SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_4_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_4_R2_val_2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 4577.21 s (23 µs/read; 2.59 M reads/minute). === Summary === Total reads processed: 197,822,142 Reads with adapters: 20,805,963 (10.5%) Reads written (passing filters): 197,822,142 (100.0%) Total basepairs processed: 19,208,738,542 bp Quality-trimmed: 4,664,617 bp (0.0%) Total written (filtered): 18,903,811,337 bp (98.4%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 20805963 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: 5.6% 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 13162651 49455535.5 0 13162651 2 3910753 12363883.9 0 3910753 3 855916 3090971.0 0 855916 4 246767 772742.7 0 246767 5 71050 193185.7 0 71050 6 17757 48296.4 0 17757 7 5666 12074.1 0 5666 8 3491 3018.5 0 3491 9 3088 754.6 0 3088 10 8720 188.7 1 2774 5946 11 7347 47.2 1 2617 4730 12 5863 11.8 1 2380 3483 13 5091 2.9 1 2163 2928 14 4505 0.7 1 1889 2616 15 3910 0.2 1 1702 2208 16 3312 0.0 1 1496 1816 17 2864 0.0 1 1321 1543 18 2335 0.0 1 1321 1014 19 2009 0.0 1 1109 900 20 4241 0.0 2 1683 870 1688 21 3929 0.0 2 1424 896 1609 22 3611 0.0 2 1362 751 1498 23 3424 0.0 2 1307 747 1370 24 3207 0.0 2 1307 697 1203 25 3021 0.0 2 1140 670 1211 26 2602 0.0 2 1079 550 973 27 2296 0.0 2 1017 493 786 28 2073 0.0 2 1048 471 554 29 1937 0.0 2 932 482 523 30 3088 0.0 3 952 471 532 1133 31 2889 0.0 3 843 454 536 1056 32 2788 0.0 3 938 425 489 936 33 2774 0.0 3 880 488 474 932 34 2632 0.0 3 841 434 472 885 35 2485 0.0 3 841 396 458 790 36 2294 0.0 3 843 374 382 695 37 2095 0.0 3 784 391 337 583 38 1848 0.0 3 780 354 320 394 39 1835 0.0 3 718 394 331 392 40 2723 0.0 4 828 349 311 434 801 41 2610 0.0 4 702 355 341 406 806 42 2498 0.0 4 746 345 313 362 732 43 2451 0.0 4 632 375 321 393 730 44 2552 0.0 4 744 384 361 393 670 45 2394 0.0 4 745 306 328 388 627 46 2310 0.0 4 793 347 303 335 532 47 2333 0.0 4 793 416 338 305 481 48 2661 0.0 4 885 551 470 396 359 49 6078 0.0 4 1973 1384 1078 891 752 50 6135 0.0 5 1767 1251 977 787 746 607 51 4724 0.0 5 1772 991 683 528 427 323 52 4122 0.0 5 1772 836 545 409 310 250 53 3642 0.0 5 1600 751 473 355 226 237 54 3455 0.0 5 1655 711 397 306 215 171 55 3031 0.0 5 1581 574 310 235 195 136 56 2955 0.0 5 1609 534 297 222 168 125 57 2873 0.0 5 1641 515 289 199 125 104 58 2682 0.0 5 1606 430 268 143 124 111 59 2363 0.0 5 1381 404 248 148 101 81 60 2161 0.0 5 1330 334 202 138 91 66 61 2085 0.0 5 1318 355 176 100 82 54 62 2073 0.0 5 1327 343 181 97 74 51 63 1960 0.0 5 1291 310 158 87 69 45 64 1913 0.0 5 1306 302 137 70 64 34 65 1841 0.0 5 1238 274 129 92 62 46 66 1885 0.0 5 1329 275 124 77 51 29 67 1828 0.0 5 1293 279 104 67 50 35 68 1991 0.0 5 1477 255 119 62 43 35 69 1818 0.0 5 1375 235 89 63 34 22 70 1542 0.0 5 1181 183 81 47 25 25 71 1614 0.0 5 1152 223 96 75 35 33 72 1529 0.0 5 1163 179 97 42 29 19 73 1379 0.0 5 1088 142 70 33 30 16 74 1312 0.0 5 1040 143 60 28 23 18 75 1298 0.0 5 1021 127 55 44 30 21 76 1275 0.0 5 1005 132 60 28 25 25 77 1214 0.0 5 959 134 61 27 21 12 78 1091 0.0 5 867 106 61 32 10 15 79 1057 0.0 5 858 105 38 20 22 14 80 1079 0.0 5 850 111 54 31 25 8 81 1043 0.0 5 829 101 48 26 19 20 82 966 0.0 5 785 93 44 21 12 11 83 935 0.0 5 751 97 39 25 13 10 84 870 0.0 5 688 82 45 21 19 15 85 880 0.0 5 702 70 54 22 17 15 86 784 0.0 5 651 56 34 21 11 11 87 830 0.0 5 675 68 24 30 16 17 88 799 0.0 5 655 51 46 22 13 12 89 716 0.0 5 581 57 28 24 14 12 90 701 0.0 5 572 59 30 17 11 12 91 637 0.0 5 520 52 28 19 9 9 92 660 0.0 5 533 55 21 20 17 14 93 626 0.0 5 518 46 25 15 11 11 94 590 0.0 5 453 68 22 19 16 12 95 611 0.0 5 508 46 24 11 12 10 96 506 0.0 5 413 39 21 11 13 9 97 564 0.0 5 457 53 16 15 12 11 98 457 0.0 5 369 37 20 14 9 8 99 501 0.0 5 411 33 25 16 10 6 100 462 0.0 5 362 36 17 16 17 14 101 446 0.0 5 377 20 17 14 8 10 102 401 0.0 5 323 30 15 11 11 11 103 456 0.0 5 379 28 23 10 5 11 104 428 0.0 5 353 26 17 8 14 10 105 433 0.0 5 363 24 12 13 10 11 106 423 0.0 5 356 26 9 20 4 8 107 439 0.0 5 367 29 15 9 8 11 108 413 0.0 5 330 30 16 14 12 11 109 533 0.0 5 420 34 20 23 21 15 110 631 0.0 5 524 30 16 21 20 20 111 696 0.0 5 578 35 25 19 24 15 112 1153 0.0 5 915 74 34 50 37 43 113 1534 0.0 5 1286 60 53 45 52 38 114 4480 0.0 5 4129 150 73 42 40 46 115 2302658 0.0 5 2301919 354 150 100 77 58 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_4_R2_val_2_val_2.fq.gz ============================================= 197822142 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 197822142 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 2417618 (1.22%)