SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-43_S40_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 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-43_S40_L005_R2_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 548.13 s (19 us/read; 3.21 M reads/minute). === Summary === Total reads processed: 29,360,787 Reads with adapters: 21,882,728 (74.5%) Reads written (passing filters): 29,360,787 (100.0%) Total basepairs processed: 2,800,831,062 bp Total written (filtered): 2,006,745,702 bp (71.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 21882728 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.3% C: 18.6% G: 19.4% T: 31.2% none/other: 1.4% Overview of removed sequences length count expect max.err error counts 1 6425203 7340196.8 0 6425203 2 222611 1835049.2 0 222611 3 166260 458762.3 0 166260 4 134732 114690.6 0 134732 5 134196 28672.6 0 134196 6 135011 7168.2 0 135011 7 131257 1792.0 0 131257 8 133293 448.0 0 133293 9 133072 112.0 0 132508 564 10 139083 28.0 1 133494 5589 11 129206 7.0 1 122603 6603 12 135888 1.8 1 129075 6813 13 130583 0.4 1 124481 6102 14 147134 0.4 1 139732 7402 15 133833 0.4 1 127812 6021 16 137078 0.4 1 131058 6020 17 149334 0.4 1 142774 6560 18 125534 0.4 1 120077 5457 19 139649 0.4 1 133483 6166 20 136761 0.4 1 130268 6493 21 140175 0.4 1 133100 7075 22 147271 0.4 1 139958 7313 23 143543 0.4 1 136929 6614 24 163549 0.4 1 155622 7927 25 134196 0.4 1 127862 6334 26 141843 0.4 1 134155 7688 27 147300 0.4 1 138248 9052 28 160950 0.4 1 153248 7702 29 147584 0.4 1 139327 8257 30 178101 0.4 1 170092 8009 31 145894 0.4 1 137843 8051 32 165208 0.4 1 158020 7188 33 172896 0.4 1 163686 9210 34 172809 0.4 1 162944 9865 35 176380 0.4 1 169628 6752 36 153064 0.4 1 145462 7602 37 154832 0.4 1 147524 7308 38 141291 0.4 1 134489 6802 39 152931 0.4 1 145358 7573 40 149737 0.4 1 142488 7249 41 155137 0.4 1 148885 6252 42 164082 0.4 1 158039 6043 43 131622 0.4 1 125602 6020 44 148796 0.4 1 142325 6471 45 244817 0.4 1 236533 8284 46 139728 0.4 1 133899 5829 47 93015 0.4 1 88475 4540 48 157918 0.4 1 152203 5715 49 96554 0.4 1 92481 4073 50 105268 0.4 1 100746 4522 51 172026 0.4 1 166528 5498 52 91291 0.4 1 87197 4094 53 94297 0.4 1 90063 4234 54 85172 0.4 1 81377 3795 55 109874 0.4 1 105657 4217 56 103483 0.4 1 99086 4397 57 97169 0.4 1 93389 3780 58 99638 0.4 1 95674 3964 59 92605 0.4 1 88599 4006 60 92416 0.4 1 88381 4035 61 97686 0.4 1 93112 4574 62 106561 0.4 1 101399 5162 63 116927 0.4 1 110869 6058 64 131591 0.4 1 124216 7375 65 167842 0.4 1 158219 9623 66 239067 0.4 1 224094 14973 67 492650 0.4 1 450060 42590 68 2022410 0.4 1 1948510 73900 69 752699 0.4 1 718139 34560 70 412515 0.4 1 392341 20174 71 210792 0.4 1 198600 12192 72 136959 0.4 1 128621 8338 73 89374 0.4 1 83274 6100 74 67577 0.4 1 62662 4915 75 53321 0.4 1 49250 4071 76 43762 0.4 1 40200 3562 77 38046 0.4 1 34750 3296 78 33166 0.4 1 30233 2933 79 28673 0.4 1 25998 2675 80 25245 0.4 1 22771 2474 81 22568 0.4 1 20288 2280 82 20201 0.4 1 18094 2107 83 18379 0.4 1 16373 2006 84 16756 0.4 1 14770 1986 85 15604 0.4 1 13663 1941 86 15098 0.4 1 13174 1924 87 15061 0.4 1 13131 1930 88 16275 0.4 1 14107 2168 89 18383 0.4 1 15987 2396 90 24307 0.4 1 21266 3041 91 35914 0.4 1 31520 4394 92 56419 0.4 1 49589 6830 93 126394 0.4 1 112535 13859 94 368652 0.4 1 332833 35819 95 594507 0.4 1 539514 54993 96 245129 0.4 1 222974 22155 97 126946 0.4 1 115180 11766 98 45559 0.4 1 41427 4132 99 42030 0.4 1 38026 4004 100 38363 0.4 1 34679 3684 101 69140 0.4 1 62160 6980 RUN STATISTICS FOR INPUT FILE: EPI-43_S40_L005_R2_001.fastq.gz ============================================= 29360787 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 8553294 (29.1%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 0 (0.0%) Total number of sequences analysed for the sequence pair length validation: 29360787 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 6787232 (23.12%)