SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_6_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_6_R2_val_2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 4370.36 s (22 µs/read; 2.67 M reads/minute). === Summary === Total reads processed: 194,821,663 Reads with adapters: 21,438,386 (11.0%) Reads written (passing filters): 194,821,663 (100.0%) Total basepairs processed: 18,333,205,768 bp Quality-trimmed: 4,157,915 bp (0.0%) Total written (filtered): 17,933,262,213 bp (97.8%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 21438386 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: 14.1% C: 5.7% G: 0.0% T: 80.0% 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 12949866 48705415.8 0 12949866 2 3934592 12176353.9 0 3934592 3 848769 3044088.5 0 848769 4 242850 761022.1 0 242850 5 72591 190255.5 0 72591 6 17494 47563.9 0 17494 7 5410 11891.0 0 5410 8 3228 2972.7 0 3228 9 2796 743.2 0 2796 10 8042 185.8 1 2625 5417 11 7096 46.4 1 2641 4455 12 5250 11.6 1 2195 3055 13 4457 2.9 1 1894 2563 14 4279 0.7 1 1816 2463 15 3797 0.2 1 1683 2114 16 3184 0.0 1 1455 1729 17 2658 0.0 1 1251 1407 18 2215 0.0 1 1277 938 19 1996 0.0 1 1120 876 20 3967 0.0 2 1547 839 1581 21 3827 0.0 2 1336 856 1635 22 3536 0.0 2 1355 747 1434 23 3344 0.0 2 1275 736 1333 24 3100 0.0 2 1205 672 1223 25 3030 0.0 2 1113 714 1203 26 2663 0.0 2 1095 564 1004 27 2481 0.0 2 1121 482 878 28 2086 0.0 2 1053 457 576 29 1941 0.0 2 993 446 502 30 2965 0.0 3 950 459 550 1006 31 2974 0.0 3 916 439 514 1105 32 2739 0.0 3 853 440 458 988 33 2697 0.0 3 899 427 465 906 34 2774 0.0 3 906 446 471 951 35 2466 0.0 3 832 409 436 789 36 2338 0.0 3 835 332 410 761 37 2074 0.0 3 703 388 353 630 38 1944 0.0 3 806 377 335 426 39 1943 0.0 3 767 369 368 439 40 2729 0.0 4 795 373 353 408 800 41 2670 0.0 4 694 349 366 459 802 42 2651 0.0 4 794 369 361 397 730 43 2546 0.0 4 630 389 352 422 753 44 2547 0.0 4 794 369 351 364 669 45 2442 0.0 4 755 331 332 382 642 46 2411 0.0 4 872 352 275 323 589 47 2458 0.0 4 847 384 351 333 543 48 2689 0.0 4 951 508 478 397 355 49 6237 0.0 4 2005 1356 1182 903 791 50 6357 0.0 5 1783 1330 980 883 770 611 51 4871 0.0 5 1839 1017 704 560 388 363 52 4332 0.0 5 1906 866 543 416 312 289 53 3637 0.0 5 1584 780 474 356 238 205 54 3622 0.0 5 1761 701 445 316 213 186 55 3139 0.0 5 1581 620 334 249 218 137 56 3022 0.0 5 1610 535 322 241 182 132 57 2967 0.0 5 1764 506 274 185 131 107 58 2875 0.0 5 1726 497 256 182 127 87 59 2370 0.0 5 1417 379 232 156 106 80 60 2177 0.0 5 1299 367 216 126 93 76 61 2200 0.0 5 1360 357 191 128 110 54 62 2185 0.0 5 1457 336 162 103 75 52 63 2044 0.0 5 1336 329 162 98 64 55 64 2079 0.0 5 1390 325 147 99 74 44 65 1986 0.0 5 1342 312 135 87 55 55 66 1851 0.0 5 1319 240 121 83 46 42 67 1930 0.0 5 1401 273 112 78 36 30 68 1895 0.0 5 1406 244 121 56 41 27 69 1928 0.0 5 1470 239 97 57 38 27 70 1666 0.0 5 1235 216 88 57 41 29 71 1621 0.0 5 1250 181 77 57 33 23 72 1584 0.0 5 1236 167 81 49 28 23 73 1532 0.0 5 1165 187 80 48 31 21 74 1397 0.0 5 1122 136 66 40 18 15 75 1439 0.0 5 1135 168 61 40 25 10 76 1474 0.0 5 1189 157 62 25 29 12 77 1396 0.0 5 1134 139 50 39 19 15 78 1279 0.0 5 1014 139 53 33 21 19 79 1197 0.0 5 935 131 52 30 26 23 80 1289 0.0 5 1011 124 63 41 27 23 81 1185 0.0 5 983 90 47 28 21 16 82 1072 0.0 5 858 110 41 27 20 16 83 974 0.0 5 786 93 40 21 19 15 84 1007 0.0 5 820 96 37 24 20 10 85 1059 0.0 5 890 85 31 17 22 14 86 980 0.0 5 808 82 35 22 18 15 87 898 0.0 5 728 81 40 27 13 9 88 924 0.0 5 756 75 34 23 22 14 89 861 0.0 5 707 69 28 22 16 19 90 853 0.0 5 688 71 36 22 24 12 91 713 0.0 5 591 57 29 12 16 8 92 733 0.0 5 591 65 39 16 14 8 93 677 0.0 5 561 53 20 19 15 9 94 694 0.0 5 557 58 33 14 21 11 95 682 0.0 5 571 58 18 14 12 9 96 575 0.0 5 445 55 34 24 10 7 97 627 0.0 5 513 51 20 20 15 8 98 564 0.0 5 443 56 27 19 9 10 99 515 0.0 5 417 38 15 14 17 14 100 490 0.0 5 388 43 27 16 9 7 101 552 0.0 5 453 34 19 19 10 17 102 511 0.0 5 399 49 20 12 16 15 103 450 0.0 5 367 37 15 11 10 10 104 422 0.0 5 342 40 15 10 8 7 105 425 0.0 5 330 36 11 24 15 9 106 422 0.0 5 345 28 15 14 13 7 107 449 0.0 5 372 29 13 10 15 10 108 458 0.0 5 352 29 22 18 16 21 109 528 0.0 5 428 35 18 16 16 15 110 670 0.0 5 560 40 24 12 13 21 111 692 0.0 5 574 38 19 23 19 19 112 1212 0.0 5 972 64 44 51 44 37 113 1610 0.0 5 1333 87 57 57 34 42 114 4750 0.0 5 4352 150 68 70 65 45 115 3130972 0.0 5 3130192 358 182 107 77 56 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_6_R2_val_2_val_2.fq.gz ============================================= 194821663 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 194821663 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 3261624 (1.67%)