SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_1_R2_val_2_val_2.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_1_R2_val_2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 3956.98 s (25 µs/read; 2.44 M reads/minute). === Summary === Total reads processed: 161,104,708 Reads with adapters: 17,645,060 (11.0%) Reads written (passing filters): 161,104,708 (100.0%) Total basepairs processed: 15,998,741,118 bp Quality-trimmed: 3,705,302 bp (0.0%) Total written (filtered): 15,671,714,831 bp (98.0%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 17645060 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: 13.9% C: 5.5% G: 0.0% T: 80.4% none/other: 0.2% WARNING: The adapter is preceded by "T" extremely often. The provided adapter sequence could be incomplete at its 5' end. Overview of removed sequences length count expect max.err error counts 1 10759713 40276177.0 0 10759713 2 3172985 10069044.2 0 3172985 3 686503 2517261.1 0 686503 4 196142 629315.3 0 196142 5 57428 157328.8 0 57428 6 14331 39332.2 0 14331 7 4632 9833.1 0 4632 8 2835 2458.3 0 2835 9 2641 614.6 0 2641 10 7444 153.6 1 2368 5076 11 6072 38.4 1 2170 3902 12 5019 9.6 1 2029 2990 13 4279 2.4 1 1807 2472 14 3713 0.6 1 1577 2136 15 3446 0.2 1 1461 1985 16 2994 0.0 1 1324 1670 17 2333 0.0 1 1048 1285 18 1902 0.0 1 1032 870 19 1773 0.0 1 1012 761 20 3542 0.0 2 1328 741 1473 21 3301 0.0 2 1151 711 1439 22 3011 0.0 2 1062 630 1319 23 2933 0.0 2 1069 649 1215 24 2630 0.0 2 1009 563 1058 25 2436 0.0 2 911 538 987 26 2231 0.0 2 854 526 851 27 1922 0.0 2 865 387 670 28 1539 0.0 2 733 364 442 29 1592 0.0 2 759 350 483 30 2502 0.0 3 730 359 458 955 31 2370 0.0 3 669 350 427 924 32 2304 0.0 3 691 322 438 853 33 2309 0.0 3 751 381 395 782 34 2118 0.0 3 667 329 364 758 35 2078 0.0 3 657 340 380 701 36 1846 0.0 3 646 281 350 569 37 1699 0.0 3 594 307 273 525 38 1609 0.0 3 647 281 305 376 39 1539 0.0 3 610 306 299 324 40 2210 0.0 4 602 282 272 323 731 41 2172 0.0 4 602 300 265 346 659 42 2003 0.0 4 540 262 262 334 605 43 2014 0.0 4 507 281 247 353 626 44 2028 0.0 4 549 268 278 337 596 45 1968 0.0 4 572 273 248 306 569 46 1873 0.0 4 615 289 234 290 445 47 1895 0.0 4 646 338 277 208 426 48 2105 0.0 4 737 424 354 330 260 49 4857 0.0 4 1505 1100 901 726 625 50 5173 0.0 5 1419 1045 850 669 608 582 51 4051 0.0 5 1512 858 563 448 372 298 52 3355 0.0 5 1364 669 454 384 269 215 53 3032 0.0 5 1332 629 376 303 221 171 54 2891 0.0 5 1390 554 375 243 187 142 55 2523 0.0 5 1221 495 315 207 177 108 56 2443 0.0 5 1374 424 245 184 120 96 57 2339 0.0 5 1323 388 243 164 117 104 58 2244 0.0 5 1323 380 198 163 110 70 59 1975 0.0 5 1154 341 197 121 88 74 60 1804 0.0 5 1058 314 163 114 93 62 61 1775 0.0 5 1063 316 152 102 80 62 62 1802 0.0 5 1138 303 146 98 60 57 63 1636 0.0 5 1036 259 153 86 57 45 64 1700 0.0 5 1106 284 117 93 61 39 65 1634 0.0 5 1107 253 133 64 40 37 66 1543 0.0 5 1076 229 109 68 38 23 67 1572 0.0 5 1122 210 104 66 45 25 68 1664 0.0 5 1249 185 103 54 43 30 69 1512 0.0 5 1139 183 90 47 36 17 70 1353 0.0 5 968 192 80 50 35 28 71 1233 0.0 5 907 155 77 38 35 21 72 1260 0.0 5 959 147 70 36 27 21 73 1208 0.0 5 911 129 77 36 25 30 74 1148 0.0 5 875 115 67 45 30 16 75 1050 0.0 5 773 122 73 40 21 21 76 1158 0.0 5 925 117 48 28 28 12 77 1156 0.0 5 916 112 53 37 17 21 78 937 0.0 5 733 107 42 25 16 14 79 893 0.0 5 684 109 42 27 13 18 80 951 0.0 5 706 119 60 21 23 22 81 892 0.0 5 710 80 43 27 17 15 82 847 0.0 5 654 88 41 25 25 14 83 788 0.0 5 619 75 42 23 18 11 84 761 0.0 5 587 80 39 19 16 20 85 829 0.0 5 658 69 37 28 19 18 86 735 0.0 5 593 65 32 25 9 11 87 695 0.0 5 547 72 35 15 12 14 88 701 0.0 5 567 67 27 10 20 10 89 669 0.0 5 526 65 33 20 17 8 90 575 0.0 5 440 56 36 17 15 11 91 560 0.0 5 443 57 25 14 13 8 92 566 0.0 5 442 43 36 21 14 10 93 529 0.0 5 415 40 26 17 20 11 94 587 0.0 5 471 48 29 22 10 7 95 542 0.0 5 416 58 29 14 15 10 96 473 0.0 5 377 43 16 15 13 9 97 504 0.0 5 387 52 28 11 12 14 98 415 0.0 5 306 48 19 16 17 9 99 457 0.0 5 347 44 18 21 16 11 100 430 0.0 5 335 32 26 18 11 8 101 427 0.0 5 328 32 26 16 14 11 102 410 0.0 5 313 40 18 16 12 11 103 389 0.0 5 298 30 27 13 11 10 104 350 0.0 5 256 37 25 15 7 10 105 379 0.0 5 295 32 16 10 13 13 106 382 0.0 5 300 28 19 14 10 11 107 385 0.0 5 311 21 21 15 11 6 108 400 0.0 5 303 33 26 12 13 13 109 449 0.0 5 344 42 25 15 11 12 110 543 0.0 5 434 33 20 19 25 12 111 580 0.0 5 463 38 27 19 21 12 112 947 0.0 5 785 50 32 27 21 32 113 1227 0.0 5 1042 51 44 33 32 25 114 3851 0.0 5 3483 141 82 64 36 45 115 2557950 0.0 5 2557183 374 205 80 57 51 WARNING: One or more of your adapter sequences may be incomplete. Please see the detailed output above. RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_1_R2_val_2_val_2.fq.gz ============================================= 161104708 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 161104708 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 2648078 (1.64%)