SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/strigg/analyses/20200320/FASTQS/EPI-120_S32_L005_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: 174202). 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-120_S32_L005_R2_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 83.31 s (3 us/read; 17.45 M reads/minute). === Summary === Total reads processed: 24,230,515 Reads with adapters: 14,689,727 (60.6%) Reads written (passing filters): 24,230,515 (100.0%) Total basepairs processed: 2,447,282,015 bp Quality-trimmed: 19,563,458 bp (0.8%) Total written (filtered): 2,253,146,459 bp (92.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14689727 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 39.5% C: 24.7% G: 6.9% T: 28.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 8721623 6057628.8 0 8721623 2 188862 1514407.2 0 188862 3 178088 378601.8 0 178088 4 135146 94650.4 0 135146 5 138529 23662.6 0 138529 6 142894 5915.7 0 142894 7 135456 1478.9 0 135456 8 185937 369.7 0 185937 9 123085 92.4 0 122587 498 10 121623 23.1 1 116941 4682 11 118149 5.8 1 112004 6145 12 117994 1.4 1 112255 5739 13 112370 0.4 1 106781 5589 14 125606 0.4 1 119543 6063 15 112656 0.4 1 107113 5543 16 114871 0.4 1 109189 5682 17 123408 0.4 1 117652 5756 18 103291 0.4 1 98274 5017 19 110822 0.4 1 105897 4925 20 105852 0.4 1 100411 5441 21 111131 0.4 1 104936 6195 22 112851 0.4 1 107208 5643 23 106174 0.4 1 100996 5178 24 114940 0.4 1 109394 5546 25 95757 0.4 1 90977 4780 26 101642 0.4 1 95817 5825 27 105078 0.4 1 98392 6686 28 106947 0.4 1 101788 5159 29 101256 0.4 1 95141 6115 30 112760 0.4 1 107757 5003 31 90711 0.4 1 85802 4909 32 96966 0.4 1 92924 4042 33 100266 0.4 1 95097 5169 34 103303 0.4 1 97611 5692 35 96319 0.4 1 92684 3635 36 87161 0.4 1 82594 4567 37 84126 0.4 1 79935 4191 38 76720 0.4 1 72811 3909 39 78646 0.4 1 74515 4131 40 79381 0.4 1 75228 4153 41 76728 0.4 1 73292 3436 42 81619 0.4 1 78586 3033 43 63253 0.4 1 59927 3326 44 71181 0.4 1 67855 3326 45 106542 0.4 1 103130 3412 46 62154 0.4 1 59265 2889 47 41213 0.4 1 38881 2332 48 70170 0.4 1 67597 2573 49 38522 0.4 1 36642 1880 50 44199 0.4 1 42000 2199 51 71287 0.4 1 69015 2272 52 34025 0.4 1 32241 1784 53 38341 0.4 1 36348 1993 54 33187 0.4 1 31441 1746 55 44345 0.4 1 42375 1970 56 42477 0.4 1 40362 2115 57 38045 0.4 1 36310 1735 58 37030 0.4 1 35270 1760 59 35127 0.4 1 33354 1773 60 35491 0.4 1 33729 1762 61 35838 0.4 1 34073 1765 62 37572 0.4 1 35739 1833 63 39060 0.4 1 37136 1924 64 38746 0.4 1 36855 1891 65 40153 0.4 1 38254 1899 66 40865 0.4 1 38970 1895 67 44637 0.4 1 42409 2228 68 84780 0.4 1 82611 2169 69 26275 0.4 1 25189 1086 70 12864 0.4 1 12087 777 71 8459 0.4 1 7830 629 72 6649 0.4 1 6168 481 73 5684 0.4 1 5242 442 74 4598 0.4 1 4253 345 75 3976 0.4 1 3699 277 76 3332 0.4 1 3073 259 77 2807 0.4 1 2594 213 78 2178 0.4 1 2032 146 79 1769 0.4 1 1639 130 80 1238 0.4 1 1147 91 81 876 0.4 1 805 71 82 660 0.4 1 608 52 83 454 0.4 1 425 29 84 238 0.4 1 219 19 85 142 0.4 1 132 10 86 101 0.4 1 89 12 87 55 0.4 1 48 7 88 42 0.4 1 36 6 89 39 0.4 1 31 8 90 42 0.4 1 35 7 91 88 0.4 1 73 15 92 127 0.4 1 107 20 93 190 0.4 1 165 25 94 325 0.4 1 294 31 95 461 0.4 1 412 49 96 448 0.4 1 413 35 97 241 0.4 1 223 18 98 76 0.4 1 71 5 99 58 0.4 1 54 4 100 54 0.4 1 48 6 101 197 0.4 1 165 32 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/strigg/analyses/20200320/FASTQS/EPI-120_S32_L005_R2_001.fastq.gz ============================================= 24230515 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 24230515 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 386975 (1.60%)