SUMMARISING RUN PARAMETERS ========================== Input filename: KO-13006-1.end2.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4 Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; 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 sequences will be trimmed by 1 bp on their 3' end to avoid problems with invalid paired-end alignments with Bowtie 1 Output file will be GZIP compressed This is cutadapt 1.16 with Python 2.7.13 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA KO-13006-1.end2.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 1040.59 s (37 us/read; 1.64 M reads/minute). === Summary === Total reads processed: 28,470,155 Reads with adapters: 11,863,720 (41.7%) Reads written (passing filters): 28,470,155 (100.0%) Total basepairs processed: 1,888,741,658 bp Quality-trimmed: 3,115,527 bp (0.2%) Total written (filtered): 1,837,103,172 bp (97.3%) === Adapter 1 === Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 11863720 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 25.2% C: 28.5% G: 23.4% T: 22.2% none/other: 0.6% Overview of removed sequences length count expect max.err error counts 1 8223951 7117538.8 0 8223951 2 1662866 1779384.7 0 1662866 3 473033 444846.2 0 473033 4 122554 111211.5 0 122554 5 48101 27802.9 0 48101 6 28427 6950.7 0 28427 7 24119 1737.7 0 24119 8 22019 434.4 0 22019 9 28003 108.6 0 27107 896 10 31063 27.2 1 22201 8862 11 36156 6.8 1 26183 9973 12 34704 1.7 1 24926 9778 13 34639 1.7 1 25182 9457 14 28807 1.7 1 20788 8019 15 34019 1.7 1 24387 9632 16 24557 1.7 1 17821 6736 17 26205 1.7 1 18086 8119 18 26263 1.7 1 19149 7114 19 36823 1.7 1 25046 11777 20 25945 1.7 1 17017 8928 21 32000 1.7 1 19633 12367 22 38300 1.7 1 18680 19620 23 36961 1.7 1 19080 17881 24 45910 1.7 1 21789 24121 25 45917 1.7 1 19781 26136 26 32436 1.7 1 14685 17751 27 30028 1.7 1 12279 17749 28 36534 1.7 1 15084 21450 29 35768 1.7 1 15325 20443 30 39480 1.7 1 17318 22162 31 51199 1.7 1 23465 27734 32 54185 1.7 1 35900 18285 33 67837 1.7 1 43816 24021 34 30750 1.7 1 19857 10893 35 71338 1.7 1 46656 24682 36 38896 1.7 1 27002 11894 37 31806 1.7 1 21454 10352 38 45171 1.7 1 30809 14362 39 16944 1.7 1 11618 5326 40 30722 1.7 1 21427 9295 41 14162 1.7 1 9719 4443 42 7294 1.7 1 4292 3002 43 6288 1.7 1 3416 2872 44 2886 1.7 1 1748 1138 45 3513 1.7 1 2145 1368 46 3222 1.7 1 2070 1152 47 2241 1.7 1 1396 845 48 2643 1.7 1 1600 1043 49 3309 1.7 1 2179 1130 50 5220 1.7 1 2207 3013 51 764 1.7 1 279 485 52 525 1.7 1 151 374 53 744 1.7 1 107 637 54 310 1.7 1 89 221 55 696 1.7 1 106 590 56 378 1.7 1 101 277 57 247 1.7 1 37 210 58 589 1.7 1 26 563 59 349 1.7 1 28 321 60 1540 1.7 1 40 1500 61 278 1.7 1 43 235 62 429 1.7 1 138 291 63 794 1.7 1 195 599 64 184 1.7 1 48 136 65 245 1.7 1 62 183 66 259 1.7 1 45 214 67 366 1.7 1 49 317 68 590 1.7 1 46 544 69 204 1.7 1 77 127 70 255 1.7 1 119 136 71 246 1.7 1 132 114 72 329 1.7 1 156 173 73 906 1.7 1 320 586 74 684 1.7 1 371 313 75 4138 1.7 1 3352 786 76 12457 1.7 1 9140 3317 RUN STATISTICS FOR INPUT FILE: KO-13006-1.end2.fastq.gz ============================================= 28470155 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 28470155 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 48891 (0.17%)