SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/owl/nightingales/C_virginica/zr2096_9_s1_R1.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 TGGAATTCTCGG /mnt/owl/nightingales/C_virginica/zr2096_9_s1_R1.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 642.13 s (20 us/read; 3.05 M reads/minute). === Summary === Total reads processed: 32,636,231 Reads with adapters: 15,181,617 (46.5%) Reads written (passing filters): 32,636,231 (100.0%) Total basepairs processed: 2,952,817,074 bp Quality-trimmed: 17,135,297 bp (0.6%) Total written (filtered): 2,891,237,315 bp (97.9%) === Adapter 1 === Sequence: TGGAATTCTCGG; Type: regular 3'; Length: 12; Trimmed: 15181617 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 26.0% C: 6.0% G: 22.4% T: 45.5% none/other: 0.2% Overview of removed sequences length count expect max.err error counts 1 12610638 8159057.8 0 12610638 2 1442340 2039764.4 0 1442340 3 531582 509941.1 0 531582 4 95137 127485.3 0 95137 5 35022 31871.3 0 35022 6 11761 7967.8 0 11761 7 6641 1992.0 0 6641 8 1081 498.0 0 1081 9 2380 124.5 0 2305 75 10 1336 31.1 1 897 439 11 1745 7.8 1 1391 354 12 464 1.9 1 241 223 13 1464 1.9 1 1054 410 14 508 1.9 1 228 280 15 1090 1.9 1 796 294 16 962 1.9 1 711 251 17 1476 1.9 1 1169 307 18 3269 1.9 1 2621 648 19 3998 1.9 1 3572 426 20 423 1.9 1 252 171 21 493 1.9 1 318 175 22 2707 1.9 1 2170 537 23 2340 1.9 1 1750 590 24 2586 1.9 1 2161 425 25 3670 1.9 1 3027 643 26 3551 1.9 1 2959 592 27 6851 1.9 1 6173 678 28 1153 1.9 1 772 381 29 2511 1.9 1 2048 463 30 2927 1.9 1 2245 682 31 3450 1.9 1 2950 500 32 4151 1.9 1 3421 730 33 3883 1.9 1 3329 554 34 5455 1.9 1 4701 754 35 4551 1.9 1 3668 883 36 15556 1.9 1 14504 1052 37 5218 1.9 1 4226 992 38 1382 1.9 1 968 414 39 2005 1.9 1 1538 467 40 2134 1.9 1 1678 456 41 3177 1.9 1 2743 434 42 2756 1.9 1 2374 382 43 2439 1.9 1 1907 532 44 5256 1.9 1 4860 396 45 3203 1.9 1 2660 543 46 7760 1.9 1 6708 1052 47 3548 1.9 1 2577 971 48 2942 1.9 1 2300 642 49 4983 1.9 1 4301 682 50 2454 1.9 1 1884 570 51 2575 1.9 1 2199 376 52 4678 1.9 1 4039 639 53 5046 1.9 1 4260 786 54 5081 1.9 1 4280 801 55 10370 1.9 1 9056 1314 56 8327 1.9 1 7346 981 57 3350 1.9 1 2716 634 58 3749 1.9 1 3200 549 59 4206 1.9 1 3503 703 60 10467 1.9 1 9588 879 61 5606 1.9 1 4394 1212 62 1447 1.9 1 1057 390 63 3144 1.9 1 2726 418 64 5419 1.9 1 4605 814 65 5300 1.9 1 4334 966 66 7570 1.9 1 6299 1271 67 9742 1.9 1 8095 1647 68 19843 1.9 1 17495 2348 69 8801 1.9 1 7537 1264 70 10433 1.9 1 9064 1369 71 19008 1.9 1 17361 1647 72 28936 1.9 1 26955 1981 73 24996 1.9 1 23010 1986 74 15927 1.9 1 14436 1491 75 10243 1.9 1 8965 1278 76 7940 1.9 1 6579 1361 77 7489 1.9 1 5918 1571 78 7812 1.9 1 5946 1866 79 7893 1.9 1 5904 1989 80 7580 1.9 1 5724 1856 81 6541 1.9 1 4992 1549 82 3574 1.9 1 2676 898 83 1916 1.9 1 1402 514 84 1792 1.9 1 1292 500 85 1878 1.9 1 1305 573 86 2019 1.9 1 1473 546 87 1878 1.9 1 1336 542 88 1652 1.9 1 1159 493 89 1526 1.9 1 1090 436 90 1545 1.9 1 1095 450 91 1490 1.9 1 1019 471 92 1360 1.9 1 965 395 93 1277 1.9 1 935 342 94 1308 1.9 1 909 399 95 1273 1.9 1 856 417 96 1326 1.9 1 913 413 97 1583 1.9 1 1056 527 98 1441 1.9 1 969 472 99 2067 1.9 1 1410 657 100 2784 1.9 1 1990 794 RUN STATISTICS FOR INPUT FILE: /mnt/owl/nightingales/C_virginica/zr2096_9_s1_R1.fastq.gz ============================================= 32636231 sequences processed in total