This is cutadapt 1.18 with Python 3.4.2 Command line parameters: -j 16 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTAT -o KOIFN_2_R1_trm.fastq.gz -p KOIFN_2_R2_trm.fastq.gz /mnt/max/b/genomics_facility/DKlab/mr/rnaseq/RNA_Seq/HI.1370.006.Index_5.KOIFN_2_R1.fastq.gz /mnt/max/b/genomics_facility/DKlab/mr/rnaseq/RNA_Seq/HI.1370.006.Index_5.KOIFN_2_R2.fastq.gz Processing reads on 16 cores in paired-end mode ... Finished in 279.36 s (5 us/read; 10.97 M reads/minute). === Summary === Total read pairs processed: 51,064,246 Read 1 with adapter: 2,789,619 (5.5%) Read 2 with adapter: 3,044,629 (6.0%) Pairs written (passing filters): 51,064,246 (100.0%) Total basepairs processed: 10,212,849,200 bp Read 1: 5,106,424,600 bp Read 2: 5,106,424,600 bp Total written (filtered): 10,168,835,490 bp (99.6%) Read 1: 5,084,779,501 bp Read 2: 5,084,055,989 bp === First read: Adapter 1 === Sequence: AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC; Type: regular 3'; Length: 34; Trimmed: 2789619 times. No. of allowed errors: 0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-34 bp: 3 Bases preceding removed adapters: A: 18.4% C: 31.4% G: 33.8% T: 16.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 3 1156800 797878.8 0 1156800 4 332911 199469.7 0 332911 5 170910 49867.4 0 170910 6 116465 12466.9 0 116465 7 100416 3116.7 0 100416 8 93341 779.2 0 93341 9 84828 194.8 0 83927 901 10 78002 48.7 1 74724 3278 11 70439 12.2 1 68263 2176 12 64123 3.0 1 60981 3142 13 58074 0.8 1 55711 2363 14 52701 0.2 1 51007 1694 15 47341 0.0 1 45776 1565 16 41922 0.0 1 40131 1791 17 37556 0.0 1 36386 1170 18 32304 0.0 1 31008 1222 74 19 28163 0.0 1 26318 1743 102 20 25064 0.0 2 23858 1042 164 21 22924 0.0 2 22012 775 137 22 20452 0.0 2 19116 1165 171 23 18202 0.0 2 17353 725 124 24 16365 0.0 2 15261 978 126 25 14583 0.0 2 13821 655 107 26 12720 0.0 2 11899 731 90 27 11497 0.0 2 10894 518 82 3 28 9830 0.0 2 9148 566 98 18 29 8632 0.0 2 8089 425 87 31 30 7461 0.0 3 6936 412 73 40 31 6478 0.0 3 5582 785 83 28 32 5806 0.0 3 5383 332 62 29 33 5274 0.0 3 4899 320 43 12 34 4615 0.0 3 4297 271 36 11 35 4043 0.0 3 3772 229 29 13 36 3693 0.0 3 3460 187 33 13 37 3321 0.0 3 3123 153 34 11 38 2776 0.0 3 2601 137 30 8 39 2473 0.0 3 2337 109 25 2 40 2112 0.0 3 1981 107 20 4 41 1859 0.0 3 1740 101 13 5 42 1626 0.0 3 1534 72 14 6 43 1370 0.0 3 1288 60 18 4 44 1220 0.0 3 1163 42 9 6 45 1103 0.0 3 1034 54 11 4 46 999 0.0 3 937 47 13 2 47 936 0.0 3 874 50 11 1 48 791 0.0 3 740 43 6 2 49 762 0.0 3 725 32 4 1 50 563 0.0 3 535 20 6 2 51 476 0.0 3 440 32 3 1 52 444 0.0 3 417 21 4 2 53 378 0.0 3 354 20 2 2 54 333 0.0 3 309 22 2 55 269 0.0 3 254 13 1 1 56 274 0.0 3 257 12 4 1 57 218 0.0 3 205 12 1 58 189 0.0 3 183 5 0 1 59 173 0.0 3 163 9 0 1 60 136 0.0 3 129 6 0 1 61 110 0.0 3 109 0 1 62 84 0.0 3 78 5 1 63 90 0.0 3 85 5 64 52 0.0 3 47 4 1 65 59 0.0 3 57 2 66 42 0.0 3 41 1 67 45 0.0 3 39 5 0 1 68 24 0.0 3 22 0 1 1 69 21 0.0 3 21 70 12 0.0 3 10 1 1 71 9 0.0 3 9 72 7 0.0 3 6 1 73 5 0.0 3 5 74 2 0.0 3 2 75 4 0.0 3 3 0 1 76 7 0.0 3 7 77 2 0.0 3 2 78 1 0.0 3 1 79 3 0.0 3 3 80 4 0.0 3 4 81 6 0.0 3 6 82 2 0.0 3 2 83 7 0.0 3 7 84 15 0.0 3 15 85 5 0.0 3 5 86 15 0.0 3 14 1 87 16 0.0 3 15 1 88 19 0.0 3 17 2 89 18 0.0 3 17 0 1 90 7 0.0 3 7 91 21 0.0 3 20 1 92 7 0.0 3 7 93 6 0.0 3 6 94 6 0.0 3 5 1 95 12 0.0 3 10 2 96 6 0.0 3 5 0 1 97 16 0.0 3 16 98 5 0.0 3 4 1 99 4 0.0 3 4 100 107 0.0 3 4 94 6 3 === Second read: Adapter 2 === Sequence: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTAT; Type: regular 3'; Length: 54; Trimmed: 3044629 times. No. of allowed errors: 0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40-49 bp: 4; 50-54 bp: 5 Bases preceding removed adapters: A: 20.9% C: 32.5% G: 36.1% T: 10.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 3 1368706 797878.8 0 1368706 4 372090 199469.7 0 372090 5 179345 49867.4 0 179345 6 117885 12466.9 0 117885 7 101547 3116.7 0 101547 8 92240 779.2 0 92240 9 83922 194.8 0 82524 1398 10 78861 48.7 1 73923 4938 11 70231 12.2 1 65772 4459 12 63751 3.0 1 61622 2129 13 57401 0.8 1 54851 2550 14 52246 0.2 1 50694 1552 15 46665 0.0 1 41859 4806 16 41528 0.0 1 39686 1842 17 37206 0.0 1 36073 1133 18 31843 0.0 1 28435 3395 13 19 27821 0.0 1 26685 1091 45 20 24805 0.0 2 22457 1557 791 21 22722 0.0 2 20236 2200 286 22 20300 0.0 2 19260 872 168 23 18040 0.0 2 17061 791 188 24 16243 0.0 2 15292 820 131 25 14467 0.0 2 13679 660 128 26 12628 0.0 2 11489 994 145 27 11402 0.0 2 10265 941 190 6 28 9766 0.0 2 8793 786 179 8 29 8549 0.0 2 7532 857 143 17 30 7385 0.0 3 6649 594 101 41 31 6423 0.0 3 4495 1687 156 85 32 5762 0.0 3 5033 450 109 170 33 5231 0.0 3 4339 649 152 91 34 4572 0.0 3 4046 402 83 41 35 3997 0.0 3 3531 373 59 34 36 3663 0.0 3 3237 331 76 18 1 37 3277 0.0 3 2940 271 52 12 2 38 2742 0.0 3 2443 238 45 15 1 39 2454 0.0 3 2211 195 33 10 5 40 2101 0.0 4 1828 210 40 17 6 41 1846 0.0 4 1631 160 34 14 7 42 1619 0.0 4 1442 136 25 11 5 43 1347 0.0 4 1004 281 39 13 10 44 1213 0.0 4 1074 102 20 8 9 45 1098 0.0 4 975 84 25 7 7 46 987 0.0 4 820 99 47 14 6 1 47 929 0.0 4 832 67 17 9 3 1 48 789 0.0 4 700 60 15 10 4 49 757 0.0 4 677 55 18 4 2 1 50 560 0.0 5 496 46 12 3 1 2 51 470 0.0 5 416 41 5 1 5 2 52 441 0.0 5 370 46 12 7 5 1 53 377 0.0 5 332 29 10 3 1 2 54 332 0.0 5 286 32 6 4 4 55 266 0.0 5 227 25 8 3 1 2 56 272 0.0 5 234 28 7 1 1 1 57 217 0.0 5 194 10 3 5 4 1 58 188 0.0 5 161 16 1 6 1 3 59 172 0.0 5 149 11 3 4 4 1 60 136 0.0 5 117 12 0 4 2 1 61 110 0.0 5 103 4 1 2 62 85 0.0 5 69 10 1 4 1 63 89 0.0 5 83 2 0 4 64 53 0.0 5 45 7 1 65 58 0.0 5 55 1 0 1 1 66 43 0.0 5 38 3 1 0 1 67 44 0.0 5 36 2 0 4 1 1 68 24 0.0 5 18 4 0 1 1 69 21 0.0 5 19 1 0 1 70 12 0.0 5 11 1 71 10 0.0 5 9 1 72 6 0.0 5 6 73 6 0.0 5 4 1 0 1 74 2 0.0 5 2 75 4 0.0 5 3 0 0 1 76 7 0.0 5 6 1 77 4 0.0 5 2 1 0 1 78 2 0.0 5 0 2 79 3 0.0 5 3 80 4 0.0 5 4 81 6 0.0 5 5 1 82 2 0.0 5 2 83 7 0.0 5 7 84 15 0.0 5 14 1 85 6 0.0 5 6 86 15 0.0 5 14 1 87 17 0.0 5 13 2 0 1 1 88 19 0.0 5 19 89 18 0.0 5 16 2 90 7 0.0 5 7 91 21 0.0 5 17 4 92 7 0.0 5 4 3 93 6 0.0 5 6 94 6 0.0 5 5 1 95 12 0.0 5 9 3 96 4 0.0 5 2 1 1 97 16 0.0 5 8 8 98 5 0.0 5 5 99 4 0.0 5 1 3 100 16 0.0 5 6 1 3 1 2 3