SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/data/geoduck_illumina/trimmed/NR006_S3_L001_R1_001_val_1.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/NR006_S3_L001_R1_001_val_1.fq.gz Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 89.69 s (26 us/read; 2.28 M reads/minute). === Summary === Total reads processed: 3,414,678 Reads with adapters: 2,142,823 (62.8%) Reads written (passing filters): 3,414,678 (100.0%) Total basepairs processed: 513,251,944 bp Quality-trimmed: 91,200 bp (0.0%) Total written (filtered): 475,253,670 bp (92.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2142823 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.9% C: 25.9% G: 18.7% T: 20.0% none/other: 4.5% Overview of removed sequences length count expect max.err error counts 1 937450 853669.5 0 937450 2 176594 213417.4 0 176594 3 79181 53354.3 0 79181 4 61172 13338.6 0 61172 5 575 3334.6 0 575 6 23757 833.7 0 23757 7 20513 208.4 0 20513 8 24548 52.1 0 24548 9 21333 13.0 0 21171 162 10 22763 3.3 1 20813 1950 11 24508 0.8 1 21879 2629 12 45457 0.2 1 41600 3857 13 1018 0.1 1 561 457 14 44363 0.1 1 40404 3959 15 823 0.1 1 411 412 16 45163 0.1 1 40778 4385 17 1267 0.1 1 786 481 18 28010 0.1 1 25271 2739 19 69106 0.1 1 63733 5373 20 477 0.1 1 296 181 21 152 0.1 1 112 40 22 379 0.1 1 225 154 23 20800 0.1 1 18900 1900 24 50883 0.1 1 46328 4555 25 1164 0.1 1 785 379 26 17657 0.1 1 16052 1605 27 16136 0.1 1 14812 1324 28 390 0.1 1 248 142 29 16537 0.1 1 14907 1630 30 18828 0.1 1 17036 1792 31 25091 0.1 1 23130 1961 32 818 0.1 1 543 275 33 26222 0.1 1 23915 2307 34 1845 0.1 1 1442 403 35 22648 0.1 1 20769 1879 36 11708 0.1 1 10747 961 37 296 0.1 1 188 108 38 10935 0.1 1 9946 989 39 11259 0.1 1 10184 1075 40 9228 0.1 1 8389 839 41 11460 0.1 1 10202 1258 42 22714 0.1 1 20755 1959 43 4407 0.1 1 3986 421 44 4019 0.1 1 3591 428 45 179 0.1 1 119 60 46 7619 0.1 1 6925 694 47 6412 0.1 1 5845 567 48 6077 0.1 1 5463 614 49 6620 0.1 1 5890 730 50 10543 0.1 1 9613 930 51 4405 0.1 1 4030 375 52 259 0.1 1 177 82 53 7095 0.1 1 6434 661 54 10793 0.1 1 9775 1018 55 462 0.1 1 388 74 56 1856 0.1 1 1649 207 57 8200 0.1 1 7510 690 58 148 0.1 1 102 46 59 300 0.1 1 224 76 60 5469 0.1 1 5029 440 61 83 0.1 1 52 31 62 89 0.1 1 64 25 63 1331 0.1 1 1206 125 64 2777 0.1 1 2523 254 65 2619 0.1 1 2410 209 66 2941 0.1 1 2671 270 67 1194 0.1 1 1080 114 68 866 0.1 1 770 96 69 572 0.1 1 506 66 70 746 0.1 1 685 61 71 1065 0.1 1 979 86 72 1080 0.1 1 978 102 73 979 0.1 1 881 98 74 963 0.1 1 897 66 75 847 0.1 1 771 76 76 894 0.1 1 815 79 77 809 0.1 1 743 66 78 755 0.1 1 681 74 79 707 0.1 1 625 82 80 697 0.1 1 620 77 81 662 0.1 1 588 74 82 553 0.1 1 498 55 83 540 0.1 1 479 61 84 554 0.1 1 510 44 85 470 0.1 1 420 50 86 455 0.1 1 416 39 87 372 0.1 1 340 32 88 399 0.1 1 361 38 89 381 0.1 1 348 33 90 360 0.1 1 322 38 91 305 0.1 1 264 41 92 313 0.1 1 259 54 93 292 0.1 1 253 39 94 244 0.1 1 205 39 95 396 0.1 1 371 25 96 233 0.1 1 193 40 97 290 0.1 1 202 88 98 513 0.1 1 412 101 99 343 0.1 1 246 97 100 379 0.1 1 196 183 101 272 0.1 1 215 57 102 338 0.1 1 165 173 103 161 0.1 1 127 34 104 159 0.1 1 140 19 105 131 0.1 1 115 16 106 119 0.1 1 103 16 107 314 0.1 1 286 28 108 113 0.1 1 98 15 109 105 0.1 1 97 8 110 107 0.1 1 97 10 111 108 0.1 1 93 15 112 99 0.1 1 88 11 113 102 0.1 1 93 9 114 77 0.1 1 69 8 115 124 0.1 1 115 9 116 109 0.1 1 97 12 117 108 0.1 1 101 7 118 94 0.1 1 87 7 119 107 0.1 1 89 18 120 94 0.1 1 84 10 121 90 0.1 1 82 8 122 99 0.1 1 89 10 123 96 0.1 1 91 5 124 91 0.1 1 79 12 125 119 0.1 1 112 7 126 106 0.1 1 99 7 127 117 0.1 1 111 6 128 121 0.1 1 115 6 129 78 0.1 1 74 4 130 142 0.1 1 128 14 131 124 0.1 1 116 8 132 102 0.1 1 98 4 133 87 0.1 1 83 4 134 132 0.1 1 123 9 135 103 0.1 1 100 3 136 107 0.1 1 100 7 137 103 0.1 1 94 9 138 87 0.1 1 83 4 139 92 0.1 1 86 6 140 51 0.1 1 46 5 141 59 0.1 1 57 2 142 81 0.1 1 74 7 143 33 0.1 1 29 4 144 36 0.1 1 24 12 145 15 0.1 1 12 3 146 24 0.1 1 21 3 147 31 0.1 1 23 8 148 78 0.1 1 51 27 149 54 0.1 1 18 36 150 414 0.1 1 14 400 151 96951 0.1 1 29 96922 RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR006_S3_L001_R1_001_val_1.fq.gz ============================================= 3414678 sequences processed in total