SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-103_S27_L005_R2_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.9.1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp File was specified to be an MspI-digested RRBS sample. Read 1 sequences with adapter contamination will be trimmed a further 2 bp from their 3' end, and Read 2 sequences will be trimmed by 2 bp from their 5' end to remove potential methylation-biased bases from the end-repair reaction All Read 2 sequences will be trimmed by 2 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /home/sam/data/geoduck_EPI/20180516_geoduck_trimgalore_rrbs/20180516_geoduck_trimmed_fastqc --threads 16 Output file will be GZIP compressed This is cutadapt 1.9.1 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -O 1 -a AGATCGGAAGAGC /home/sam/data/geoduck_EPI/20180516_geoduck_trimgalore_rrbs/EPI-103_S27_L005_R2_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 394.49 s (19 us/read; 3.11 M reads/minute). === Summary === Total reads processed: 20,420,261 Reads with adapters: 12,148,428 (59.5%) Reads written (passing filters): 20,420,261 (100.0%) Total basepairs processed: 2,046,731,649 bp Total written (filtered): 1,922,510,622 bp (93.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 12148428 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 40.5% C: 24.3% G: 6.2% T: 29.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 7615522 5105065.2 0 7615522 2 156088 1276266.3 0 156088 3 142929 319066.6 0 142929 4 112165 79766.6 0 112165 5 114907 19941.7 0 114907 6 120133 4985.4 0 120133 7 113434 1246.4 0 113434 8 149954 311.6 0 149954 9 106498 77.9 0 106050 448 10 103617 19.5 1 99671 3946 11 99440 4.9 1 94360 5080 12 98688 1.2 1 93968 4720 13 93937 0.3 1 89334 4603 14 104436 0.3 1 99267 5169 15 93846 0.3 1 89181 4665 16 95720 0.3 1 90978 4742 17 102660 0.3 1 97875 4785 18 84709 0.3 1 80452 4257 19 90844 0.3 1 86508 4336 20 85337 0.3 1 81119 4218 21 90486 0.3 1 85508 4978 22 90660 0.3 1 85954 4706 23 85854 0.3 1 81574 4280 24 91736 0.3 1 87241 4495 25 75307 0.3 1 71549 3758 26 78986 0.3 1 74510 4476 27 80970 0.3 1 75748 5222 28 82783 0.3 1 78843 3940 29 77865 0.3 1 73021 4844 30 87301 0.3 1 83499 3802 31 69645 0.3 1 65899 3746 32 75320 0.3 1 72173 3147 33 76984 0.3 1 72990 3994 34 78365 0.3 1 73880 4485 35 72496 0.3 1 69700 2796 36 65080 0.3 1 61658 3422 37 61694 0.3 1 58485 3209 38 55831 0.3 1 52992 2839 39 56581 0.3 1 53610 2971 40 56009 0.3 1 53110 2899 41 55086 0.3 1 52630 2456 42 59200 0.3 1 57077 2123 43 44458 0.3 1 42120 2338 44 48971 0.3 1 46748 2223 45 73709 0.3 1 71380 2329 46 41539 0.3 1 39617 1922 47 26482 0.3 1 24884 1598 48 47529 0.3 1 45810 1719 49 25518 0.3 1 24295 1223 50 29159 0.3 1 27660 1499 51 47154 0.3 1 45608 1546 52 22021 0.3 1 20888 1133 53 24448 0.3 1 23150 1298 54 20732 0.3 1 19645 1087 55 27876 0.3 1 26660 1216 56 26476 0.3 1 25092 1384 57 23846 0.3 1 22663 1183 58 23343 0.3 1 22239 1104 59 21714 0.3 1 20629 1085 60 21553 0.3 1 20419 1134 61 21625 0.3 1 20540 1085 62 22433 0.3 1 21272 1161 63 22522 0.3 1 21440 1082 64 22371 0.3 1 21234 1137 65 22367 0.3 1 21301 1066 66 21985 0.3 1 20946 1039 67 23677 0.3 1 22475 1202 68 42865 0.3 1 41698 1167 69 13316 0.3 1 12645 671 70 6610 0.3 1 6143 467 71 4387 0.3 1 4027 360 72 3408 0.3 1 3161 247 73 2853 0.3 1 2613 240 74 2447 0.3 1 2266 181 75 1965 0.3 1 1810 155 76 1583 0.3 1 1442 141 77 1295 0.3 1 1193 102 78 1024 0.3 1 939 85 79 788 0.3 1 717 71 80 528 0.3 1 490 38 81 404 0.3 1 368 36 82 280 0.3 1 250 30 83 178 0.3 1 163 15 84 126 0.3 1 111 15 85 86 0.3 1 74 12 86 39 0.3 1 33 6 87 48 0.3 1 39 9 88 35 0.3 1 26 9 89 25 0.3 1 22 3 90 44 0.3 1 42 2 91 56 0.3 1 42 14 92 102 0.3 1 83 19 93 124 0.3 1 100 24 94 238 0.3 1 208 30 95 306 0.3 1 268 38 96 303 0.3 1 262 41 97 138 0.3 1 121 17 98 48 0.3 1 42 6 99 22 0.3 1 20 2 100 37 0.3 1 31 6 101 109 0.3 1 89 20 RUN STATISTICS FOR INPUT FILE: EPI-103_S27_L005_R2_001.fastq.gz ============================================= 20420261 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 2250578 (11.0%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 0 (0.0%) Total number of sequences analysed for the sequence pair length validation: 20420261 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 70602 (0.35%)