SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/data/geoduck_illumina/trimmed/NR013_AD013_S2_L002_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_L002_R2_001_val_2.fq.gz Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 9482.79 s (25 us/read; 2.40 M reads/minute). === Summary === Total reads processed: 379,535,476 Reads with adapters: 158,202,642 (41.7%) Reads written (passing filters): 379,535,476 (100.0%) Total basepairs processed: 49,672,679,182 bp Quality-trimmed: 30,573,885 bp (0.1%) Total written (filtered): 48,791,766,215 bp (98.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 158202642 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 32.0% C: 22.9% G: 15.3% T: 29.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 109580322 94883869.0 0 109580322 2 26576548 23720967.2 0 26576548 3 7597769 5930241.8 0 7597769 4 2680993 1482560.5 0 2680993 5 226898 370640.1 0 226898 6 150660 92660.0 0 150660 7 122142 23165.0 0 122142 8 131733 5791.3 0 131733 9 90844 1447.8 0 86022 4822 10 150905 362.0 1 107502 43403 11 135349 90.5 1 97607 37742 12 252946 22.6 1 199121 53825 13 3530 5.7 1 1331 2199 14 168638 5.7 1 128925 39713 15 195609 5.7 1 158466 37143 16 1950 5.7 1 608 1342 17 154612 5.7 1 121576 33036 18 83683 5.7 1 65735 17948 19 170549 5.7 1 131905 38644 20 113819 5.7 1 88764 25055 21 99079 5.7 1 77374 21705 22 121474 5.7 1 94946 26528 23 131152 5.7 1 101603 29549 24 248335 5.7 1 190265 58070 25 123183 5.7 1 98568 24615 26 116509 5.7 1 93505 23004 27 85593 5.7 1 63827 21766 28 187504 5.7 1 154503 33001 29 63599 5.7 1 44467 19132 30 187277 5.7 1 152585 34692 31 82799 5.7 1 60937 21862 32 355185 5.7 1 306261 48924 33 158641 5.7 1 124646 33995 34 64822 5.7 1 45842 18980 35 195418 5.7 1 164137 31281 36 58936 5.7 1 42343 16593 37 108180 5.7 1 83522 24658 38 35568 5.7 1 25724 9844 39 64341 5.7 1 47554 16787 40 20127 5.7 1 13603 6524 41 106196 5.7 1 85625 20571 42 153301 5.7 1 126849 26452 43 68625 5.7 1 52544 16081 44 121927 5.7 1 96858 25069 45 262336 5.7 1 224010 38326 46 116328 5.7 1 90525 25803 47 58043 5.7 1 44637 13406 48 248028 5.7 1 209929 38099 49 75167 5.7 1 58530 16637 50 31491 5.7 1 21928 9563 51 198900 5.7 1 165930 32970 52 287281 5.7 1 253422 33859 53 78856 5.7 1 63865 14991 54 119169 5.7 1 97179 21990 55 55266 5.7 1 43255 12011 56 35422 5.7 1 25390 10032 57 60972 5.7 1 46938 14034 58 72809 5.7 1 56312 16497 59 38555 5.7 1 27522 11033 60 31487 5.7 1 21444 10043 61 31013 5.7 1 21204 9809 62 31200 5.7 1 21560 9640 63 34441 5.7 1 24740 9701 64 55775 5.7 1 44093 11682 65 78736 5.7 1 63960 14776 66 90620 5.7 1 73458 17162 67 95517 5.7 1 76780 18737 68 97188 5.7 1 77764 19424 69 99204 5.7 1 79345 19859 70 99963 5.7 1 79546 20417 71 100406 5.7 1 79933 20473 72 99798 5.7 1 79578 20220 73 99683 5.7 1 79316 20367 74 99331 5.7 1 78979 20352 75 98621 5.7 1 78425 20196 76 97932 5.7 1 77457 20475 77 97135 5.7 1 77151 19984 78 97028 5.7 1 77056 19972 79 96260 5.7 1 76466 19794 80 94810 5.7 1 75454 19356 81 94602 5.7 1 75244 19358 82 94004 5.7 1 74771 19233 83 92945 5.7 1 73823 19122 84 92419 5.7 1 73182 19237 85 91632 5.7 1 72790 18842 86 91035 5.7 1 72317 18718 87 90050 5.7 1 71548 18502 88 89894 5.7 1 71506 18388 89 87725 5.7 1 69845 17880 90 87185 5.7 1 69399 17786 91 84618 5.7 1 66960 17658 92 84186 5.7 1 66945 17241 93 82900 5.7 1 65834 17066 94 81370 5.7 1 64473 16897 95 80429 5.7 1 63919 16510 96 79457 5.7 1 63127 16330 97 78199 5.7 1 62179 16020 98 77342 5.7 1 61569 15773 99 75264 5.7 1 59801 15463 100 74042 5.7 1 58980 15062 101 72181 5.7 1 57310 14871 102 70827 5.7 1 56161 14666 103 69379 5.7 1 55477 13902 104 66924 5.7 1 53369 13555 105 64860 5.7 1 51608 13252 106 63171 5.7 1 50167 13004 107 60966 5.7 1 48666 12300 108 59572 5.7 1 47230 12342 109 57458 5.7 1 45484 11974 110 54410 5.7 1 43114 11296 111 53126 5.7 1 41972 11154 112 51049 5.7 1 40361 10688 113 49939 5.7 1 39585 10354 114 48143 5.7 1 38288 9855 115 46204 5.7 1 36627 9577 116 44751 5.7 1 35508 9243 117 42469 5.7 1 33654 8815 118 41251 5.7 1 32738 8513 119 39131 5.7 1 31188 7943 120 37000 5.7 1 29225 7775 121 34921 5.7 1 27767 7154 122 32786 5.7 1 26075 6711 123 30986 5.7 1 24656 6330 124 29117 5.7 1 23102 6015 125 27519 5.7 1 21859 5660 126 25495 5.7 1 20373 5122 127 23925 5.7 1 19306 4619 128 20431 5.7 1 16762 3669 129 19497 5.7 1 16497 3000 130 15325 5.7 1 13045 2280 131 13886 5.7 1 12078 1808 132 10761 5.7 1 9519 1242 133 9402 5.7 1 8413 989 134 7873 5.7 1 7096 777 135 6890 5.7 1 6211 679 136 5416 5.7 1 4918 498 137 4724 5.7 1 4317 407 138 3681 5.7 1 3347 334 139 2838 5.7 1 2579 259 140 2088 5.7 1 1837 251 141 1592 5.7 1 1358 234 142 1256 5.7 1 990 266 143 1102 5.7 1 852 250 144 825 5.7 1 603 222 145 848 5.7 1 562 286 146 752 5.7 1 465 287 147 697 5.7 1 449 248 148 750 5.7 1 456 294 149 606 5.7 1 356 250 150 664 5.7 1 440 224 151 51839 5.7 1 50778 1061 RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR013_AD013_S2_L002_R2_001_val_2.fq.gz ============================================= 379535476 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 379535476 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 942696 (0.25%)