SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/owl/nightingales/C_virginica/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 Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /home/sam/20180409_trimgalore_autotrim_Cvirginica_MBD/20180409_fastqc_trimgalore_autotrim_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 /mnt/owl/nightingales/C_virginica/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 589.50 s (18 us/read; 3.32 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: /mnt/owl/nightingales/C_virginica/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): 206893 (0.63%)