SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_5_R1_val_1_val_1.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG' (user defined) Maximum trimming error rate: 0.1 (default) Optional adapter 2 sequence (only used for read 2 of paired-end files): 'GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG' Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/poly-G --threads 28 Output file will be GZIP compressed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_5_R1_val_1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 3403.76 s (23 µs/read; 2.62 M reads/minute). === Summary === Total reads processed: 148,556,552 Reads with adapters: 16,348,719 (11.0%) Reads written (passing filters): 148,556,552 (100.0%) Total basepairs processed: 14,222,653,957 bp Quality-trimmed: 3,116,855 bp (0.0%) Total written (filtered): 14,037,493,557 bp (98.7%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 16348719 times No. of allowed errors: 1-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40-49 bp: 4; 50 bp: 5 Bases preceding removed adapters: A: 23.8% C: 4.8% G: 0.0% T: 71.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 10087226 37139138.0 0 10087226 2 3044735 9284784.5 0 3044735 3 662617 2321196.1 0 662617 4 193189 580299.0 0 193189 5 59703 145074.8 0 59703 6 16899 36268.7 0 16899 7 7655 9067.2 0 7655 8 5339 2266.8 0 5339 9 5357 566.7 0 5357 10 9717 141.7 1 4825 4892 11 8684 35.4 1 4481 4203 12 7228 8.9 1 3838 3390 13 6672 2.2 1 3545 3127 14 5739 0.6 1 3098 2641 15 5182 0.1 1 2835 2347 16 4430 0.0 1 2445 1985 17 3681 0.0 1 2096 1585 18 2991 0.0 1 1941 1050 19 2765 0.0 1 1802 963 20 4178 0.0 2 1889 923 1366 21 3608 0.0 2 1769 845 994 22 3426 0.0 2 1681 752 993 23 3245 0.0 2 1611 752 882 24 3168 0.0 2 1546 795 827 25 2860 0.0 2 1462 703 695 26 2590 0.0 2 1282 661 647 27 2606 0.0 2 1370 660 576 28 2305 0.0 2 1243 625 437 29 2214 0.0 2 1274 548 392 30 2746 0.0 3 1225 535 395 591 31 2617 0.0 3 1100 536 411 570 32 2592 0.0 3 1102 541 347 602 33 2496 0.0 3 1071 520 377 528 34 2387 0.0 3 1060 520 346 461 35 2489 0.0 3 1060 538 407 484 36 2277 0.0 3 1007 500 335 435 37 2253 0.0 3 1091 474 310 378 38 2174 0.0 3 1085 464 330 295 39 2071 0.0 3 973 527 272 299 40 2461 0.0 4 976 435 323 287 440 41 2440 0.0 4 997 462 310 261 410 42 2312 0.0 4 918 404 312 280 398 43 2466 0.0 4 961 494 315 298 398 44 2329 0.0 4 894 446 305 248 436 45 2111 0.0 4 877 400 265 250 319 46 2173 0.0 4 947 408 255 240 323 47 2079 0.0 4 926 443 243 198 269 48 2346 0.0 4 1014 523 320 264 225 49 4688 0.0 4 1911 1077 728 544 428 50 5022 0.0 5 1938 1083 746 542 418 295 51 3927 0.0 5 1952 786 435 328 252 174 52 3420 0.0 5 1796 654 384 265 189 132 53 3205 0.0 5 1750 617 354 233 165 86 54 3066 0.0 5 1824 554 298 184 106 100 55 2851 0.0 5 1732 525 281 160 84 69 56 2911 0.0 5 1917 496 227 132 81 58 57 3141 0.0 5 2209 466 199 132 79 56 58 3509 0.0 5 2662 403 191 124 77 52 59 3416 0.0 5 2617 414 185 96 63 41 60 2295 0.0 5 1592 364 152 96 51 40 61 2258 0.0 5 1608 332 163 70 48 37 62 2452 0.0 5 1837 296 164 70 53 32 63 3119 0.0 5 2469 364 132 80 49 25 64 4389 0.0 5 3792 323 128 73 53 20 65 2328 0.0 5 1731 296 147 83 40 31 66 2647 0.0 5 2068 307 143 64 35 30 67 2261 0.0 5 1697 303 143 58 38 22 68 2493 0.0 5 1955 295 108 76 42 17 69 2990 0.0 5 2445 282 135 74 40 14 70 5283 0.0 5 4796 284 108 42 32 21 71 11806 0.0 5 11259 346 91 57 33 20 72 82817 0.0 5 82198 393 108 54 39 25 73 124837 0.0 5 124239 362 112 57 35 32 74 1207358 0.0 5 1206776 348 115 59 36 24 75 55484 0.0 5 55039 247 82 53 43 20 76 36184 0.0 5 35783 219 90 54 18 20 77 245197 0.0 5 244795 227 80 50 23 22 78 16995 0.0 5 16622 196 76 44 33 24 79 144664 0.0 5 144307 196 83 40 22 16 80 32559 0.0 5 32271 162 44 44 24 14 81 17777 0.0 5 17437 156 85 57 21 21 82 50121 0.0 5 49830 133 76 44 25 13 83 4753 0.0 5 4469 147 68 25 25 19 84 18019 0.0 5 17720 132 84 45 26 12 85 4428 0.0 5 4200 113 47 28 25 15 86 791 0.0 5 552 117 58 36 18 10 87 775 0.0 5 534 115 67 28 18 13 88 657 0.0 5 469 80 42 32 24 10 89 642 0.0 5 453 85 43 27 17 17 90 627 0.0 5 424 91 51 24 12 25 91 566 0.0 5 392 81 32 32 9 20 92 500 0.0 5 350 63 36 24 15 12 93 513 0.0 5 338 74 33 30 22 16 94 431 0.0 5 282 59 38 20 19 13 95 392 0.0 5 268 42 43 15 18 6 96 376 0.0 5 244 59 30 24 9 10 97 352 0.0 5 233 56 34 13 7 9 98 321 0.0 5 209 47 25 22 13 5 99 278 0.0 5 176 38 32 15 11 6 100 285 0.0 5 194 41 18 13 10 9 101 233 0.0 5 156 32 17 14 10 4 102 229 0.0 5 158 34 11 13 9 4 103 160 0.0 5 105 18 12 9 8 8 104 148 0.0 5 100 17 9 6 10 6 105 132 0.0 5 83 21 11 7 7 3 106 115 0.0 5 78 11 10 9 4 3 107 116 0.0 5 82 8 7 7 6 6 108 106 0.0 5 69 13 13 5 1 5 109 76 0.0 5 54 5 4 5 4 4 110 60 0.0 5 42 3 5 3 5 2 111 41 0.0 5 32 2 2 1 0 4 112 52 0.0 5 36 7 2 6 0 1 113 31 0.0 5 21 3 3 1 2 1 114 47 0.0 5 39 5 0 3 115 169 0.0 5 161 5 0 1 1 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_5_R1_val_1_val_1.fq.gz ============================================= 148556552 sequences processed in total