SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/strigg/analyses/20200320/FASTQS/EPI-229_S36_L004_R2_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.6.4_dev Cutadapt version: 2.4 Python version: could not detect Number of cores used for trimming: 8 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Using Illumina adapter for trimming (count: 343561). Second best hit was Nextera (count: 1) 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 All Read 1 sequences will be trimmed by 8 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 8 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 8 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 8 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /gscratch/scrubbed/strigg/analyses/20200320/TG_FASTQS/FastQC --threads 28 Output file will be GZIP compressed This is cutadapt 2.4 with Python 3.7.6 Command line parameters: -j 8 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/strigg/analyses/20200320/FASTQS/EPI-229_S36_L004_R2_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 57.46 s (3 us/read; 21.85 M reads/minute). === Summary === Total reads processed: 20,924,617 Reads with adapters: 14,487,017 (69.2%) Reads written (passing filters): 20,924,617 (100.0%) Total basepairs processed: 2,113,386,317 bp Quality-trimmed: 34,559,374 bp (1.6%) Total written (filtered): 1,743,965,869 bp (82.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14487017 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 34.7% C: 23.3% G: 11.4% T: 30.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 5636220 5231154.2 0 5636220 2 186576 1307788.6 0 186576 3 149497 326947.1 0 149497 4 126375 81736.8 0 126375 5 125827 20434.2 0 125827 6 129238 5108.5 0 129238 7 128200 1277.1 0 128200 8 135400 319.3 0 135400 9 130130 79.8 0 129582 548 10 134421 20.0 1 131006 3415 11 121869 5.0 1 118185 3684 12 127267 1.2 1 123176 4091 13 123603 0.3 1 119710 3893 14 136177 0.3 1 131738 4439 15 129248 0.3 1 125494 3754 16 130274 0.3 1 126378 3896 17 136327 0.3 1 132005 4322 18 121709 0.3 1 118066 3643 19 129392 0.3 1 125273 4119 20 130050 0.3 1 126027 4023 21 130651 0.3 1 126444 4207 22 136897 0.3 1 132288 4609 23 129926 0.3 1 125733 4193 24 137834 0.3 1 133187 4647 25 125067 0.3 1 121134 3933 26 126502 0.3 1 121930 4572 27 126810 0.3 1 121655 5155 28 135447 0.3 1 130862 4585 29 128992 0.3 1 124272 4720 30 143056 0.3 1 138483 4573 31 122746 0.3 1 118554 4192 32 133091 0.3 1 128956 4135 33 136587 0.3 1 131962 4625 34 134539 0.3 1 129498 5041 35 135777 0.3 1 131788 3989 36 130081 0.3 1 125611 4470 37 130061 0.3 1 125914 4147 38 121071 0.3 1 117142 3929 39 121951 0.3 1 117678 4273 40 123073 0.3 1 118721 4352 41 126784 0.3 1 122619 4165 42 125600 0.3 1 121685 3915 43 109843 0.3 1 106088 3755 44 115477 0.3 1 111575 3902 45 142871 0.3 1 138531 4340 46 110167 0.3 1 106709 3458 47 86638 0.3 1 83512 3126 48 118981 0.3 1 115288 3693 49 90421 0.3 1 87579 2842 50 90762 0.3 1 87587 3175 51 126142 0.3 1 122846 3296 52 81474 0.3 1 78929 2545 53 82704 0.3 1 80227 2477 54 72722 0.3 1 70496 2226 55 88906 0.3 1 86340 2566 56 84829 0.3 1 82131 2698 57 79289 0.3 1 76813 2476 58 76459 0.3 1 74110 2349 59 73817 0.3 1 71416 2401 60 69400 0.3 1 67043 2357 61 68978 0.3 1 66753 2225 62 70653 0.3 1 68188 2465 63 70607 0.3 1 68126 2481 64 70133 0.3 1 67654 2479 65 72850 0.3 1 70063 2787 66 77203 0.3 1 74045 3158 67 111327 0.3 1 102605 8722 68 469756 0.3 1 457080 12676 69 189839 0.3 1 182984 6855 70 96560 0.3 1 92673 3887 71 49264 0.3 1 47041 2223 72 33091 0.3 1 31452 1639 73 22986 0.3 1 21745 1241 74 17842 0.3 1 16814 1028 75 14600 0.3 1 13725 875 76 12514 0.3 1 11758 756 77 11082 0.3 1 10392 690 78 9525 0.3 1 8913 612 79 8144 0.3 1 7551 593 80 6686 0.3 1 6193 493 81 5722 0.3 1 5310 412 82 4881 0.3 1 4508 373 83 4009 0.3 1 3672 337 84 3439 0.3 1 3160 279 85 2799 0.3 1 2542 257 86 2425 0.3 1 2144 281 87 2316 0.3 1 2060 256 88 2238 0.3 1 1972 266 89 2495 0.3 1 2203 292 90 3131 0.3 1 2728 403 91 4329 0.3 1 3836 493 92 6491 0.3 1 5761 730 93 14019 0.3 1 12612 1407 94 41673 0.3 1 37890 3783 95 72635 0.3 1 66605 6030 96 31509 0.3 1 28786 2723 97 21403 0.3 1 19581 1822 98 8966 0.3 1 8248 718 99 9140 0.3 1 8322 818 100 9750 0.3 1 8929 821 101 18762 0.3 1 16818 1944 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/strigg/analyses/20200320/FASTQS/EPI-229_S36_L004_R2_001.fastq.gz ============================================= 20924617 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 20924617 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1591638 (7.61%)