SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_32psu_2_S2_L002_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: 617121). Second best hit was smallRNA (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 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 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 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 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/20200427/TG_PE_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/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_32psu_2_S2_L002_R1_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 61.80 s (3 us/read; 17.17 M reads/minute). === Summary === Total reads processed: 17,682,252 Reads with adapters: 14,725,601 (83.3%) Reads written (passing filters): 17,682,252 (100.0%) Total basepairs processed: 2,652,337,800 bp Quality-trimmed: 5,252,718 bp (0.2%) Total written (filtered): 1,953,712,678 bp (73.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14725601 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.6% C: 12.9% G: 21.9% T: 35.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1730837 4420563.0 0 1730837 2 274288 1105140.8 0 274288 3 164540 276285.2 0 164540 4 98245 69071.3 0 98245 5 85133 17267.8 0 85133 6 82977 4317.0 0 82977 7 68628 1079.2 0 68628 8 92219 269.8 0 92219 9 82148 67.5 0 81058 1090 10 81207 16.9 1 75933 5274 11 91764 4.2 1 83517 8247 12 88451 1.1 1 81680 6771 13 90852 0.3 1 83635 7217 14 92006 0.3 1 84006 8000 15 95802 0.3 1 88019 7783 16 94793 0.3 1 86152 8641 17 117965 0.3 1 106745 11220 18 99003 0.3 1 91800 7203 19 85234 0.3 1 78539 6695 20 103603 0.3 1 95615 7988 21 115441 0.3 1 106021 9420 22 96644 0.3 1 89824 6820 23 112899 0.3 1 103928 8971 24 106903 0.3 1 96909 9994 25 114269 0.3 1 105193 9076 26 105406 0.3 1 97809 7597 27 119549 0.3 1 109420 10129 28 117559 0.3 1 108344 9215 29 126569 0.3 1 115202 11367 30 135359 0.3 1 126047 9312 31 102444 0.3 1 94598 7846 32 135060 0.3 1 124361 10699 33 113717 0.3 1 104773 8944 34 130221 0.3 1 118947 11274 35 139590 0.3 1 127417 12173 36 127748 0.3 1 118449 9299 37 156612 0.3 1 144323 12289 38 124619 0.3 1 114023 10596 39 136370 0.3 1 126274 10096 40 143456 0.3 1 132041 11415 41 145337 0.3 1 132898 12439 42 139531 0.3 1 126917 12614 43 211559 0.3 1 197954 13605 44 73750 0.3 1 66328 7422 45 151399 0.3 1 140473 10926 46 138024 0.3 1 127568 10456 47 150595 0.3 1 139553 11042 48 147780 0.3 1 136652 11128 49 162871 0.3 1 149899 12972 50 141270 0.3 1 131458 9812 51 154346 0.3 1 142859 11487 52 160748 0.3 1 148256 12492 53 167551 0.3 1 155619 11932 54 139669 0.3 1 129569 10100 55 162273 0.3 1 150174 12099 56 200304 0.3 1 186484 13820 57 127569 0.3 1 117186 10383 58 167466 0.3 1 156693 10773 59 150014 0.3 1 138880 11134 60 160710 0.3 1 148928 11782 61 158834 0.3 1 147715 11119 62 178143 0.3 1 165938 12205 63 141715 0.3 1 130934 10781 64 158746 0.3 1 148093 10653 65 176936 0.3 1 164216 12720 66 182618 0.3 1 169484 13134 67 198670 0.3 1 182225 16445 68 365118 0.3 1 345570 19548 69 68264 0.3 1 62074 6190 70 29092 0.3 1 24265 4827 71 103442 0.3 1 96474 6968 72 142212 0.3 1 133025 9187 73 149684 0.3 1 139925 9759 74 148896 0.3 1 138764 10132 75 148109 0.3 1 137782 10327 76 146530 0.3 1 136141 10389 77 146539 0.3 1 136490 10049 78 139703 0.3 1 129860 9843 79 137432 0.3 1 127635 9797 80 135397 0.3 1 125660 9737 81 133287 0.3 1 123761 9526 82 129169 0.3 1 119849 9320 83 125954 0.3 1 117089 8865 84 121677 0.3 1 112941 8736 85 117830 0.3 1 109511 8319 86 114988 0.3 1 106799 8189 87 110799 0.3 1 103288 7511 88 109823 0.3 1 102149 7674 89 103812 0.3 1 96531 7281 90 101371 0.3 1 94159 7212 91 96555 0.3 1 89763 6792 92 92588 0.3 1 86028 6560 93 86787 0.3 1 80806 5981 94 84568 0.3 1 78482 6086 95 78600 0.3 1 72903 5697 96 74361 0.3 1 69003 5358 97 69748 0.3 1 64791 4957 98 65245 0.3 1 60478 4767 99 62580 0.3 1 57800 4780 100 56847 0.3 1 52715 4132 101 53263 0.3 1 49277 3986 102 48648 0.3 1 45084 3564 103 45338 0.3 1 42014 3324 104 41917 0.3 1 38870 3047 105 37301 0.3 1 34586 2715 106 33679 0.3 1 31071 2608 107 30205 0.3 1 27947 2258 108 27998 0.3 1 25811 2187 109 24717 0.3 1 22799 1918 110 22343 0.3 1 20572 1771 111 20279 0.3 1 18723 1556 112 17492 0.3 1 16037 1455 113 14993 0.3 1 13741 1252 114 13102 0.3 1 12018 1084 115 11167 0.3 1 10176 991 116 9702 0.3 1 8851 851 117 8008 0.3 1 7282 726 118 6784 0.3 1 6194 590 119 5714 0.3 1 5190 524 120 4836 0.3 1 4363 473 121 3994 0.3 1 3606 388 122 3193 0.3 1 2889 304 123 2794 0.3 1 2493 301 124 2161 0.3 1 1934 227 125 1832 0.3 1 1606 226 126 1531 0.3 1 1356 175 127 1197 0.3 1 1054 143 128 960 0.3 1 854 106 129 853 0.3 1 753 100 130 591 0.3 1 514 77 131 531 0.3 1 470 61 132 430 0.3 1 380 50 133 462 0.3 1 411 51 134 470 0.3 1 418 52 135 263 0.3 1 225 38 136 146 0.3 1 127 19 137 106 0.3 1 90 16 138 84 0.3 1 66 18 139 59 0.3 1 48 11 140 48 0.3 1 41 7 141 28 0.3 1 20 8 142 22 0.3 1 17 5 143 22 0.3 1 15 7 144 21 0.3 1 19 2 145 41 0.3 1 38 3 146 29 0.3 1 26 3 147 81 0.3 1 70 11 148 47 0.3 1 39 8 149 50 0.3 1 42 8 150 504 0.3 1 392 112 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_32psu_2_S2_L002_R1_001.fastq.gz ============================================= 17682252 sequences processed in total