: 13,208,659 (76.9%) Reads written (passing filters): 17,174,050 (100.0%) Total basepairs processed: 2,576,107,500 bp Quality-trimmed: 11,281,504 bp (0.4%) Total written (filtered): 2,040,417,795 bp (79.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 13208659 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.5% C: 12.8% G: 23.5% T: 35.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2393304 4293512.5 0 2393304 2 355208 1073378.1 0 355208 3 207534 268344.5 0 207534 4 112818 67086.1 0 112818 5 98722 16771.5 0 98722 6 88016 4192.9 0 88016 7 70973 1048.2 0 70973 8 100906 262.1 0 100906 9 80596 65.5 0 80310 286 10 85921 16.4 1 80103 5818 11 93456 4.1 1 85698 7758 12 91973 1.0 1 84465 7508 13 105255 0.3 1 96925 8330 14 97607 0.3 1 89028 8579 15 80440 0.3 1 74131 6309 16 114723 0.3 1 105648 9075 17 95977 0.3 1 87931 8046 18 85383 0.3 1 78648 6735 19 112212 0.3 1 103391 8821 20 104516 0.3 1 96596 7920 21 91790 0.3 1 84587 7203 22 103890 0.3 1 96083 7807 23 109193 0.3 1 100822 8371 24 108259 0.3 1 99753 8506 25 121670 0.3 1 113120 8550 26 100521 0.3 1 92626 7895 27 113578 0.3 1 104198 9380 28 101690 0.3 1 94983 6707 29 113641 0.3 1 105222 8419 30 108610 0.3 1 101210 7400 31 120920 0.3 1 112244 8676 32 104000 0.3 1 96851 7149 33 120229 0.3 1 111277 8952 34 153685 0.3 1 142847 10838 35 83436 0.3 1 77543 5893 36 120970 0.3 1 112035 8935 37 127408 0.3 1 118333 9075 38 119755 0.3 1 112084 7671 39 113420 0.3 1 106417 7003 40 129274 0.3 1 120419 8855 41 124811 0.3 1 116558 8253 42 127899 0.3 1 119534 8365 43 115450 0.3 1 107954 7496 44 133939 0.3 1 124786 9153 45 139673 0.3 1 130506 9167 46 102301 0.3 1 95697 6604 47 129785 0.3 1 121923 7862 48 125953 0.3 1 118248 7705 49 131617 0.3 1 122911 8706 50 126447 0.3 1 118299 8148 51 153054 0.3 1 143414 9640 52 111902 0.3 1 104877 7025 53 136845 0.3 1 129094 7751 54 100542 0.3 1 94550 5992 55 131225 0.3 1 123466 7759 56 134910 0.3 1 126386 8524 57 127245 0.3 1 120240 7005 58 123733 0.3 1 116761 6972 59 122876 0.3 1 115856 7020 60 129560 0.3 1 122153 7407 61 129535 0.3 1 122248 7287 62 141327 0.3 1 132778 8549 63 187124 0.3 1 177463 9661 64 148865 0.3 1 142160 6705 65 101493 0.3 1 96017 5476 66 109966 0.3 1 103977 5989 67 109147 0.3 1 102972 6175 68 110252 0.3 1 104088 6164 69 109266 0.3 1 102978 6288 70 115917 0.3 1 109437 6480 71 118081 0.3 1 111469 6612 72 111629 0.3 1 105360 6269 73 116346 0.3 1 109876 6470 74 106757 0.3 1 100604 6153 75 101733 0.3 1 95970 5763 76 99872 0.3 1 94223 5649 77 99194 0.3 1 93520 5674 78 93229 0.3 1 87953 5276 79 90739 0.3 1 85605 5134 80 89347 0.3 1 84416 4931 81 88970 0.3 1 84141 4829 82 84536 0.3 1 79929 4607 83 81530 0.3 1 77128 4402 84 78480 0.3 1 74228 4252 85 77346 0.3 1 73110 4236 86 75912 0.3 1 71909 4003 87 75393 0.3 1 71530 3863 88 73839 0.3 1 69922 3917 89 65607 0.3 1 62233 3374 90 63315 0.3 1 59995 3320 91 59514 0.3 1 56442 3072 92 55456 0.3 1 52465 2991 93 52632 0.3 1 49948 2684 94 51163 0.3 1 48481 2682 95 47871 0.3 1 45320 2551 96 45902 0.3 1 43474 2428 97 43468 0.3 1 41231 2237 98 40225 0.3 1 38177 2048 99 39861 0.3 1 37850 2011 100 35922 0.3 1 34182 1740 101 31906 0.3 1 30324 1582 102 28881 0.3 1 27260 1621 103 26612 0.3 1 25202 1410 104 25092 0.3 1 23747 1345 105 22553 0.3 1 21323 1230 106 20249 0.3 1 19195 1054 107 18698 0.3 1 17704 994 108 16333 0.3 1 15423 910 109 15105 0.3 1 14342 763 110 13538 0.3 1 12818 720 111 12635 0.3 1 11928 707 112 10864 0.3 1 10306 558 113 9370 0.3 1 8881 489 114 8127 0.3 1 7692 435 115 6826 0.3 1 6440 386 116 5914 0.3 1 5590 324 117 5167 0.3 1 4841 326 118 4505 0.3 1 4244 261 119 3657 0.3 1 3441 216 120 3157 0.3 1 2964 193 121 2768 0.3 1 2620 148 122 2319 0.3 1 2199 120 123 2119 0.3 1 1978 141 124 1696 0.3 1 1576 120 125 1359 0.3 1 1259 100 126 1191 0.3 1 1105 86 127 1007 0.3 1 955 52 128 721 0.3 1 673 48 129 632 0.3 1 599 33 130 537 0.3 1 494 43 131 454 0.3 1 423 31 132 387 0.3 1 367 20 133 461 0.3 1 442 19 134 637 0.3 1 611 26 135 279 0.3 1 264 15 136 164 0.3 1 153 11 137 121 0.3 1 110 11 138 99 0.3 1 89 10 139 86 0.3 1 79 7 140 59 0.3 1 52 7 141 49 0.3 1 44 5 142 39 0.3 1 36 3 143 48 0.3 1 45 3 144 41 0.3 1 36 5 145 47 0.3 1 41 6 146 121 0.3 1 118 3 147 643 0.3 1 616 27 148 431 0.3 1 416 15 149 244 0.3 1 225 19 150 2704 0.3 1 2570 134 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_26psu_2_S14_L002_R2_001.fastq.gz ============================================= 17174050 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 22162 (0.1%)