SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-188_S21_L003_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-188_S21_L003_R1_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 461.70 s (19 us/read; 3.15 M reads/minute). === Summary === Total reads processed: 24,209,277 Reads with adapters: 17,010,941 (70.3%) Reads written (passing filters): 24,209,277 (100.0%) Total basepairs processed: 2,398,939,499 bp Total written (filtered): 1,794,827,099 bp (74.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 17010941 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 21.5% C: 17.2% G: 25.5% T: 33.5% none/other: 2.3% Overview of removed sequences length count expect max.err error counts 1 3080226 6052319.2 0 3080226 2 756005 1513079.8 0 756005 3 317167 378270.0 0 317167 4 231881 94567.5 0 231881 5 136551 23641.9 0 136551 6 135081 5910.5 0 135081 7 127119 1477.6 0 127119 8 142856 369.4 0 142856 9 139816 92.4 0 138682 1134 10 135167 23.1 1 129743 5424 11 138432 5.8 1 131953 6479 12 133945 1.4 1 127983 5962 13 130279 0.4 1 124563 5716 14 145360 0.4 1 135285 10075 15 139536 0.4 1 129610 9926 16 150691 0.4 1 139208 11483 17 145583 0.4 1 134995 10588 18 135528 0.4 1 126181 9347 19 151360 0.4 1 138851 12509 20 141725 0.4 1 132028 9697 21 163432 0.4 1 150292 13140 22 152576 0.4 1 141863 10713 23 144099 0.4 1 133472 10627 24 154253 0.4 1 142476 11777 25 145098 0.4 1 134749 10349 26 164301 0.4 1 151086 13215 27 152998 0.4 1 144154 8844 28 145681 0.4 1 138321 7360 29 164631 0.4 1 155445 9186 30 156746 0.4 1 148941 7805 31 169461 0.4 1 159497 9964 32 162852 0.4 1 154656 8196 33 170498 0.4 1 161670 8828 34 160532 0.4 1 152486 8046 35 160949 0.4 1 152689 8260 36 160980 0.4 1 153183 7797 37 173871 0.4 1 164923 8948 38 171544 0.4 1 162201 9343 39 167227 0.4 1 159810 7417 40 173095 0.4 1 164213 8882 41 239880 0.4 1 229508 10372 42 165745 0.4 1 159000 6745 43 81658 0.4 1 77317 4341 44 156045 0.4 1 149093 6952 45 152668 0.4 1 146191 6477 46 150931 0.4 1 144501 6430 47 162554 0.4 1 155033 7521 48 153571 0.4 1 146525 7046 49 163066 0.4 1 155347 7719 50 148399 0.4 1 141991 6408 51 148733 0.4 1 142414 6319 52 143686 0.4 1 137485 6201 53 138467 0.4 1 133090 5377 54 138260 0.4 1 132442 5818 55 144896 0.4 1 139183 5713 56 137458 0.4 1 131975 5483 57 130926 0.4 1 125497 5429 58 129492 0.4 1 124571 4921 59 126757 0.4 1 121844 4913 60 117489 0.4 1 113102 4387 61 122458 0.4 1 117839 4619 62 127115 0.4 1 122545 4570 63 119624 0.4 1 115354 4270 64 117716 0.4 1 113772 3944 65 109892 0.4 1 106086 3806 66 103064 0.4 1 99428 3636 67 100441 0.4 1 96880 3561 68 92346 0.4 1 88866 3480 69 98902 0.4 1 95340 3562 70 95464 0.4 1 91592 3872 71 108217 0.4 1 103672 4545 72 119545 0.4 1 113302 6243 73 198646 0.4 1 182675 15971 74 641987 0.4 1 618165 23822 75 500751 0.4 1 482278 18473 76 319758 0.4 1 307425 12333 77 201977 0.4 1 194124 7853 78 124043 0.4 1 119337 4706 79 69619 0.4 1 66705 2914 80 44716 0.4 1 42875 1841 81 27468 0.4 1 26205 1263 82 18563 0.4 1 17722 841 83 14140 0.4 1 13454 686 84 11524 0.4 1 10945 579 85 9955 0.4 1 9485 470 86 8489 0.4 1 8053 436 87 7214 0.4 1 6837 377 88 6045 0.4 1 5738 307 89 5851 0.4 1 5526 325 90 7049 0.4 1 6707 342 91 9472 0.4 1 8982 490 92 15546 0.4 1 14836 710 93 37252 0.4 1 35530 1722 94 111298 0.4 1 106703 4595 95 192040 0.4 1 184222 7818 96 91221 0.4 1 87072 4149 97 66316 0.4 1 63222 3094 98 29873 0.4 1 28272 1601 99 32611 0.4 1 30842 1769 100 43518 0.4 1 40566 2952 101 89402 0.4 1 80800 8602 RUN STATISTICS FOR INPUT FILE: EPI-188_S21_L003_R1_001.fastq.gz ============================================= 24209277 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 4133270 (17.1%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 16504583 (68.2%)