SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/data/geoduck_illumina/trimmed/NR013_AD013_S2_L001_R2_001_val_2.fq.gz Trimming mode: paired-end Trim Galore version: 0.4.4 Cutadapt version: 1.9.1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp Output file will be GZIP compressed This is cutadapt 1.9.1 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /home/sam/data/geoduck_illumina/trimmed/NR013_AD013_S2_L001_R2_001_val_2.fq.gz Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 7839.82 s (25 us/read; 2.37 M reads/minute). === Summary === Total reads processed: 309,877,704 Reads with adapters: 125,884,928 (40.6%) Reads written (passing filters): 309,877,704 (100.0%) Total basepairs processed: 39,922,240,804 bp Quality-trimmed: 30,422,029 bp (0.1%) Total written (filtered): 39,426,232,820 bp (98.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 125884928 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 32.1% C: 23.1% G: 15.3% T: 29.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 88845909 77469426.0 0 88845909 2 22125586 19367356.5 0 22125586 3 6391789 4841839.1 0 6391789 4 2247257 1210459.8 0 2247257 5 199820 302614.9 0 199820 6 110118 75653.7 0 110118 7 87861 18913.4 0 87861 8 95299 4728.4 0 95299 9 63978 1182.1 0 59832 4146 10 105395 295.5 1 75720 29675 11 89578 73.9 1 66659 22919 12 173465 18.5 1 138196 35269 13 2389 4.6 1 887 1502 14 113395 4.6 1 87505 25890 15 135634 4.6 1 111210 24424 16 1253 4.6 1 397 856 17 104209 4.6 1 83034 21175 18 56976 4.6 1 45269 11707 19 114574 4.6 1 90053 24521 20 75891 4.6 1 60021 15870 21 61297 4.6 1 49070 12227 22 78310 4.6 1 62289 16021 23 85866 4.6 1 66959 18907 24 167954 4.6 1 130753 37201 25 73002 4.6 1 58910 14092 26 70090 4.6 1 56535 13555 27 47016 4.6 1 35691 11325 28 117783 4.6 1 97694 20089 29 33129 4.6 1 23153 9976 30 112586 4.6 1 92542 20044 31 48002 4.6 1 35771 12231 32 193298 4.6 1 165534 27764 33 87671 4.6 1 68658 19013 34 32056 4.6 1 22676 9380 35 109513 4.6 1 91086 18427 36 39661 4.6 1 30104 9557 37 57789 4.6 1 44412 13377 38 30027 4.6 1 23398 6629 39 42527 4.6 1 32645 9882 40 18198 4.6 1 13575 4623 41 61586 4.6 1 49843 11743 42 83440 4.6 1 68575 14865 43 42319 4.6 1 32603 9716 44 66878 4.6 1 52939 13939 45 115546 4.6 1 95285 20261 46 62010 4.6 1 47751 14259 47 39415 4.6 1 31070 8345 48 114841 4.6 1 94405 20436 49 50075 4.6 1 39582 10493 50 22207 4.6 1 15934 6273 51 93791 4.6 1 76265 17526 52 129976 4.6 1 111177 18799 53 52101 4.6 1 42431 9670 54 70208 4.6 1 57057 13151 55 41534 4.6 1 33481 8053 56 22914 4.6 1 17128 5786 57 38141 4.6 1 29953 8188 58 44206 4.6 1 34293 9913 59 25694 4.6 1 18853 6841 60 18689 4.6 1 13090 5599 61 16750 4.6 1 11632 5118 62 17922 4.6 1 12604 5318 63 19917 4.6 1 14689 5228 64 30669 4.6 1 23972 6697 65 39466 4.6 1 31318 8148 66 43956 4.6 1 34720 9236 67 45097 4.6 1 35359 9738 68 45768 4.6 1 35779 9989 69 45954 4.6 1 35668 10286 70 46047 4.6 1 35770 10277 71 45745 4.6 1 35257 10488 72 45607 4.6 1 35117 10490 73 45024 4.6 1 34813 10211 74 44498 4.6 1 34307 10191 75 44017 4.6 1 34003 10014 76 43540 4.6 1 33431 10109 77 43090 4.6 1 33125 9965 78 42637 4.6 1 32752 9885 79 41853 4.6 1 32164 9689 80 41286 4.6 1 31721 9565 81 40929 4.6 1 31441 9488 82 40505 4.6 1 31156 9349 83 39595 4.6 1 30373 9222 84 39003 4.6 1 29871 9132 85 38856 4.6 1 29840 9016 86 38308 4.6 1 29168 9140 87 37828 4.6 1 28974 8854 88 37411 4.6 1 28579 8832 89 36119 4.6 1 27688 8431 90 35621 4.6 1 27246 8375 91 35130 4.6 1 26933 8197 92 34667 4.6 1 26480 8187 93 33625 4.6 1 25771 7854 94 33191 4.6 1 25409 7782 95 32138 4.6 1 24554 7584 96 32105 4.6 1 24550 7555 97 31392 4.6 1 24148 7244 98 30486 4.6 1 23462 7024 99 29633 4.6 1 22786 6847 100 28698 4.6 1 22036 6662 101 28001 4.6 1 21491 6510 102 27082 4.6 1 20760 6322 103 26784 4.6 1 20505 6279 104 25275 4.6 1 19359 5916 105 24641 4.6 1 18707 5934 106 23433 4.6 1 17836 5597 107 22242 4.6 1 16750 5492 108 21167 4.6 1 15837 5330 109 20140 4.6 1 15032 5108 110 19354 4.6 1 14351 5003 111 18430 4.6 1 13727 4703 112 17600 4.6 1 13157 4443 113 16947 4.6 1 12800 4147 114 16325 4.6 1 12306 4019 115 15895 4.6 1 11983 3912 116 15307 4.6 1 11534 3773 117 14514 4.6 1 10941 3573 118 13913 4.6 1 10507 3406 119 13245 4.6 1 10078 3167 120 12231 4.6 1 9245 2986 121 11796 4.6 1 8977 2819 122 10638 4.6 1 8118 2520 123 10402 4.6 1 7982 2420 124 9446 4.6 1 7197 2249 125 9015 4.6 1 6866 2149 126 8486 4.6 1 6462 2024 127 7804 4.6 1 6024 1780 128 6749 4.6 1 5384 1365 129 6747 4.6 1 5588 1159 130 5261 4.6 1 4337 924 131 5109 4.6 1 4384 725 132 3835 4.6 1 3252 583 133 3353 4.6 1 2896 457 134 2940 4.6 1 2598 342 135 2590 4.6 1 2262 328 136 2123 4.6 1 1857 266 137 1846 4.6 1 1629 217 138 1530 4.6 1 1332 198 139 1244 4.6 1 1106 138 140 1074 4.6 1 916 158 141 858 4.6 1 679 179 142 851 4.6 1 632 219 143 728 4.6 1 535 193 144 621 4.6 1 433 188 145 543 4.6 1 369 174 146 592 4.6 1 362 230 147 522 4.6 1 326 196 148 596 4.6 1 302 294 149 511 4.6 1 299 212 150 928 4.6 1 667 261 151 37859 4.6 1 36758 1101 RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR013_AD013_S2_L001_R2_001_val_2.fq.gz ============================================= 309877704 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 309877704 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 827042 (0.27%)