SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_4_R1_val_1_val_1.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_R1_val_1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 4467.36 s (23 µs/read; 2.66 M reads/minute). === Summary === Total reads processed: 197,822,142 Reads with adapters: 21,373,406 (10.8%) Reads written (passing filters): 197,822,142 (100.0%) Total basepairs processed: 19,209,489,295 bp Quality-trimmed: 3,593,209 bp (0.0%) Total written (filtered): 18,997,290,406 bp (98.9%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 21373406 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: 22.0% C: 5.0% G: 0.0% T: 73.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 13485831 49455535.5 0 13485831 2 4067387 12363883.9 0 4067387 3 882409 3090971.0 0 882409 4 254872 772742.7 0 254872 5 75779 193185.7 0 75779 6 22085 48296.4 0 22085 7 9677 12074.1 0 9677 8 6853 3018.5 0 6853 9 6827 754.6 0 6827 10 12720 188.7 1 6450 6270 11 10888 47.2 1 5671 5217 12 9323 11.8 1 4929 4394 13 8458 2.9 1 4556 3902 14 7529 0.7 1 4004 3525 15 6746 0.2 1 3631 3115 16 5766 0.0 1 3241 2525 17 4821 0.0 1 2682 2139 18 3902 0.0 1 2520 1382 19 3556 0.0 1 2302 1254 20 5372 0.0 2 2427 1194 1751 21 4669 0.0 2 2220 1057 1392 22 4499 0.0 2 2227 991 1281 23 4267 0.0 2 2123 993 1151 24 4214 0.0 2 2090 1033 1091 25 3743 0.0 2 1875 930 938 26 3303 0.0 2 1666 855 782 27 3257 0.0 2 1753 740 764 28 2989 0.0 2 1680 760 549 29 2825 0.0 2 1611 708 506 30 3334 0.0 3 1430 679 520 705 31 3407 0.0 3 1494 697 506 710 32 3435 0.0 3 1492 689 552 702 33 3310 0.0 3 1423 675 552 660 34 3155 0.0 3 1370 667 528 590 35 3028 0.0 3 1323 638 498 569 36 2910 0.0 3 1303 647 463 497 37 2833 0.0 3 1250 647 419 517 38 2746 0.0 3 1352 657 418 319 39 2696 0.0 3 1315 626 399 356 40 3077 0.0 4 1187 613 391 362 524 41 3176 0.0 4 1271 628 426 367 484 42 3037 0.0 4 1179 582 382 357 537 43 3063 0.0 4 1216 630 384 327 506 44 2911 0.0 4 1180 564 380 337 450 45 2820 0.0 4 1175 548 401 321 375 46 2771 0.0 4 1201 564 338 286 382 47 2786 0.0 4 1200 647 377 269 293 48 3099 0.0 4 1396 651 456 345 251 49 5860 0.0 4 2520 1306 889 662 483 50 6145 0.0 5 2495 1308 835 640 478 389 51 4637 0.0 5 2526 851 516 343 226 175 52 4015 0.0 5 2360 697 416 249 173 120 53 3730 0.0 5 2301 638 341 204 144 102 54 3634 0.0 5 2355 630 288 173 104 84 55 3463 0.0 5 2325 529 278 160 107 64 56 3460 0.0 5 2443 489 228 157 88 55 57 3797 0.0 5 2800 463 245 141 86 62 58 4018 0.0 5 3150 410 211 118 72 57 59 3950 0.0 5 3147 402 171 99 86 45 60 2713 0.0 5 1972 376 172 78 68 47 61 2824 0.0 5 2134 362 148 87 54 39 62 3006 0.0 5 2381 332 148 71 51 23 63 3731 0.0 5 3126 328 120 86 48 23 64 4553 0.0 5 3934 333 116 83 59 28 65 2834 0.0 5 2186 319 174 84 39 32 66 3268 0.0 5 2630 353 147 80 33 25 67 2811 0.0 5 2183 343 150 68 41 26 68 3220 0.0 5 2627 329 132 66 45 21 69 3876 0.0 5 3306 343 111 56 41 19 70 7126 0.0 5 6537 371 107 59 32 20 71 17595 0.0 5 17045 333 109 48 41 19 72 97387 0.0 5 96737 428 103 59 34 26 73 201695 0.0 5 201076 384 120 70 27 18 74 1277550 0.0 5 1276974 365 105 55 31 20 75 59639 0.0 5 59128 274 110 63 33 31 76 53289 0.0 5 52818 263 112 46 32 18 77 259250 0.0 5 258872 195 80 54 27 22 78 26245 0.0 5 25834 217 91 50 37 16 79 147142 0.0 5 146785 166 90 44 35 22 80 33506 0.0 5 33118 195 86 63 18 26 81 20536 0.0 5 20146 189 87 59 35 20 82 52938 0.0 5 52648 150 62 47 19 12 83 8773 0.0 5 8430 167 84 49 23 20 84 28873 0.0 5 28554 180 62 37 27 13 85 7709 0.0 5 7426 133 58 54 25 13 86 1268 0.0 5 1014 113 75 27 19 20 87 999 0.0 5 745 123 59 35 17 20 88 836 0.0 5 604 102 58 26 21 25 89 833 0.0 5 614 107 50 28 16 18 90 842 0.0 5 598 118 53 31 23 19 91 791 0.0 5 560 98 53 40 26 14 92 674 0.0 5 500 80 43 26 16 9 93 663 0.0 5 490 74 47 25 13 14 94 610 0.0 5 446 74 39 21 17 13 95 568 0.0 5 411 64 34 22 18 19 96 495 0.0 5 349 63 30 21 20 12 97 461 0.0 5 328 50 27 28 13 15 98 452 0.0 5 329 50 32 14 13 14 99 375 0.0 5 265 48 19 24 10 9 100 399 0.0 5 280 51 30 8 22 8 101 274 0.0 5 195 32 19 15 6 7 102 290 0.0 5 210 31 17 12 4 16 103 233 0.0 5 160 21 18 13 11 10 104 188 0.0 5 120 30 12 9 10 7 105 182 0.0 5 126 27 7 8 5 9 106 146 0.0 5 103 11 12 12 3 5 107 123 0.0 5 83 15 6 5 7 7 108 117 0.0 5 82 12 7 4 7 5 109 88 0.0 5 67 7 7 4 3 110 76 0.0 5 56 4 6 4 3 3 111 88 0.0 5 72 7 2 3 1 3 112 70 0.0 5 55 6 1 2 5 1 113 49 0.0 5 32 5 3 4 2 3 114 46 0.0 5 37 2 3 0 1 3 115 211 0.0 5 202 5 1 3 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_4_R1_val_1_val_1.fq.gz ============================================= 197822142 sequences processed in total