SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/data/geoduck_illumina/trimmed/AD002_S9_L002_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/AD002_S9_L002_R1_001_val_1.fq.gz Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 5175.37 s (24 us/read; 2.46 M reads/minute). === Summary === Total reads processed: 212,571,014 Reads with adapters: 82,462,079 (38.8%) Reads written (passing filters): 212,571,014 (100.0%) Total basepairs processed: 26,380,336,744 bp Quality-trimmed: 11,282,411 bp (0.0%) Total written (filtered): 26,072,320,126 bp (98.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 82462079 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 32.8% C: 22.7% G: 14.3% T: 30.1% none/other: 0.2% Overview of removed sequences length count expect max.err error counts 1 59039996 53142753.5 0 59039996 2 14966438 13285688.4 0 14966438 3 3831679 3321422.1 0 3831679 4 1480847 830355.5 0 1480847 5 163128 207588.9 0 163128 6 38541 51897.2 0 38541 7 22951 12974.3 0 22951 8 27327 3243.6 0 27327 9 22259 810.9 0 19747 2512 10 31473 202.7 1 19843 11630 11 30840 50.7 1 21362 9478 12 50070 12.7 1 39221 10849 13 2844 3.2 1 1464 1380 14 47563 3.2 1 37749 9814 15 2742 3.2 1 1398 1344 16 55622 3.2 1 42339 13283 17 4406 3.2 1 2343 2063 18 38657 3.2 1 30067 8590 19 76638 3.2 1 63646 12992 20 785 3.2 1 335 450 21 1199 3.2 1 405 794 22 2135 3.2 1 907 1228 23 33554 3.2 1 25117 8437 24 69371 3.2 1 55342 14029 25 3521 3.2 1 1864 1657 26 30185 3.2 1 22674 7511 27 23530 3.2 1 19348 4182 28 1332 3.2 1 573 759 29 30080 3.2 1 22282 7798 30 36733 3.2 1 28722 8011 31 43072 3.2 1 34257 8815 32 5026 3.2 1 2892 2134 33 54705 3.2 1 41452 13253 34 25607 3.2 1 20697 4910 35 1315 3.2 1 598 717 36 29363 3.2 1 22625 6738 37 37853 3.2 1 28899 8954 38 22367 3.2 1 16611 5756 39 31698 3.2 1 24957 6741 40 28603 3.2 1 22260 6343 41 36993 3.2 1 27714 9279 42 67000 3.2 1 53293 13707 43 12117 3.2 1 10136 1981 44 17331 3.2 1 12768 4563 45 1153 3.2 1 533 620 46 32065 3.2 1 25213 6852 47 25756 3.2 1 20118 5638 48 28466 3.2 1 21563 6903 49 37422 3.2 1 27270 10152 50 55745 3.2 1 44380 11365 51 21907 3.2 1 17848 4059 52 3678 3.2 1 2299 1379 53 50349 3.2 1 40043 10306 54 73367 3.2 1 59796 13571 55 6120 3.2 1 4526 1594 56 18476 3.2 1 14265 4211 57 66431 3.2 1 54830 11601 58 2492 3.2 1 1488 1004 59 7423 3.2 1 4507 2916 60 51321 3.2 1 43286 8035 61 1057 3.2 1 524 533 62 2916 3.2 1 1514 1402 63 16873 3.2 1 12893 3980 64 34310 3.2 1 28027 6283 65 36670 3.2 1 29768 6902 66 38998 3.2 1 32040 6958 67 27680 3.2 1 21977 5703 68 30139 3.2 1 23969 6170 69 9433 3.2 1 6500 2933 70 10154 3.2 1 7699 2455 71 16385 3.2 1 13467 2918 72 19640 3.2 1 16226 3414 73 21512 3.2 1 17701 3811 74 22493 3.2 1 18430 4063 75 22985 3.2 1 18770 4215 76 23564 3.2 1 19042 4522 77 23835 3.2 1 19293 4542 78 23686 3.2 1 19111 4575 79 23946 3.2 1 19361 4585 80 23986 3.2 1 19298 4688 81 23804 3.2 1 19288 4516 82 23811 3.2 1 19206 4605 83 23556 3.2 1 18944 4612 84 23072 3.2 1 18538 4534 85 23578 3.2 1 18987 4591 86 23342 3.2 1 18729 4613 87 23024 3.2 1 18465 4559 88 22665 3.2 1 18278 4387 89 22267 3.2 1 17848 4419 90 22426 3.2 1 18024 4402 91 22119 3.2 1 17670 4449 92 21903 3.2 1 17527 4376 93 21581 3.2 1 17328 4253 94 20982 3.2 1 16814 4168 95 20719 3.2 1 16547 4172 96 20401 3.2 1 16240 4161 97 20127 3.2 1 16014 4113 98 19866 3.2 1 15899 3967 99 19812 3.2 1 15778 4034 100 19194 3.2 1 15304 3890 101 18736 3.2 1 14893 3843 102 18130 3.2 1 14414 3716 103 17646 3.2 1 14103 3543 104 17379 3.2 1 13812 3567 105 16898 3.2 1 13401 3497 106 16141 3.2 1 12757 3384 107 15731 3.2 1 12435 3296 108 15140 3.2 1 11901 3239 109 14543 3.2 1 11434 3109 110 14054 3.2 1 10931 3123 111 13746 3.2 1 10800 2946 112 13320 3.2 1 10353 2967 113 12601 3.2 1 9841 2760 114 12035 3.2 1 9427 2608 115 11563 3.2 1 9102 2461 116 11244 3.2 1 8830 2414 117 10939 3.2 1 8547 2392 118 10488 3.2 1 8214 2274 119 9944 3.2 1 7746 2198 120 9315 3.2 1 7136 2179 121 9004 3.2 1 7044 1960 122 8319 3.2 1 6468 1851 123 7911 3.2 1 6134 1777 124 7343 3.2 1 5701 1642 125 6984 3.2 1 5463 1521 126 6625 3.2 1 5163 1462 127 6127 3.2 1 4776 1351 128 5503 3.2 1 4353 1150 129 5386 3.2 1 4334 1052 130 4455 3.2 1 3636 819 131 4178 3.2 1 3487 691 132 3362 3.2 1 2811 551 133 3044 3.2 1 2598 446 134 2477 3.2 1 2143 334 135 2320 3.2 1 2028 292 136 1849 3.2 1 1616 233 137 1640 3.2 1 1429 211 138 1271 3.2 1 1112 159 139 1045 3.2 1 941 104 140 761 3.2 1 666 95 141 600 3.2 1 528 72 142 478 3.2 1 401 77 143 396 3.2 1 338 58 144 395 3.2 1 338 57 145 377 3.2 1 304 73 146 314 3.2 1 248 66 147 287 3.2 1 225 62 148 291 3.2 1 201 90 149 349 3.2 1 241 108 150 1019 3.2 1 426 593 151 158198 3.2 1 58633 99565 RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/AD002_S9_L002_R1_001_val_1.fq.gz ============================================= 212571014 sequences processed in total