SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-104_S28_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-104_S28_L005_R1_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 572.62 s (19 us/read; 3.16 M reads/minute). === Summary === Total reads processed: 30,166,064 Reads with adapters: 16,283,585 (54.0%) Reads written (passing filters): 30,166,064 (100.0%) Total basepairs processed: 3,034,733,228 bp Total written (filtered): 2,784,101,302 bp (91.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 16283585 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 27.0% C: 7.3% G: 23.4% T: 42.3% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 6305810 7541516.0 0 6305810 2 1472488 1885379.0 0 1472488 3 575629 471344.8 0 575629 4 377143 117836.2 0 377143 5 180188 29459.0 0 180188 6 184663 7364.8 0 184663 7 171765 1841.2 0 171765 8 214518 460.3 0 214518 9 171541 115.1 0 170138 1403 10 159371 28.8 1 152601 6770 11 168267 7.2 1 159963 8304 12 159243 1.8 1 151918 7325 13 148012 0.4 1 141358 6654 14 167390 0.4 1 158225 9165 15 155120 0.4 1 147768 7352 16 169540 0.4 1 160118 9422 17 158189 0.4 1 150423 7766 18 143080 0.4 1 136700 6380 19 158475 0.4 1 149214 9261 20 141509 0.4 1 135224 6285 21 162106 0.4 1 152666 9440 22 146856 0.4 1 140058 6798 23 138370 0.4 1 131541 6829 24 147090 0.4 1 138965 8125 25 131471 0.4 1 125435 6036 26 149677 0.4 1 141437 8240 27 131260 0.4 1 124959 6301 28 124421 0.4 1 118796 5625 29 137945 0.4 1 131145 6800 30 123265 0.4 1 118015 5250 31 134029 0.4 1 126996 7033 32 119383 0.4 1 114170 5213 33 134816 0.4 1 127680 7136 34 123117 0.4 1 117219 5898 35 112962 0.4 1 107580 5382 36 119220 0.4 1 113931 5289 37 115946 0.4 1 110843 5103 38 107999 0.4 1 103070 4929 39 103997 0.4 1 99466 4531 40 115602 0.4 1 109613 5989 41 157625 0.4 1 151472 6153 42 88501 0.4 1 84718 3783 43 59016 0.4 1 56250 2766 44 94600 0.4 1 90433 4167 45 89575 0.4 1 85803 3772 46 87528 0.4 1 83813 3715 47 93931 0.4 1 89437 4494 48 87241 0.4 1 83143 4098 49 88165 0.4 1 83905 4260 50 79264 0.4 1 75909 3355 51 74943 0.4 1 71753 3190 52 70554 0.4 1 67610 2944 53 70410 0.4 1 67578 2832 54 70419 0.4 1 67536 2883 55 71075 0.4 1 68387 2688 56 67470 0.4 1 64709 2761 57 65638 0.4 1 63117 2521 58 60614 0.4 1 58480 2134 59 60033 0.4 1 57871 2162 60 54513 0.4 1 52621 1892 61 54454 0.4 1 52566 1888 62 56521 0.4 1 54594 1927 63 53410 0.4 1 51457 1953 64 52933 0.4 1 51203 1730 65 48480 0.4 1 46746 1734 66 47534 0.4 1 45865 1669 67 44039 0.4 1 42473 1566 68 40358 0.4 1 38946 1412 69 41003 0.4 1 39567 1436 70 39244 0.4 1 37921 1323 71 35438 0.4 1 34257 1181 72 33298 0.4 1 31993 1305 73 37228 0.4 1 35277 1951 74 65399 0.4 1 63558 1841 75 27070 0.4 1 26176 894 76 14129 0.4 1 13581 548 77 8862 0.4 1 8536 326 78 6162 0.4 1 5940 222 79 4046 0.4 1 3884 162 80 2994 0.4 1 2883 111 81 2010 0.4 1 1919 91 82 1372 0.4 1 1320 52 83 957 0.4 1 905 52 84 692 0.4 1 669 23 85 456 0.4 1 425 31 86 315 0.4 1 305 10 87 204 0.4 1 185 19 88 156 0.4 1 136 20 89 168 0.4 1 151 17 90 206 0.4 1 192 14 91 312 0.4 1 282 30 92 427 0.4 1 387 40 93 803 0.4 1 752 51 94 1807 0.4 1 1717 90 95 2819 0.4 1 2689 130 96 1652 0.4 1 1573 79 97 993 0.4 1 920 73 98 357 0.4 1 318 39 99 307 0.4 1 267 40 100 614 0.4 1 485 129 101 1768 0.4 1 1328 440 RUN STATISTICS FOR INPUT FILE: EPI-104_S28_L005_R1_001.fastq.gz ============================================= 30166064 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 3004157 (10.0%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 16274794 (54.0%)