SUMMARISING RUN PARAMETERS ========================== Input filename: L142.AHFFJVBGX5.end1.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.end1.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 21397.12 s (42 us/read; 1.43 M reads/minute). === Summary === Total reads processed: 510,810,213 Reads with adapters: 174,759,177 (34.2%) Reads written (passing filters): 510,810,213 (100.0%) Total basepairs processed: 38,821,576,188 bp Quality-trimmed: 277,163,488 bp (0.7%) Total written (filtered): 37,538,541,296 bp (96.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 174759177 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 34.4% C: 26.0% G: 17.4% T: 16.4% none/other: 5.8% Overview of removed sequences length count expect max.err error counts 1 122005781 127702553.2 0 122005781 2 27467535 31925638.3 0 27467535 3 7817684 7981409.6 0 7817684 4 2957131 1995352.4 0 2957131 5 1011418 498838.1 0 1011418 6 740136 124709.5 0 740136 7 198265 31177.4 0 198265 8 187197 7794.3 0 187197 9 209885 1948.6 0 200650 9235 10 192286 487.1 1 163305 28981 11 145674 121.8 1 121397 24277 12 122817 30.4 1 106531 16286 13 170971 7.6 1 149949 21022 14 90932 7.6 1 77543 13389 15 150660 7.6 1 132164 18496 16 66619 7.6 1 55809 10810 17 112955 7.6 1 96597 16358 18 89206 7.6 1 77451 11755 19 72797 7.6 1 63007 9790 20 71760 7.6 1 61704 10056 21 60904 7.6 1 52770 8134 22 58404 7.6 1 50634 7770 23 48351 7.6 1 41213 7138 24 43304 7.6 1 36612 6692 25 51011 7.6 1 43643 7368 26 26790 7.6 1 22249 4541 27 32314 7.6 1 27106 5208 28 34209 7.6 1 28625 5584 29 27404 7.6 1 22066 5338 30 22815 7.6 1 18776 4039 31 18543 7.6 1 14888 3655 32 22266 7.6 1 18319 3947 33 12752 7.6 1 9329 3423 34 18884 7.6 1 14733 4151 35 9698 7.6 1 6733 2965 36 12920 7.6 1 9216 3704 37 13544 7.6 1 9208 4336 38 10824 7.6 1 7021 3803 39 13610 7.6 1 7847 5763 40 17209 7.6 1 5797 11412 41 27818 7.6 1 8513 19305 42 27115 7.6 1 8496 18619 43 41780 7.6 1 7478 34302 44 22588 7.6 1 8986 13602 45 39237 7.6 1 2344 36893 46 41235 7.6 1 5821 35414 47 130821 7.6 1 2478 128343 48 226418 7.6 1 7111 219307 49 68844 7.6 1 6685 62159 50 34626 7.6 1 1553 33073 51 46213 7.6 1 2148 44065 52 29064 7.6 1 1950 27114 53 12425 7.6 1 796 11629 54 25973 7.6 1 904 25069 55 27299 7.6 1 1043 26256 56 17887 7.6 1 1091 16796 57 18962 7.6 1 616 18346 58 10145 7.6 1 536 9609 59 6575 7.6 1 851 5724 60 3795 7.6 1 233 3562 61 6950 7.6 1 301 6649 62 6473 7.6 1 1151 5322 63 6196 7.6 1 568 5628 64 4947 7.6 1 511 4436 65 10512 7.6 1 1028 9484 66 4738 7.6 1 1406 3332 67 1972 7.6 1 285 1687 68 3381 7.6 1 860 2521 69 7763 7.6 1 1842 5921 70 17844 7.6 1 2441 15403 71 75957 7.6 1 2978 72979 72 336346 7.6 1 4736 331610 73 1061290 7.6 1 7061 1054229 74 2787670 7.6 1 15108 2772562 75 3633295 7.6 1 30593 3602702 76 1497558 7.6 1 48387 1449171 RUN STATISTICS FOR INPUT FILE: L142.AHFFJVBGX5.end1.fastq.gz ============================================= 510810213 sequences processed in total