SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/CTRL_16C_26psu_2_S21_L002_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/CTRL_16C_26psu_2_S21_L002_R1_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 505.76 s (38 us/read; 1.59 M reads/minute). === Summary === Total reads processed: 13,408,232 Reads with adapters: 11,662,676 (87.0%) Reads written (passing filters): 13,408,232 (100.0%) Total basepairs processed: 2,011,234,800 bp Quality-trimmed: 4,075,788 bp (0.2%) Total written (filtered): 1,423,488,059 bp (70.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11662676 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.8% C: 12.5% G: 23.6% T: 35.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 950454 3352058.0 0 950454 2 175107 838014.5 0 175107 3 106043 209503.6 0 106043 4 68134 52375.9 0 68134 5 61886 13094.0 0 61886 6 61175 3273.5 0 61175 7 51159 818.4 0 51159 8 64511 204.6 0 64511 9 64557 51.1 0 63785 772 10 60792 12.8 1 57082 3710 11 68970 3.2 1 63184 5786 12 66553 0.8 1 61883 4670 13 68274 0.2 1 63204 5070 14 71364 0.2 1 65643 5721 15 74174 0.2 1 68692 5482 16 73515 0.2 1 67346 6169 17 90659 0.2 1 82653 8006 18 76471 0.2 1 71237 5234 19 67430 0.2 1 62447 4983 20 80487 0.2 1 74742 5745 21 89676 0.2 1 82775 6901 22 76355 0.2 1 71205 5150 23 90468 0.2 1 83777 6691 24 85067 0.2 1 77644 7423 25 91076 0.2 1 84134 6942 26 84890 0.2 1 79317 5573 27 95709 0.2 1 88308 7401 28 95026 0.2 1 88099 6927 29 98118 0.2 1 89948 8170 30 107848 0.2 1 101119 6729 31 84062 0.2 1 78313 5749 32 103994 0.2 1 96660 7334 33 98133 0.2 1 90574 7559 34 120505 0.2 1 111057 9448 35 94055 0.2 1 87482 6573 36 107881 0.2 1 100206 7675 37 113227 0.2 1 104836 8391 38 107162 0.2 1 98615 8547 39 126650 0.2 1 117366 9284 40 101784 0.2 1 94417 7367 41 130084 0.2 1 120107 9977 42 108652 0.2 1 99173 9479 43 179621 0.2 1 169283 10338 44 59500 0.2 1 54067 5433 45 124819 0.2 1 116443 8376 46 119134 0.2 1 110810 8324 47 129268 0.2 1 120606 8662 48 119694 0.2 1 111395 8299 49 138243 0.2 1 127784 10459 50 121057 0.2 1 113597 7460 51 131350 0.2 1 122521 8829 52 138351 0.2 1 127802 10549 53 154024 0.2 1 144429 9595 54 116951 0.2 1 108870 8081 55 139783 0.2 1 130545 9238 56 165267 0.2 1 155186 10081 57 126758 0.2 1 117494 9264 58 142781 0.2 1 134977 7804 59 117589 0.2 1 109427 8162 60 144831 0.2 1 135423 9408 61 138318 0.2 1 129552 8766 62 148945 0.2 1 139636 9309 63 129691 0.2 1 120718 8973 64 134879 0.2 1 126688 8191 65 146410 0.2 1 137112 9298 66 156960 0.2 1 146744 10216 67 171283 0.2 1 158133 13150 68 312723 0.2 1 296738 15985 69 76525 0.2 1 70767 5758 70 28798 0.2 1 24712 4086 71 79564 0.2 1 74491 5073 72 122325 0.2 1 115172 7153 73 132393 0.2 1 124378 8015 74 131213 0.2 1 123087 8126 75 128592 0.2 1 120236 8356 76 128119 0.2 1 119430 8689 77 126752 0.2 1 118441 8311 78 121397 0.2 1 113322 8075 79 118367 0.2 1 110488 7879 80 116333 0.2 1 108557 7776 81 115083 0.2 1 107691 7392 82 111285 0.2 1 103893 7392 83 107858 0.2 1 100817 7041 84 105350 0.2 1 98390 6960 85 102602 0.2 1 95870 6732 86 97359 0.2 1 90922 6437 87 94015 0.2 1 87784 6231 88 92275 0.2 1 86366 5909 89 87740 0.2 1 82108 5632 90 86642 0.2 1 80943 5699 91 81958 0.2 1 76615 5343 92 78763 0.2 1 73589 5174 93 72932 0.2 1 68198 4734 94 70403 0.2 1 65851 4552 95 65162 0.2 1 60795 4367 96 61147 0.2 1 56990 4157 97 57845 0.2 1 54051 3794 98 54088 0.2 1 50353 3735 99 50912 0.2 1 47388 3524 100 46451 0.2 1 43306 3145 101 43581 0.2 1 40541 3040 102 39156 0.2 1 36546 2610 103 35574 0.2 1 33122 2452 104 32789 0.2 1 30678 2111 105 29034 0.2 1 27055 1979 106 26298 0.2 1 24343 1955 107 23552 0.2 1 21942 1610 108 21227 0.2 1 19666 1561 109 18723 0.2 1 17348 1375 110 16933 0.2 1 15728 1205 111 14813 0.2 1 13715 1098 112 12788 0.2 1 11763 1025 113 11310 0.2 1 10437 873 114 9920 0.2 1 9142 778 115 8131 0.2 1 7451 680 116 6933 0.2 1 6415 518 117 5884 0.2 1 5388 496 118 5136 0.2 1 4702 434 119 4097 0.2 1 3751 346 120 3546 0.2 1 3238 308 121 2947 0.2 1 2707 240 122 2422 0.2 1 2210 212 123 1924 0.2 1 1761 163 124 1733 0.2 1 1576 157 125 1418 0.2 1 1276 142 126 1305 0.2 1 1178 127 127 1104 0.2 1 1004 100 128 823 0.2 1 732 91 129 659 0.2 1 593 66 130 710 0.2 1 634 76 131 875 0.2 1 812 63 132 926 0.2 1 862 64 133 1378 0.2 1 1297 81 134 1693 0.2 1 1594 99 135 721 0.2 1 691 30 136 229 0.2 1 205 24 137 172 0.2 1 157 15 138 80 0.2 1 66 14 139 66 0.2 1 55 11 140 62 0.2 1 53 9 141 37 0.2 1 35 2 142 33 0.2 1 27 6 143 21 0.2 1 19 2 144 18 0.2 1 17 1 145 32 0.2 1 28 4 146 69 0.2 1 67 2 147 283 0.2 1 250 33 148 183 0.2 1 166 17 149 88 0.2 1 79 9 150 625 0.2 1 537 88 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/CTRL_16C_26psu_2_S21_L002_R1_001.fastq.gz ============================================= 13408232 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 7650 (0.1%)