SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/Downloads/zr2096/Raw_data/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 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 TGGAATTCTCGG /home/sam/Downloads/zr2096/Raw_data/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 635.85 s (19 us/read; 3.08 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: /home/sam/Downloads/zr2096/Raw_data/zr2096_9_s1_R1.fastq.gz ============================================= 32636231 sequences processed in total