SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-42_S39_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-42_S39_L005_R2_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 572.09 s (19 us/read; 3.15 M reads/minute). === Summary === Total reads processed: 30,041,436 Reads with adapters: 20,795,246 (69.2%) Reads written (passing filters): 30,041,436 (100.0%) Total basepairs processed: 2,997,554,126 bp Total written (filtered): 2,540,344,516 bp (84.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 20795246 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 35.7% C: 23.6% G: 9.3% T: 31.1% none/other: 0.3% Overview of removed sequences length count expect max.err error counts 1 8136675 7510359.0 0 8136675 2 251809 1877589.8 0 251809 3 230932 469397.4 0 230932 4 181015 117349.4 0 181015 5 186864 29337.3 0 186864 6 183967 7334.3 0 183967 7 177624 1833.6 0 177624 8 183343 458.4 0 183343 9 178845 114.6 0 178222 623 10 189141 28.6 1 181854 7287 11 175298 7.2 1 166402 8896 12 183586 1.8 1 174990 8596 13 174337 0.4 1 166139 8198 14 196405 0.4 1 187207 9198 15 181417 0.4 1 173210 8207 16 186101 0.4 1 177957 8144 17 196591 0.4 1 188099 8492 18 170641 0.4 1 163199 7442 19 183929 0.4 1 175883 8046 20 183745 0.4 1 175351 8394 21 188399 0.4 1 178962 9437 22 198395 0.4 1 188822 9573 23 189859 0.4 1 181499 8360 24 208299 0.4 1 198915 9384 25 181384 0.4 1 173214 8170 26 188247 0.4 1 178567 9680 27 196730 0.4 1 185317 11413 28 207628 0.4 1 198298 9330 29 197454 0.4 1 186515 10939 30 224209 0.4 1 214780 9429 31 188845 0.4 1 179382 9463 32 200318 0.4 1 192436 7882 33 215998 0.4 1 205431 10567 34 220950 0.4 1 209377 11573 35 212011 0.4 1 204273 7738 36 200582 0.4 1 190998 9584 37 200374 0.4 1 191398 8976 38 181260 0.4 1 173107 8153 39 191952 0.4 1 183040 8912 40 190909 0.4 1 182087 8822 41 194772 0.4 1 187250 7522 42 195555 0.4 1 188935 6620 43 167355 0.4 1 159901 7454 44 179529 0.4 1 172248 7281 45 245723 0.4 1 237849 7874 46 175212 0.4 1 168187 7025 47 122362 0.4 1 116622 5740 48 187347 0.4 1 180694 6653 49 127861 0.4 1 122635 5226 50 136692 0.4 1 130717 5975 51 206009 0.4 1 199505 6504 52 120762 0.4 1 115609 5153 53 125924 0.4 1 120244 5680 54 111678 0.4 1 106624 5054 55 144675 0.4 1 139144 5531 56 136968 0.4 1 131145 5823 57 128391 0.4 1 123278 5113 58 129921 0.4 1 124971 4950 59 123007 0.4 1 117818 5189 60 121787 0.4 1 116631 5156 61 124526 0.4 1 119208 5318 62 129625 0.4 1 123889 5736 63 132623 0.4 1 126952 5671 64 132349 0.4 1 126447 5902 65 139096 0.4 1 133237 5859 66 146035 0.4 1 139623 6412 67 181569 0.4 1 171576 9993 68 440815 0.4 1 429177 11638 69 157089 0.4 1 150867 6222 70 73617 0.4 1 69753 3864 71 45539 0.4 1 42636 2903 72 36979 0.4 1 34398 2581 73 32199 0.4 1 29940 2259 74 27493 0.4 1 25611 1882 75 24085 0.4 1 22355 1730 76 22046 0.4 1 20468 1578 77 20197 0.4 1 18715 1482 78 17557 0.4 1 16188 1369 79 15214 0.4 1 14054 1160 80 12541 0.4 1 11577 964 81 10613 0.4 1 9782 831 82 8104 0.4 1 7536 568 83 6403 0.4 1 5903 500 84 4716 0.4 1 4340 376 85 3171 0.4 1 2905 266 86 2007 0.4 1 1836 171 87 1400 0.4 1 1261 139 88 804 0.4 1 700 104 89 702 0.4 1 606 96 90 770 0.4 1 674 96 91 950 0.4 1 804 146 92 1352 0.4 1 1146 206 93 2171 0.4 1 1866 305 94 5407 0.4 1 4716 691 95 8719 0.4 1 7689 1030 96 5937 0.4 1 5218 719 97 4538 0.4 1 3972 566 98 1758 0.4 1 1529 229 99 1273 0.4 1 1086 187 100 2477 0.4 1 2007 470 101 13182 0.4 1 10971 2211 RUN STATISTICS FOR INPUT FILE: EPI-42_S39_L005_R2_001.fastq.gz ============================================= 30041436 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 4758616 (15.8%) 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 (937821) or CGA (340816) in total: 1278637 (4.3%) Total number of sequences analysed for the sequence pair length validation: 30041436 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 415630 (1.38%)