SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_8_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_8_R2_val_2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 3712.28 s (23 µs/read; 2.61 M reads/minute). === Summary === Total reads processed: 161,309,784 Reads with adapters: 16,896,270 (10.5%) Reads written (passing filters): 161,309,784 (100.0%) Total basepairs processed: 15,578,772,993 bp Quality-trimmed: 3,804,929 bp (0.0%) Total written (filtered): 15,335,395,137 bp (98.4%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 16896270 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: 80.1% none/other: 0.5% 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 10728037 40327446.0 0 10728037 2 3180063 10081861.5 0 3180063 3 691498 2520465.4 0 691498 4 197818 630116.3 0 197818 5 57457 157529.1 0 57457 6 14925 39382.3 0 14925 7 4931 9845.6 0 4931 8 2970 2461.4 0 2970 9 2471 615.3 0 2471 10 7191 153.8 1 2354 4837 11 6228 38.5 1 2128 4100 12 4726 9.6 1 1910 2816 13 4051 2.4 1 1635 2416 14 3706 0.6 1 1490 2216 15 3246 0.2 1 1309 1937 16 2653 0.0 1 1157 1496 17 2166 0.0 1 958 1208 18 1769 0.0 1 973 796 19 1532 0.0 1 802 730 20 3450 0.0 2 1284 747 1419 21 3180 0.0 2 1108 663 1409 22 2895 0.0 2 1071 593 1231 23 2833 0.0 2 1050 569 1214 24 2456 0.0 2 874 518 1064 25 2467 0.0 2 861 536 1070 26 2066 0.0 2 814 434 818 27 1864 0.0 2 779 402 683 28 1632 0.0 2 815 358 459 29 1580 0.0 2 734 401 445 30 2562 0.0 3 768 358 435 1001 31 2434 0.0 3 718 369 431 916 32 2228 0.0 3 711 317 359 841 33 2276 0.0 3 757 329 375 815 34 2236 0.0 3 704 351 383 798 35 2068 0.0 3 614 347 365 742 36 1840 0.0 3 654 305 324 557 37 1696 0.0 3 597 309 272 518 38 1509 0.0 3 641 288 253 327 39 1472 0.0 3 576 285 270 341 40 2241 0.0 4 666 285 282 346 662 41 2041 0.0 4 512 291 260 312 666 42 2161 0.0 4 619 283 258 335 666 43 1948 0.0 4 449 261 247 324 667 44 1987 0.0 4 588 275 256 314 554 45 1967 0.0 4 558 278 228 327 576 46 1794 0.0 4 607 254 213 283 437 47 1933 0.0 4 632 311 295 221 474 48 2119 0.0 4 755 408 356 296 304 49 4916 0.0 4 1461 1110 903 806 636 50 5146 0.0 5 1361 1044 802 788 608 543 51 3975 0.0 5 1470 790 601 468 344 302 52 3305 0.0 5 1337 648 486 373 268 193 53 2886 0.0 5 1208 576 399 302 242 159 54 2707 0.0 5 1290 506 332 252 183 144 55 2434 0.0 5 1219 460 280 209 149 117 56 2350 0.0 5 1217 439 250 194 138 112 57 2227 0.0 5 1235 411 226 147 115 93 58 2143 0.0 5 1243 357 221 150 100 72 59 1834 0.0 5 1033 324 179 132 106 60 60 1724 0.0 5 1013 292 167 115 81 56 61 1663 0.0 5 1030 264 139 98 83 49 62 1748 0.0 5 1109 286 163 83 52 55 63 1624 0.0 5 1010 289 141 96 59 29 64 1591 0.0 5 1029 267 114 90 55 36 65 1494 0.0 5 989 216 130 74 51 34 66 1428 0.0 5 986 212 106 59 43 22 67 1450 0.0 5 1025 195 86 65 40 39 68 1575 0.0 5 1147 214 106 39 45 24 69 1440 0.0 5 1021 192 101 66 39 21 70 1287 0.0 5 950 172 66 52 23 24 71 1204 0.0 5 872 164 71 46 28 23 72 1277 0.0 5 975 149 61 43 25 24 73 1162 0.0 5 893 121 72 31 24 21 74 1068 0.0 5 801 134 59 31 18 25 75 999 0.0 5 781 107 48 20 24 19 76 1043 0.0 5 829 107 40 26 26 15 77 1028 0.0 5 797 120 52 22 21 16 78 919 0.0 5 720 92 47 24 22 14 79 824 0.0 5 645 89 43 18 18 11 80 957 0.0 5 748 98 52 26 16 17 81 889 0.0 5 727 80 39 23 10 10 82 777 0.0 5 626 71 40 22 12 6 83 708 0.0 5 567 63 30 21 12 15 84 702 0.0 5 545 71 35 27 12 12 85 738 0.0 5 591 72 21 22 21 11 86 684 0.0 5 576 53 20 15 12 8 87 650 0.0 5 518 60 30 21 12 9 88 640 0.0 5 535 48 25 12 8 12 89 583 0.0 5 462 47 25 22 16 11 90 583 0.0 5 475 53 26 7 9 13 91 505 0.0 5 403 38 22 19 13 10 92 495 0.0 5 387 43 22 16 13 14 93 540 0.0 5 437 52 17 15 11 8 94 522 0.0 5 440 40 17 13 9 3 95 509 0.0 5 414 33 24 17 11 10 96 449 0.0 5 365 31 20 9 14 10 97 459 0.0 5 359 36 27 13 17 7 98 415 0.0 5 335 34 17 13 6 10 99 451 0.0 5 368 31 20 11 12 9 100 404 0.0 5 328 30 21 8 12 5 101 399 0.0 5 319 31 20 12 10 7 102 381 0.0 5 300 30 18 11 10 12 103 375 0.0 5 300 28 17 11 5 14 104 376 0.0 5 297 33 15 13 11 7 105 404 0.0 5 320 37 18 11 7 11 106 346 0.0 5 284 24 11 11 11 5 107 400 0.0 5 319 34 9 14 14 10 108 349 0.0 5 276 34 6 12 7 14 109 473 0.0 5 384 31 24 14 10 10 110 568 0.0 5 456 31 18 25 18 20 111 564 0.0 5 459 35 24 18 13 15 112 983 0.0 5 792 69 24 31 33 34 113 1309 0.0 5 1098 64 39 39 34 35 114 4066 0.0 5 3711 151 69 56 39 40 115 1831773 0.0 5 1831021 391 142 89 78 52 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_8_R2_val_2_val_2.fq.gz ============================================= 161309784 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 161309784 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1927048 (1.19%)