SUMMARISING RUN PARAMETERS ========================== Input filename: L142.AHFFJVBGX5.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: '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 9 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 9 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 6 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 6 bp from their 3' end to avoid poor qualities or biases Output file will be GZIP compressed This is cutadapt 1.16 with Python 2.7.14 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC L142.AHFFJVBGX5.end2.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 22180.52 s (43 us/read; 1.38 M reads/minute). === Summary === Total reads processed: 510,810,213 Reads with adapters: 171,523,248 (33.6%) Reads written (passing filters): 510,810,213 (100.0%) Total basepairs processed: 38,821,576,188 bp Quality-trimmed: 495,336,333 bp (1.3%) Total written (filtered): 38,044,184,168 bp (98.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 171523248 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 39.5% C: 26.0% G: 17.4% T: 17.0% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 128798207 127702553.2 0 128798207 2 27531422 31925638.3 0 27531422 3 7793796 7981409.6 0 7793796 4 2983469 1995352.4 0 2983469 5 1025074 498838.1 0 1025074 6 734851 124709.5 0 734851 7 203930 31177.4 0 203930 8 185613 7794.3 0 185613 9 193965 1948.6 0 184884 9081 10 213927 487.1 1 183165 30762 11 127342 121.8 1 100507 26835 12 148027 30.4 1 127706 20321 13 122493 7.6 1 103252 19241 14 148115 7.6 1 127156 20959 15 97131 7.6 1 83059 14072 16 91766 7.6 1 76482 15284 17 109513 7.6 1 94239 15274 18 74759 7.6 1 63286 11473 19 94308 7.6 1 81147 13161 20 79238 7.6 1 68813 10425 21 44382 7.6 1 34899 9483 22 43492 7.6 1 36969 6523 23 52126 7.6 1 43782 8344 24 55423 7.6 1 47041 8382 25 31092 7.6 1 25177 5915 26 40474 7.6 1 32683 7791 27 50330 7.6 1 40461 9869 28 22674 7.6 1 18451 4223 29 26871 7.6 1 19984 6887 30 20888 7.6 1 16806 4082 31 19715 7.6 1 15531 4184 32 17286 7.6 1 13525 3761 33 19135 7.6 1 14992 4143 34 15155 7.6 1 10634 4521 35 15469 7.6 1 11084 4385 36 13266 7.6 1 10081 3185 37 10106 7.6 1 6964 3142 38 7744 7.6 1 5064 2680 39 11805 7.6 1 8056 3749 40 4474 7.6 1 2398 2076 41 6653 7.6 1 4375 2278 42 8318 7.6 1 5584 2734 43 5319 7.6 1 3080 2239 44 6014 7.6 1 3593 2421 45 6525 7.6 1 4063 2462 46 6602 7.6 1 3509 3093 47 4138 7.6 1 2430 1708 48 5123 7.6 1 2686 2437 49 4538 7.6 1 2537 2001 50 2802 7.6 1 1318 1484 51 2868 7.6 1 1405 1463 52 2706 7.6 1 1304 1402 53 2424 7.6 1 1323 1101 54 3244 7.6 1 1969 1275 55 2059 7.6 1 1042 1017 56 2500 7.6 1 1468 1032 57 3467 7.6 1 2407 1060 58 2317 7.6 1 1603 714 59 1702 7.6 1 994 708 60 2286 7.6 1 1603 683 61 1986 7.6 1 1367 619 62 2911 7.6 1 2099 812 63 3934 7.6 1 3050 884 64 3280 7.6 1 2609 671 65 2648 7.6 1 1916 732 66 3265 7.6 1 2576 689 67 2258 7.6 1 1584 674 68 3880 7.6 1 3068 812 69 3256 7.6 1 2579 677 70 5498 7.6 1 4768 730 71 2336 7.6 1 1678 658 72 3991 7.6 1 3227 764 73 3295 7.6 1 2517 778 74 4758 7.6 1 3469 1289 75 13693 7.6 1 10591 3102 76 101801 7.6 1 91252 10549 RUN STATISTICS FOR INPUT FILE: L142.AHFFJVBGX5.end2.fastq.gz ============================================= 510810213 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 510810213 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 11797865 (2.31%)