SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/data/geoduck_illumina/trimmed/NR013_AD013_S2_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/NR013_AD013_S2_L002_R1_001_val_1.fq.gz Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 9397.15 s (25 us/read; 2.42 M reads/minute). === Summary === Total reads processed: 379,535,476 Reads with adapters: 157,413,392 (41.5%) Reads written (passing filters): 379,535,476 (100.0%) Total basepairs processed: 48,465,312,024 bp Quality-trimmed: 27,720,181 bp (0.1%) Total written (filtered): 47,689,069,992 bp (98.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 157413392 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 32.2% C: 23.6% G: 14.5% T: 29.6% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 110667740 94883869.0 0 110667740 2 26663149 23720967.2 0 26663149 3 7393392 5930241.8 0 7393392 4 2653451 1482560.5 0 2653451 5 254168 370640.1 0 254168 6 128511 92660.0 0 128511 7 88935 23165.0 0 88935 8 105904 5791.3 0 105904 9 92612 1447.8 0 88170 4442 10 114990 362.0 1 85274 29716 11 123270 90.5 1 91224 32046 12 208554 22.6 1 169873 38681 13 11285 5.7 1 6138 5147 14 194395 5.7 1 161652 32743 15 8680 5.7 1 4299 4381 16 223910 5.7 1 178592 45318 17 15102 5.7 1 8422 6680 18 154776 5.7 1 123797 30979 19 313056 5.7 1 268766 44290 20 3143 5.7 1 1583 1560 21 3876 5.7 1 1369 2507 22 8827 5.7 1 3921 4906 23 127107 5.7 1 99437 27670 24 274885 5.7 1 228223 46662 25 12392 5.7 1 6883 5509 26 115765 5.7 1 90881 24884 27 92682 5.7 1 78305 14377 28 4103 5.7 1 1994 2109 29 103986 5.7 1 82555 21431 30 131306 5.7 1 107052 24254 31 162960 5.7 1 133400 29560 32 14793 5.7 1 8688 6105 33 194807 5.7 1 157828 36979 34 4998 5.7 1 2683 2315 35 105963 5.7 1 82175 23788 36 137630 5.7 1 110316 27314 37 159200 5.7 1 129691 29509 38 6660 5.7 1 3982 2678 39 127764 5.7 1 98518 29246 40 199028 5.7 1 153865 45163 41 9971 5.7 1 5999 3972 42 136600 5.7 1 101299 35301 43 178520 5.7 1 129574 48946 44 262367 5.7 1 204880 57487 45 52027 5.7 1 41943 10084 46 73660 5.7 1 52825 20835 47 8441 5.7 1 5143 3298 48 174363 5.7 1 139828 34535 49 108253 5.7 1 83992 24261 50 108727 5.7 1 83186 25541 51 161423 5.7 1 124375 37048 52 175183 5.7 1 140943 34240 53 74326 5.7 1 61229 13097 54 16107 5.7 1 11671 4436 55 194176 5.7 1 167170 27006 56 185187 5.7 1 155240 29947 57 17080 5.7 1 13135 3945 58 31574 5.7 1 22573 9001 59 182957 5.7 1 156639 26318 60 10462 5.7 1 6373 4089 61 24520 5.7 1 15594 8926 62 128782 5.7 1 109288 19494 63 5151 5.7 1 2694 2457 64 13518 5.7 1 8092 5426 65 51853 5.7 1 40861 10992 66 103903 5.7 1 87611 16292 67 66440 5.7 1 53152 13288 68 88880 5.7 1 72897 15983 69 82619 5.7 1 66722 15897 70 96138 5.7 1 77885 18253 71 25150 5.7 1 16131 9019 72 27241 5.7 1 19801 7440 73 45344 5.7 1 36516 8828 74 57484 5.7 1 47405 10079 75 64067 5.7 1 52679 11388 76 68089 5.7 1 55772 12317 77 70462 5.7 1 57543 12919 78 72065 5.7 1 58687 13378 79 72745 5.7 1 58952 13793 80 72785 5.7 1 58704 14081 81 73449 5.7 1 59389 14060 82 73456 5.7 1 59165 14291 83 72939 5.7 1 58314 14625 84 72785 5.7 1 58258 14527 85 72185 5.7 1 57856 14329 86 71613 5.7 1 57074 14539 87 70864 5.7 1 56677 14187 88 71145 5.7 1 56961 14184 89 69194 5.7 1 55323 13871 90 69287 5.7 1 55262 14025 91 68129 5.7 1 54295 13834 92 67451 5.7 1 53886 13565 93 65864 5.7 1 52572 13292 94 64955 5.7 1 51832 13123 95 64272 5.7 1 51150 13122 96 63370 5.7 1 50414 12956 97 61971 5.7 1 49449 12522 98 61411 5.7 1 48937 12474 99 60080 5.7 1 47918 12162 100 59076 5.7 1 46891 12185 101 57691 5.7 1 45837 11854 102 56341 5.7 1 44779 11562 103 54946 5.7 1 43824 11122 104 53301 5.7 1 42151 11150 105 51774 5.7 1 41142 10632 106 50125 5.7 1 39682 10443 107 48776 5.7 1 38650 10126 108 47554 5.7 1 37248 10306 109 45662 5.7 1 36058 9604 110 43668 5.7 1 34299 9369 111 42524 5.7 1 33304 9220 112 41006 5.7 1 32171 8835 113 39805 5.7 1 31283 8522 114 38467 5.7 1 30150 8317 115 36917 5.7 1 28981 7936 116 35474 5.7 1 27902 7572 117 33548 5.7 1 26390 7158 118 32583 5.7 1 25558 7025 119 31091 5.7 1 24329 6762 120 29303 5.7 1 22921 6382 121 27728 5.7 1 21825 5903 122 25972 5.7 1 20442 5530 123 24465 5.7 1 19214 5251 124 22898 5.7 1 17993 4905 125 21621 5.7 1 16995 4626 126 20014 5.7 1 15694 4320 127 18987 5.7 1 15019 3968 128 16876 5.7 1 13491 3385 129 16593 5.7 1 13625 2968 130 13421 5.7 1 10974 2447 131 12382 5.7 1 10375 2007 132 9875 5.7 1 8394 1481 133 8952 5.7 1 7759 1193 134 7501 5.7 1 6524 977 135 6534 5.7 1 5675 859 136 5217 5.7 1 4621 596 137 4587 5.7 1 4093 494 138 3588 5.7 1 3198 390 139 2812 5.7 1 2534 278 140 2065 5.7 1 1837 228 141 1568 5.7 1 1398 170 142 1250 5.7 1 1114 136 143 1100 5.7 1 961 139 144 839 5.7 1 710 129 145 842 5.7 1 725 117 146 755 5.7 1 637 118 147 688 5.7 1 589 99 148 799 5.7 1 669 130 149 662 5.7 1 532 130 150 933 5.7 1 583 350 151 101421 5.7 1 50281 51140 RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR013_AD013_S2_L002_R1_001_val_1.fq.gz ============================================= 379535476 sequences processed in total