SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-136_S36_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 File was specified to be a non-directional MspI-digested RRBS sample. Sequences starting with either 'CAA' or 'CGA' will have the first 2 bp trimmed off to remove potential methylation-biased bases from the end-repair reaction Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /home/sam/data/geoduck_EPI/20180514_geoduck_trimgalore_rrbs/20180514_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/20180514_geoduck_trimgalore_rrbs/EPI-136_S36_L005_R2_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 533.21 s (19 us/read; 3.14 M reads/minute). === Summary === Total reads processed: 27,877,100 Reads with adapters: 18,235,204 (65.4%) Reads written (passing filters): 27,877,100 (100.0%) Total basepairs processed: 2,791,944,028 bp Total written (filtered): 2,500,528,990 bp (89.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 18235204 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 37.8% C: 25.8% G: 8.1% T: 28.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 8830708 6969275.0 0 8830708 2 223620 1742318.8 0 223620 3 222819 435579.7 0 222819 4 171586 108894.9 0 171586 5 178207 27223.7 0 178207 6 184291 6805.9 0 184291 7 177176 1701.5 0 177176 8 243550 425.4 0 243550 9 166885 106.3 0 166239 646 10 164528 26.6 1 158546 5982 11 162059 6.6 1 153810 8249 12 161648 1.7 1 154291 7357 13 157259 0.4 1 149832 7427 14 176096 0.4 1 167890 8206 15 161318 0.4 1 153689 7629 16 165648 0.4 1 157868 7780 17 176379 0.4 1 168490 7889 18 150377 0.4 1 143355 7022 19 161766 0.4 1 154763 7003 20 157269 0.4 1 149555 7714 21 168485 0.4 1 159353 9132 22 173935 0.4 1 165331 8604 23 164041 0.4 1 156338 7703 24 177570 0.4 1 169449 8121 25 152221 0.4 1 144997 7224 26 162098 0.4 1 153065 9033 27 171605 0.4 1 160984 10621 28 171813 0.4 1 163977 7836 29 170374 0.4 1 160337 10037 30 187363 0.4 1 179436 7927 31 155123 0.4 1 147109 8014 32 163663 0.4 1 157193 6470 33 173247 0.4 1 164629 8618 34 183693 0.4 1 173704 9989 35 164322 0.4 1 158176 6146 36 158088 0.4 1 149952 8136 37 149474 0.4 1 142475 6999 38 139192 0.4 1 132415 6777 39 143749 0.4 1 136504 7245 40 145519 0.4 1 138251 7268 41 140810 0.4 1 134948 5862 42 150551 0.4 1 145244 5307 43 120653 0.4 1 114731 5922 44 132545 0.4 1 126808 5737 45 196999 0.4 1 190839 6160 46 118182 0.4 1 113102 5080 47 79736 0.4 1 75384 4352 48 132135 0.4 1 127680 4455 49 75444 0.4 1 72034 3410 50 87410 0.4 1 83190 4220 51 136170 0.4 1 132113 4057 52 66357 0.4 1 63035 3322 53 75959 0.4 1 72317 3642 54 65006 0.4 1 61788 3218 55 86638 0.4 1 83064 3574 56 81679 0.4 1 77850 3829 57 73982 0.4 1 70748 3234 58 71608 0.4 1 68565 3043 59 66500 0.4 1 63345 3155 60 66875 0.4 1 63624 3251 61 67272 0.4 1 64153 3119 62 69714 0.4 1 66454 3260 63 71148 0.4 1 67870 3278 64 70123 0.4 1 67053 3070 65 69904 0.4 1 66807 3097 66 69345 0.4 1 66362 2983 67 72243 0.4 1 68843 3400 68 129450 0.4 1 126200 3250 69 40640 0.4 1 38975 1665 70 19901 0.4 1 18817 1084 71 12711 0.4 1 11872 839 72 9880 0.4 1 9208 672 73 8188 0.4 1 7601 587 74 6707 0.4 1 6229 478 75 5414 0.4 1 5052 362 76 4438 0.4 1 4128 310 77 3509 0.4 1 3230 279 78 2751 0.4 1 2568 183 79 2172 0.4 1 2011 161 80 1450 0.4 1 1344 106 81 1052 0.4 1 972 80 82 739 0.4 1 679 60 83 447 0.4 1 415 32 84 264 0.4 1 236 28 85 153 0.4 1 145 8 86 82 0.4 1 78 4 87 62 0.4 1 59 3 88 26 0.4 1 24 2 89 33 0.4 1 27 6 90 30 0.4 1 25 5 91 55 0.4 1 50 5 92 77 0.4 1 68 9 93 96 0.4 1 84 12 94 197 0.4 1 176 21 95 277 0.4 1 245 32 96 284 0.4 1 263 21 97 145 0.4 1 133 12 98 43 0.4 1 39 4 99 31 0.4 1 29 2 100 30 0.4 1 30 101 118 0.4 1 108 10 RUN STATISTICS FOR INPUT FILE: EPI-136_S36_L005_R2_001.fastq.gz ============================================= 27877100 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 3635713 (13.0%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 0 (0.0%) RRBS reads trimmed by 2 bp at the start when read started with CAA (933804) or CGA (266820) in total: 1200624 (4.3%) Total number of sequences analysed for the sequence pair length validation: 27877100 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 83484 (0.30%)