SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-169_S12_L002_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-169_S12_L002_R2_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 411.91 s (19 us/read; 3.18 M reads/minute). === Summary === Total reads processed: 21,849,611 Reads with adapters: 15,148,389 (69.3%) Reads written (passing filters): 21,849,611 (100.0%) Total basepairs processed: 2,179,085,176 bp Total written (filtered): 1,855,948,164 bp (85.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 15148389 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 35.9% C: 22.8% G: 10.0% T: 30.8% none/other: 0.5% Overview of removed sequences length count expect max.err error counts 1 5874903 5462402.8 0 5874903 2 200511 1365600.7 0 200511 3 163464 341400.2 0 163464 4 140402 85350.0 0 140402 5 139893 21337.5 0 139893 6 141505 5334.4 0 141505 7 138441 1333.6 0 138441 8 145834 333.4 0 145834 9 142309 83.3 0 141634 675 10 144848 20.8 1 140400 4448 11 136699 5.2 1 131250 5449 12 143099 1.3 1 137420 5679 13 137181 0.3 1 131980 5201 14 152833 0.3 1 146742 6091 15 142020 0.3 1 136420 5600 16 143810 0.3 1 138246 5564 17 152447 0.3 1 146552 5895 18 135894 0.3 1 130727 5167 19 145672 0.3 1 140162 5510 20 144022 0.3 1 138285 5737 21 149044 0.3 1 142759 6285 22 154652 0.3 1 148218 6434 23 148194 0.3 1 142233 5961 24 160644 0.3 1 153727 6917 25 141191 0.3 1 135511 5680 26 145503 0.3 1 138785 6718 27 149567 0.3 1 141888 7679 28 159035 0.3 1 152444 6591 29 153133 0.3 1 145895 7238 30 169047 0.3 1 162582 6465 31 146124 0.3 1 139725 6399 32 154883 0.3 1 149189 5694 33 165200 0.3 1 158027 7173 34 167347 0.3 1 159812 7535 35 162067 0.3 1 156482 5585 36 152029 0.3 1 145655 6374 37 156975 0.3 1 150888 6087 38 138292 0.3 1 132874 5418 39 145751 0.3 1 139959 5792 40 146164 0.3 1 140436 5728 41 147724 0.3 1 142707 5017 42 145393 0.3 1 140969 4424 43 126351 0.3 1 121534 4817 44 132379 0.3 1 127711 4668 45 174480 0.3 1 169492 4988 46 127193 0.3 1 123065 4128 47 91659 0.3 1 88127 3532 48 132541 0.3 1 128709 3832 49 93781 0.3 1 90629 3152 50 98686 0.3 1 95164 3522 51 140484 0.3 1 136846 3638 52 83709 0.3 1 80711 2998 53 86708 0.3 1 83588 3120 54 76999 0.3 1 74108 2891 55 92989 0.3 1 90104 2885 56 90043 0.3 1 86865 3178 57 83175 0.3 1 80202 2973 58 79827 0.3 1 77052 2775 59 76818 0.3 1 74048 2770 60 75005 0.3 1 72125 2880 61 74977 0.3 1 72126 2851 62 76690 0.3 1 73657 3033 63 76111 0.3 1 73174 2937 64 75306 0.3 1 72358 2948 65 78030 0.3 1 75039 2991 66 83493 0.3 1 79983 3510 67 109259 0.3 1 102576 6683 68 299307 0.3 1 292172 7135 69 99019 0.3 1 95468 3551 70 46975 0.3 1 44944 2031 71 27069 0.3 1 25589 1480 72 20646 0.3 1 19445 1201 73 16983 0.3 1 15844 1139 74 14209 0.3 1 13279 930 75 12031 0.3 1 11253 778 76 10633 0.3 1 9931 702 77 9617 0.3 1 8946 671 78 8436 0.3 1 7900 536 79 7349 0.3 1 6878 471 80 6052 0.3 1 5670 382 81 5024 0.3 1 4670 354 82 4166 0.3 1 3866 300 83 3315 0.3 1 3081 234 84 2715 0.3 1 2497 218 85 2020 0.3 1 1844 176 86 1425 0.3 1 1293 132 87 1219 0.3 1 1079 140 88 963 0.3 1 843 120 89 976 0.3 1 871 105 90 1128 0.3 1 1008 120 91 1470 0.3 1 1315 155 92 2099 0.3 1 1857 242 93 3969 0.3 1 3556 413 94 11125 0.3 1 10109 1016 95 19517 0.3 1 17801 1716 96 10658 0.3 1 9714 944 97 8606 0.3 1 7835 771 98 3455 0.3 1 3115 340 99 3533 0.3 1 3200 333 100 5505 0.3 1 4946 559 101 16736 0.3 1 14870 1866 RUN STATISTICS FOR INPUT FILE: EPI-169_S12_L002_R2_001.fastq.gz ============================================= 21849611 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 3049059 (14.0%) 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 (664649) or CGA (217263) in total: 881912 (4.0%) Total number of sequences analysed for the sequence pair length validation: 21849611 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 455655 (2.09%)