SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/CTRL_16C_26psu_1_S19_L002_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: 537596). 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 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/CTRL_16C_26psu_1_S19_L002_R2_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 71.63 s (4 us/read; 15.49 M reads/minute). === Summary === Total reads processed: 18,490,322 Reads with adapters: 14,450,091 (78.1%) Reads written (passing filters): 18,490,322 (100.0%) Total basepairs processed: 2,773,548,300 bp Quality-trimmed: 11,878,254 bp (0.4%) Total written (filtered): 2,174,052,769 bp (78.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14450091 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.0% C: 12.4% G: 24.6% T: 35.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2377683 4622580.5 0 2377683 2 369953 1155645.1 0 369953 3 212079 288911.3 0 212079 4 120512 72227.8 0 120512 5 108962 18057.0 0 108962 6 97421 4514.2 0 97421 7 79386 1128.6 0 79386 8 113054 282.1 0 113054 9 87971 70.5 0 87624 347 10 96473 17.6 1 89879 6594 11 101734 4.4 1 93536 8198 12 102089 1.1 1 93747 8342 13 117081 0.3 1 107549 9532 14 108685 0.3 1 98929 9756 15 89117 0.3 1 82133 6984 16 127440 0.3 1 117058 10382 17 108227 0.3 1 99362 8865 18 94672 0.3 1 87210 7462 19 124816 0.3 1 114994 9822 20 116877 0.3 1 108056 8821 21 101808 0.3 1 94028 7780 22 115329 0.3 1 106403 8926 23 122296 0.3 1 112903 9393 24 121720 0.3 1 111954 9766 25 136356 0.3 1 126910 9446 26 113979 0.3 1 104759 9220 27 127054 0.3 1 116622 10432 28 113808 0.3 1 106074 7734 29 126916 0.3 1 117431 9485 30 122281 0.3 1 113729 8552 31 135760 0.3 1 126137 9623 32 117176 0.3 1 109066 8110 33 136110 0.3 1 125744 10366 34 171537 0.3 1 159519 12018 35 95945 0.3 1 89044 6901 36 137046 0.3 1 126917 10129 37 143037 0.3 1 132698 10339 38 133329 0.3 1 124497 8832 39 127534 0.3 1 119434 8100 40 144687 0.3 1 134651 10036 41 140384 0.3 1 131070 9314 42 144299 0.3 1 134780 9519 43 129916 0.3 1 121294 8622 44 151641 0.3 1 141122 10519 45 160400 0.3 1 149699 10701 46 114273 0.3 1 106605 7668 47 144997 0.3 1 136130 8867 48 143166 0.3 1 134124 9042 49 148482 0.3 1 138822 9660 50 140955 0.3 1 131828 9127 51 174978 0.3 1 163816 11162 52 126038 0.3 1 118003 8035 53 153652 0.3 1 144809 8843 54 111499 0.3 1 104710 6789 55 148731 0.3 1 140120 8611 56 152852 0.3 1 143418 9434 57 145621 0.3 1 137708 7913 58 139629 0.3 1 131703 7926 59 139468 0.3 1 131381 8087 60 145979 0.3 1 137374 8605 61 147098 0.3 1 138678 8420 62 160909 0.3 1 151040 9869 63 208484 0.3 1 197875 10609 64 163339 0.3 1 155950 7389 65 115211 0.3 1 108911 6300 66 124628 0.3 1 117681 6947 67 122836 0.3 1 115645 7191 68 124659 0.3 1 117627 7032 69 121178 0.3 1 114114 7064 70 126813 0.3 1 119514 7299 71 132039 0.3 1 124540 7499 72 125242 0.3 1 118005 7237 73 130262 0.3 1 123006 7256 74 119815 0.3 1 112862 6953 75 114051 0.3 1 107533 6518 76 111158 0.3 1 104747 6411 77 111769 0.3 1 105274 6495 78 104990 0.3 1 98882 6108 79 101071 0.3 1 95399 5672 80 100953 0.3 1 95281 5672 81 99176 0.3 1 93590 5586 82 94350 0.3 1 89142 5208 83 91413 0.3 1 86366 5047 84 87258 0.3 1 82554 4704 85 85916 0.3 1 81265 4651 86 84604 0.3 1 80107 4497 87 84396 0.3 1 79885 4511 88 82425 0.3 1 78207 4218 89 73764 0.3 1 69903 3861 90 71339 0.3 1 67438 3901 91 67256 0.3 1 63682 3574 92 62204 0.3 1 58897 3307 93 60201 0.3 1 57003 3198 94 58001 0.3 1 54921 3080 95 54924 0.3 1 52030 2894 96 52451 0.3 1 49666 2785 97 48389 0.3 1 45913 2476 98 44117 0.3 1 41843 2274 99 42086 0.3 1 39795 2291 100 38235 0.3 1 36240 1995 101 35522 0.3 1 33621 1901 102 32226 0.3 1 30512 1714 103 29643 0.3 1 27969 1674 104 28709 0.3 1 27141 1568 105 25222 0.3 1 23921 1301 106 23132 0.3 1 21958 1174 107 20950 0.3 1 19852 1098 108 19130 0.3 1 18127 1003 109 16951 0.3 1 16010 941 110 15532 0.3 1 14697 835 111 14263 0.3 1 13491 772 112 12448 0.3 1 11737 711 113 11105 0.3 1 10532 573 114 9378 0.3 1 8878 500 115 8004 0.3 1 7541 463 116 7028 0.3 1 6643 385 117 5705 0.3 1 5388 317 118 5009 0.3 1 4724 285 119 4196 0.3 1 3948 248 120 3592 0.3 1 3360 232 121 3098 0.3 1 2900 198 122 2572 0.3 1 2409 163 123 2164 0.3 1 2037 127 124 1827 0.3 1 1705 122 125 1543 0.3 1 1435 108 126 1244 0.3 1 1160 84 127 1099 0.3 1 1018 81 128 829 0.3 1 778 51 129 718 0.3 1 677 41 130 539 0.3 1 503 36 131 460 0.3 1 425 35 132 375 0.3 1 343 32 133 337 0.3 1 318 19 134 432 0.3 1 410 22 135 267 0.3 1 250 17 136 145 0.3 1 136 9 137 88 0.3 1 77 11 138 77 0.3 1 69 8 139 43 0.3 1 40 3 140 29 0.3 1 26 3 141 28 0.3 1 23 5 142 25 0.3 1 23 2 143 30 0.3 1 30 144 16 0.3 1 15 1 145 18 0.3 1 15 3 146 29 0.3 1 26 3 147 70 0.3 1 66 4 148 40 0.3 1 37 3 149 46 0.3 1 43 3 150 248 0.3 1 232 16 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/CTRL_16C_26psu_1_S19_L002_R2_001.fastq.gz ============================================= 18490322 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 18490322 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 136982 (0.74%)