SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-145_S38_L005_R1_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-145_S38_L005_R1_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 492.85 s (19 us/read; 3.11 M reads/minute). === Summary === Total reads processed: 25,512,585 Reads with adapters: 13,462,867 (52.8%) Reads written (passing filters): 25,512,585 (100.0%) Total basepairs processed: 2,565,582,121 bp Total written (filtered): 2,360,157,346 bp (92.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 13462867 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 26.5% C: 6.9% G: 24.0% T: 42.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 5384149 6378146.2 0 5384149 2 1237292 1594536.6 0 1237292 3 477009 398634.1 0 477009 4 309917 99658.5 0 309917 5 137040 24914.6 0 137040 6 141942 6228.7 0 141942 7 136148 1557.2 0 136148 8 171177 389.3 0 171177 9 135399 97.3 0 133468 1931 10 133448 24.3 1 126740 6708 11 130125 6.1 1 122855 7270 12 125898 1.5 1 118969 6929 13 116678 0.4 1 110165 6513 14 132694 0.4 1 124241 8453 15 124998 0.4 1 117617 7381 16 132595 0.4 1 124021 8574 17 123113 0.4 1 115921 7192 18 112438 0.4 1 106149 6289 19 124941 0.4 1 116847 8094 20 112746 0.4 1 106313 6433 21 127996 0.4 1 119498 8498 22 119702 0.4 1 112924 6778 23 108578 0.4 1 101909 6669 24 115103 0.4 1 107691 7412 25 103741 0.4 1 97616 6125 26 117200 0.4 1 109613 7587 27 104031 0.4 1 98124 5907 28 98557 0.4 1 93052 5505 29 108148 0.4 1 101932 6216 30 99778 0.4 1 94283 5495 31 108016 0.4 1 101293 6723 32 95644 0.4 1 90292 5352 33 100731 0.4 1 94926 5805 34 93831 0.4 1 88461 5370 35 89167 0.4 1 84380 4787 36 91082 0.4 1 85811 5271 37 94050 0.4 1 88609 5441 38 84452 0.4 1 79768 4684 39 88850 0.4 1 83456 5394 40 91247 0.4 1 85377 5870 41 121186 0.4 1 115345 5841 42 75479 0.4 1 71992 3487 43 40810 0.4 1 37835 2975 44 75435 0.4 1 71186 4249 45 72435 0.4 1 68506 3929 46 71403 0.4 1 67533 3870 47 76572 0.4 1 72143 4429 48 72445 0.4 1 68125 4320 49 70073 0.4 1 65861 4212 50 63534 0.4 1 60031 3503 51 60224 0.4 1 57144 3080 52 56247 0.4 1 53180 3067 53 55602 0.4 1 52726 2876 54 54986 0.4 1 52065 2921 55 56139 0.4 1 53298 2841 56 54038 0.4 1 51174 2864 57 53287 0.4 1 50653 2634 58 48844 0.4 1 46522 2322 59 47462 0.4 1 45186 2276 60 43320 0.4 1 41302 2018 61 43293 0.4 1 41363 1930 62 46050 0.4 1 43964 2086 63 46698 0.4 1 44589 2109 64 47166 0.4 1 45141 2025 65 42305 0.4 1 40382 1923 66 39994 0.4 1 38101 1893 67 35239 0.4 1 33620 1619 68 29963 0.4 1 28613 1350 69 31106 0.4 1 29738 1368 70 28521 0.4 1 27223 1298 71 26440 0.4 1 25220 1220 72 26667 0.4 1 25266 1401 73 32662 0.4 1 30250 2412 74 63500 0.4 1 61317 2183 75 30106 0.4 1 28878 1228 76 17455 0.4 1 16715 740 77 11059 0.4 1 10533 526 78 7356 0.4 1 7042 314 79 4765 0.4 1 4538 227 80 3213 0.4 1 3065 148 81 2121 0.4 1 2031 90 82 1473 0.4 1 1401 72 83 1045 0.4 1 993 52 84 785 0.4 1 747 38 85 571 0.4 1 550 21 86 411 0.4 1 386 25 87 395 0.4 1 365 30 88 384 0.4 1 351 33 89 332 0.4 1 305 27 90 419 0.4 1 388 31 91 626 0.4 1 571 55 92 1086 0.4 1 1021 65 93 2726 0.4 1 2569 157 94 7140 0.4 1 6743 397 95 11307 0.4 1 10758 549 96 4586 0.4 1 4334 252 97 2022 0.4 1 1877 145 98 673 0.4 1 618 55 99 584 0.4 1 538 46 100 538 0.4 1 460 78 101 913 0.4 1 679 234 RUN STATISTICS FOR INPUT FILE: EPI-145_S38_L005_R1_001.fastq.gz ============================================= 25512585 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 2604076 (10.2%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 13457613 (52.7%)