SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-200_S25_L003_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-200_S25_L003_R2_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 518.14 s (19 us/read; 3.23 M reads/minute). === Summary === Total reads processed: 27,883,056 Reads with adapters: 20,474,522 (73.4%) Reads written (passing filters): 27,883,056 (100.0%) Total basepairs processed: 2,739,407,094 bp Total written (filtered): 2,135,073,442 bp (77.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 20474522 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 32.4% C: 22.2% G: 14.5% T: 29.7% none/other: 1.2% Overview of removed sequences length count expect max.err error counts 1 6532203 6970764.0 0 6532203 2 225379 1742691.0 0 225379 3 195408 435672.8 0 195408 4 156137 108918.2 0 156137 5 159127 27229.5 0 159127 6 160234 6807.4 0 160234 7 155399 1701.8 0 155399 8 172977 425.5 0 172977 9 157743 106.4 0 157053 690 10 160523 26.6 1 155802 4721 11 152500 6.6 1 146379 6121 12 157149 1.7 1 151234 5915 13 151621 0.4 1 145943 5678 14 166588 0.4 1 160218 6370 15 159308 0.4 1 153406 5902 16 160981 0.4 1 155015 5966 17 169923 0.4 1 163858 6065 18 152796 0.4 1 147249 5547 19 162511 0.4 1 156693 5818 20 162675 0.4 1 156626 6049 21 167660 0.4 1 160792 6868 22 173825 0.4 1 167008 6817 23 168111 0.4 1 161684 6427 24 181998 0.4 1 174707 7291 25 164001 0.4 1 157761 6240 26 171198 0.4 1 163712 7486 27 177230 0.4 1 168634 8596 28 184046 0.4 1 176911 7135 29 180546 0.4 1 172480 8066 30 195286 0.4 1 188257 7029 31 172745 0.4 1 165749 6996 32 180578 0.4 1 174175 6403 33 193761 0.4 1 185927 7834 34 201168 0.4 1 192411 8757 35 189111 0.4 1 182948 6163 36 189594 0.4 1 182157 7437 37 190030 0.4 1 183018 7012 38 174462 0.4 1 167787 6675 39 183209 0.4 1 176227 6982 40 183906 0.4 1 176681 7225 41 185051 0.4 1 178579 6472 42 183560 0.4 1 177735 5825 43 169361 0.4 1 163103 6258 44 175270 0.4 1 169212 6058 45 222583 0.4 1 215828 6755 46 174867 0.4 1 168962 5905 47 130889 0.4 1 125990 4899 48 181431 0.4 1 175880 5551 49 134444 0.4 1 129935 4509 50 140723 0.4 1 135870 4853 51 195590 0.4 1 190346 5244 52 124955 0.4 1 120529 4426 53 132657 0.4 1 128390 4267 54 118048 0.4 1 114129 3919 55 143427 0.4 1 139149 4278 56 138526 0.4 1 134032 4494 57 130226 0.4 1 126136 4090 58 127981 0.4 1 124030 3951 59 123093 0.4 1 118912 4181 60 121118 0.4 1 117027 4091 61 120770 0.4 1 116536 4234 62 124599 0.4 1 120198 4401 63 127882 0.4 1 123325 4557 64 130175 0.4 1 125277 4898 65 143185 0.4 1 137473 5712 66 164641 0.4 1 157506 7135 67 273256 0.4 1 251345 21911 68 1154348 0.4 1 1125480 28868 69 430444 0.4 1 416026 14418 70 222164 0.4 1 214264 7900 71 116120 0.4 1 111140 4980 72 78601 0.4 1 75090 3511 73 54066 0.4 1 51389 2677 74 42699 0.4 1 40351 2348 75 35345 0.4 1 33406 1939 76 30396 0.4 1 28671 1725 77 27095 0.4 1 25514 1581 78 24030 0.4 1 22640 1390 79 21351 0.4 1 20028 1323 80 18244 0.4 1 17147 1097 81 15500 0.4 1 14548 952 82 13580 0.4 1 12740 840 83 11493 0.4 1 10705 788 84 9834 0.4 1 9129 705 85 7987 0.4 1 7411 576 86 7228 0.4 1 6674 554 87 6851 0.4 1 6249 602 88 6811 0.4 1 6240 571 89 7467 0.4 1 6781 686 90 9441 0.4 1 8600 841 91 12571 0.4 1 11502 1069 92 18843 0.4 1 17302 1541 93 40413 0.4 1 37313 3100 94 119490 0.4 1 111344 8146 95 209944 0.4 1 196046 13898 96 90833 0.4 1 84802 6031 97 63109 0.4 1 58929 4180 98 26253 0.4 1 24471 1782 99 27079 0.4 1 25134 1945 100 29087 0.4 1 27001 2086 101 53850 0.4 1 48953 4897 RUN STATISTICS FOR INPUT FILE: EPI-200_S25_L003_R2_001.fastq.gz ============================================= 27883056 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 5292548 (19.0%) 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: 27883056 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 2782361 (9.98%)