SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_5_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_5_R2_val_2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 3388.77 s (23 µs/read; 2.63 M reads/minute). === Summary === Total reads processed: 148,556,552 Reads with adapters: 16,112,459 (10.8%) Reads written (passing filters): 148,556,552 (100.0%) Total basepairs processed: 14,221,637,036 bp Quality-trimmed: 3,330,879 bp (0.0%) Total written (filtered): 13,952,076,286 bp (98.1%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 16112459 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: 14.2% C: 5.5% G: 0.0% T: 80.1% 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 9950820 37139138.0 0 9950820 2 2984814 9284784.5 0 2984814 3 647858 2321196.1 0 647858 4 187678 580299.0 0 187678 5 55129 145074.8 0 55129 6 13530 36268.7 0 13530 7 4375 9067.2 0 4375 8 2680 2266.8 0 2680 9 2366 566.7 0 2366 10 6997 141.7 1 2195 4802 11 5387 35.4 1 2012 3375 12 4607 8.9 1 1880 2727 13 3936 2.2 1 1647 2289 14 3478 0.6 1 1550 1928 15 3181 0.1 1 1415 1766 16 2711 0.0 1 1239 1472 17 2220 0.0 1 1025 1195 18 1768 0.0 1 1023 745 19 1737 0.0 1 997 740 20 3353 0.0 2 1293 716 1344 21 3164 0.0 2 1139 688 1337 22 2949 0.0 2 1046 696 1207 23 2822 0.0 2 1072 605 1145 24 2630 0.0 2 1048 567 1015 25 2510 0.0 2 961 595 954 26 2183 0.0 2 904 483 796 27 1976 0.0 2 870 407 699 28 1660 0.0 2 817 405 438 29 1616 0.0 2 808 383 425 30 2500 0.0 3 793 393 429 885 31 2429 0.0 3 762 371 431 865 32 2269 0.0 3 739 402 354 774 33 2248 0.0 3 754 320 410 764 34 2248 0.0 3 725 381 378 764 35 2015 0.0 3 652 348 370 645 36 1900 0.0 3 703 295 323 579 37 1754 0.0 3 645 311 281 517 38 1607 0.0 3 648 337 288 334 39 1537 0.0 3 600 319 265 353 40 2416 0.0 4 726 318 264 361 747 41 2263 0.0 4 641 323 285 349 665 42 2140 0.0 4 635 305 260 327 613 43 2064 0.0 4 535 306 301 339 583 44 2107 0.0 4 627 329 289 313 549 45 2039 0.0 4 646 297 291 309 496 46 1921 0.0 4 681 287 238 259 456 47 2000 0.0 4 722 331 270 256 421 48 2195 0.0 4 790 445 396 300 264 49 5025 0.0 4 1669 1087 885 777 607 50 5294 0.0 5 1552 1082 842 755 575 488 51 4060 0.0 5 1662 767 591 397 338 305 52 3554 0.0 5 1619 665 472 325 237 236 53 3217 0.0 5 1544 607 388 281 216 181 54 2841 0.0 5 1429 550 345 234 149 134 55 2733 0.0 5 1422 496 300 217 180 118 56 2576 0.0 5 1430 470 260 192 125 99 57 2471 0.0 5 1451 416 243 168 107 86 58 2244 0.0 5 1374 361 178 123 123 85 59 2056 0.0 5 1265 348 184 118 93 48 60 1979 0.0 5 1197 345 201 109 74 53 61 1869 0.0 5 1209 287 165 98 60 50 62 1871 0.0 5 1231 297 156 92 49 46 63 1837 0.0 5 1214 281 145 82 61 54 64 1843 0.0 5 1260 271 139 90 49 34 65 1784 0.0 5 1252 262 124 63 50 33 66 1771 0.0 5 1285 247 111 55 41 32 67 1687 0.0 5 1257 232 88 51 35 24 68 1798 0.0 5 1325 237 91 72 35 38 69 1667 0.0 5 1259 186 110 53 32 27 70 1540 0.0 5 1107 209 96 65 38 25 71 1468 0.0 5 1106 184 74 51 33 20 72 1405 0.0 5 1055 178 75 46 27 24 73 1333 0.0 5 1034 161 55 33 32 18 74 1332 0.0 5 1011 159 68 41 35 18 75 1204 0.0 5 936 146 53 37 22 10 76 1328 0.0 5 1033 136 65 42 30 22 77 1250 0.0 5 957 129 62 52 34 16 78 1111 0.0 5 881 115 44 26 28 17 79 1051 0.0 5 813 122 56 28 22 10 80 1088 0.0 5 881 109 49 19 14 16 81 1017 0.0 5 834 81 35 27 22 18 82 922 0.0 5 734 90 38 26 19 15 83 922 0.0 5 723 88 51 26 22 12 84 885 0.0 5 719 73 43 21 15 14 85 860 0.0 5 680 87 45 18 15 15 86 831 0.0 5 676 64 43 22 13 13 87 772 0.0 5 619 53 40 28 18 14 88 813 0.0 5 646 79 36 20 17 15 89 731 0.0 5 569 69 37 30 18 8 90 695 0.0 5 545 69 30 22 14 15 91 614 0.0 5 502 39 28 23 14 8 92 601 0.0 5 487 55 26 16 10 7 93 572 0.0 5 464 46 21 18 13 10 94 591 0.0 5 460 61 28 17 11 14 95 618 0.0 5 499 49 24 24 9 13 96 498 0.0 5 393 52 21 15 7 10 97 551 0.0 5 426 51 23 24 13 14 98 480 0.0 5 376 41 22 20 15 6 99 505 0.0 5 402 41 27 16 10 9 100 454 0.0 5 363 36 24 9 13 9 101 482 0.0 5 379 36 17 23 10 17 102 445 0.0 5 358 33 21 16 12 5 103 415 0.0 5 321 30 23 16 14 11 104 392 0.0 5 302 34 21 15 13 7 105 391 0.0 5 314 30 16 11 11 9 106 344 0.0 5 271 29 19 9 8 8 107 387 0.0 5 299 34 19 17 11 7 108 339 0.0 5 264 25 15 14 10 11 109 425 0.0 5 339 26 20 15 13 12 110 554 0.0 5 472 28 18 12 13 11 111 582 0.0 5 481 31 19 16 16 19 112 931 0.0 5 801 41 26 17 27 19 113 1206 0.0 5 1016 68 35 22 38 27 114 3723 0.0 5 3403 148 60 53 30 29 115 2069837 0.0 5 2069167 326 160 77 58 49 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_5_R2_val_2_val_2.fq.gz ============================================= 148556552 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 148556552 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 2163491 (1.46%)