SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/Downloads/zr2096/Raw_data/zr2096_9_s1_R2.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'TGGAATTCTCGG' (Illumina small RNA adapter; auto-detected) Maximum trimming error rate: 0.1 (default) Optional adapter 2 sequence (only used for read 2 of paired-end files): 'GATCGTCGGACT' Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 18 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir ~/Downloads/20180411_trimgalore_10bp_Cvirginica_MBD/20180411_fastqc_trim_10bp_Cvirginica_MBD --threads 18 Output file will be GZIP compressed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a GATCGTCGGACT /home/sam/Downloads/zr2096/Raw_data/zr2096_9_s1_R2.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 590.96 s (18 us/read; 3.31 M reads/minute). === Summary === Total reads processed: 32,636,231 Reads with adapters: 6,933,718 (21.2%) Reads written (passing filters): 32,636,231 (100.0%) Total basepairs processed: 2,953,164,569 bp Quality-trimmed: 15,971,942 bp (0.5%) Total written (filtered): 2,909,626,875 bp (98.5%) === Adapter 1 === Sequence: GATCGTCGGACT; Type: regular 3'; Length: 12; Trimmed: 6933718 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 21.9% C: 15.5% G: 32.2% T: 30.2% none/other: 0.3% Overview of removed sequences length count expect max.err error counts 1 4900033 8159057.8 0 4900033 2 1191999 2039764.4 0 1191999 3 470362 509941.1 0 470362 4 21023 127485.3 0 21023 5 12967 31871.3 0 12967 6 7282 7967.8 0 7282 7 1811 1992.0 0 1811 8 435 498.0 0 435 9 481 124.5 0 198 283 10 1434 31.1 1 782 652 11 1674 7.8 1 1367 307 12 213 1.9 1 106 107 13 694 1.9 1 511 183 14 2537 1.9 1 1999 538 15 316 1.9 1 164 152 16 213 1.9 1 97 116 17 1642 1.9 1 1247 395 18 1903 1.9 1 1461 442 19 1281 1.9 1 921 360 20 3271 1.9 1 2708 563 21 3897 1.9 1 3346 551 22 468 1.9 1 255 213 23 387 1.9 1 228 159 24 3004 1.9 1 2368 636 25 5277 1.9 1 4575 702 26 648 1.9 1 405 243 27 5067 1.9 1 4503 564 28 938 1.9 1 574 364 29 2100 1.9 1 1610 490 30 13896 1.9 1 12017 1879 31 647 1.9 1 314 333 32 345 1.9 1 176 169 33 698 1.9 1 395 303 34 1142 1.9 1 653 489 35 3037 1.9 1 2327 710 36 9549 1.9 1 8468 1081 37 3124 1.9 1 2736 388 38 1105 1.9 1 759 346 39 4549 1.9 1 3948 601 40 4610 1.9 1 4139 471 41 654 1.9 1 426 228 42 2179 1.9 1 1700 479 43 6444 1.9 1 5773 671 44 562 1.9 1 400 162 45 2238 1.9 1 1894 344 46 6367 1.9 1 5909 458 47 390 1.9 1 259 131 48 1800 1.9 1 1528 272 49 2601 1.9 1 2186 415 50 1731 1.9 1 1354 377 51 2961 1.9 1 2546 415 52 2473 1.9 1 2039 434 53 3086 1.9 1 2521 565 54 3482 1.9 1 2740 742 55 6328 1.9 1 5447 881 56 5780 1.9 1 4872 908 57 3575 1.9 1 2861 714 58 4364 1.9 1 3506 858 59 3677 1.9 1 2728 949 60 7389 1.9 1 6051 1338 61 6585 1.9 1 5394 1191 62 6101 1.9 1 4946 1155 63 9196 1.9 1 7785 1411 64 28226 1.9 1 26305 1921 65 25732 1.9 1 24150 1582 66 14246 1.9 1 13037 1209 67 9091 1.9 1 7832 1259 68 7572 1.9 1 6223 1349 69 3523 1.9 1 2800 723 70 2859 1.9 1 2152 707 71 2576 1.9 1 1839 737 72 2588 1.9 1 1806 782 73 2465 1.9 1 1682 783 74 2652 1.9 1 1780 872 75 2849 1.9 1 1849 1000 76 3382 1.9 1 2131 1251 77 4110 1.9 1 2610 1500 78 4963 1.9 1 3113 1850 79 4818 1.9 1 3134 1684 80 4781 1.9 1 3026 1755 81 4149 1.9 1 2674 1475 82 2282 1.9 1 1452 830 83 1393 1.9 1 884 509 84 1336 1.9 1 836 500 85 1386 1.9 1 855 531 86 1574 1.9 1 1033 541 87 1509 1.9 1 996 513 88 1306 1.9 1 831 475 89 1136 1.9 1 753 383 90 1152 1.9 1 716 436 91 1120 1.9 1 671 449 92 1002 1.9 1 606 396 93 932 1.9 1 556 376 94 965 1.9 1 599 366 95 972 1.9 1 581 391 96 1081 1.9 1 649 432 97 1225 1.9 1 747 478 98 1239 1.9 1 691 548 99 2175 1.9 1 1245 930 100 3329 1.9 1 2050 1279 RUN STATISTICS FOR INPUT FILE: /home/sam/Downloads/zr2096/Raw_data/zr2096_9_s1_R2.fastq.gz ============================================= 32636231 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 32636231 Number of sequence pairs removed because at least one read was shorter than the length cutoff (18 bp): 788690 (2.42%)