SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/strigg/analyses/20200320/FASTQS/EPI-41_S38_L005_R1_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: 336735). Second best hit was Nextera (count: 0) 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-41_S38_L005_R1_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 77.60 s (3 us/read; 19.94 M reads/minute). === Summary === Total reads processed: 25,784,248 Reads with adapters: 16,123,696 (62.5%) Reads written (passing filters): 25,784,248 (100.0%) Total basepairs processed: 2,604,209,048 bp Quality-trimmed: 18,982,430 bp (0.7%) Total written (filtered): 2,166,486,166 bp (83.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 16123696 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 22.6% C: 11.2% G: 29.5% T: 36.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 4261224 6446062.0 0 4261224 2 985208 1611515.5 0 985208 3 386593 402878.9 0 386593 4 267747 100719.7 0 267747 5 153542 25179.9 0 153542 6 142058 6295.0 0 142058 7 127484 1573.7 0 127484 8 141235 393.4 0 141235 9 146968 98.4 0 145699 1269 10 137799 24.6 1 130983 6816 11 148428 6.1 1 140164 8264 12 136200 1.5 1 129144 7056 13 135738 0.4 1 128519 7219 14 149617 0.4 1 140119 9498 15 147158 0.4 1 138484 8674 16 156671 0.4 1 146341 10330 17 156855 0.4 1 147063 9792 18 140692 0.4 1 133061 7631 19 153237 0.4 1 142906 10331 20 146851 0.4 1 138448 8403 21 163392 0.4 1 152027 11365 22 152561 0.4 1 143480 9081 23 145452 0.4 1 136644 8808 24 150690 0.4 1 140804 9886 25 146993 0.4 1 138057 8936 26 157169 0.4 1 146608 10561 27 152089 0.4 1 143272 8817 28 146009 0.4 1 138084 7925 29 160017 0.4 1 150511 9506 30 145418 0.4 1 138046 7372 31 159900 0.4 1 150120 9780 32 147184 0.4 1 139501 7683 33 171046 0.4 1 160373 10673 34 153175 0.4 1 145094 8081 35 155093 0.4 1 146247 8846 36 162248 0.4 1 152777 9471 37 164902 0.4 1 156272 8630 38 154829 0.4 1 145972 8857 39 167776 0.4 1 158083 9693 40 171017 0.4 1 161557 9460 41 237943 0.4 1 226993 10950 42 134399 0.4 1 128102 6297 43 70463 0.4 1 66102 4361 44 138798 0.4 1 131703 7095 45 142862 0.4 1 134968 7894 46 131743 0.4 1 124887 6856 47 147562 0.4 1 139149 8413 48 135682 0.4 1 127789 7893 49 152328 0.4 1 143084 9244 50 130308 0.4 1 123261 7047 51 135670 0.4 1 127967 7703 52 136431 0.4 1 128310 8121 53 121608 0.4 1 115016 6592 54 122994 0.4 1 115844 7150 55 134548 0.4 1 126839 7709 56 123749 0.4 1 116620 7129 57 113087 0.4 1 106349 6738 58 120087 0.4 1 113743 6344 59 116904 0.4 1 110667 6237 60 103542 0.4 1 98238 5304 61 116409 0.4 1 110389 6020 62 117850 0.4 1 111964 5886 63 105605 0.4 1 100278 5327 64 100906 0.4 1 96174 4732 65 95073 0.4 1 90841 4232 66 90350 0.4 1 86323 4027 67 92045 0.4 1 87927 4118 68 85640 0.4 1 81988 3652 69 90424 0.4 1 86699 3725 70 82750 0.4 1 79136 3614 71 85980 0.4 1 82062 3918 72 94547 0.4 1 89994 4553 73 119365 0.4 1 110854 8511 74 283657 0.4 1 273441 10216 75 165095 0.4 1 158881 6214 76 83945 0.4 1 80506 3439 77 49946 0.4 1 47787 2159 78 32346 0.4 1 30986 1360 79 20265 0.4 1 19397 868 80 14549 0.4 1 13856 693 81 10084 0.4 1 9648 436 82 7616 0.4 1 7237 379 83 5789 0.4 1 5521 268 84 4616 0.4 1 4370 246 85 3664 0.4 1 3478 186 86 2886 0.4 1 2709 177 87 2229 0.4 1 2112 117 88 1656 0.4 1 1545 111 89 1569 0.4 1 1479 90 90 1904 0.4 1 1804 100 91 2512 0.4 1 2346 166 92 3661 0.4 1 3413 248 93 8067 0.4 1 7646 421 94 22127 0.4 1 21054 1073 95 37776 0.4 1 36021 1755 96 19364 0.4 1 18276 1088 97 13594 0.4 1 12782 812 98 5497 0.4 1 5114 383 99 5436 0.4 1 5027 409 100 9228 0.4 1 8419 809 101 28701 0.4 1 25459 3242 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/strigg/analyses/20200320/FASTQS/EPI-41_S38_L005_R1_001.fastq.gz ============================================= 25784248 sequences processed in total