SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/CTRL_8C_26psu_2_S18_L001_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: 751160). Second best hit was Nextera (count: 1) 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_8C_26psu_2_S18_L001_R1_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 53.93 s (3 us/read; 18.89 M reads/minute). === Summary === Total reads processed: 16,982,389 Reads with adapters: 15,316,406 (90.2%) Reads written (passing filters): 16,982,389 (100.0%) Total basepairs processed: 2,547,358,350 bp Quality-trimmed: 5,122,052 bp (0.2%) Total written (filtered): 1,661,718,543 bp (65.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 15316406 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.1% C: 17.9% G: 21.3% T: 32.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 934198 4245597.2 0 934198 2 161909 1061399.3 0 161909 3 105071 265349.8 0 105071 4 65361 66337.5 0 65361 5 61151 16584.4 0 61151 6 60130 4146.1 0 60130 7 51265 1036.5 0 51265 8 64755 259.1 0 64755 9 64351 64.8 0 63580 771 10 61337 16.2 1 58020 3317 11 70221 4.0 1 64705 5516 12 66216 1.0 1 61889 4327 13 69137 0.3 1 64630 4507 14 70780 0.3 1 65742 5038 15 75204 0.3 1 70097 5107 16 73779 0.3 1 68019 5760 17 90043 0.3 1 82540 7503 18 81214 0.3 1 76392 4822 19 66550 0.3 1 62390 4160 20 83867 0.3 1 78220 5647 21 92423 0.3 1 86031 6392 22 79989 0.3 1 75306 4683 23 93784 0.3 1 87424 6360 24 89031 0.3 1 81718 7313 25 96197 0.3 1 89537 6660 26 88926 0.3 1 83710 5216 27 100077 0.3 1 92668 7409 28 100613 0.3 1 93553 7060 29 104938 0.3 1 96491 8447 30 117488 0.3 1 110880 6608 31 89018 0.3 1 83492 5526 32 107667 0.3 1 100716 6951 33 110564 0.3 1 102547 8017 34 137673 0.3 1 127216 10457 35 119092 0.3 1 112273 6819 36 94075 0.3 1 88092 5983 37 125638 0.3 1 116775 8863 38 138305 0.3 1 128145 10160 39 120373 0.3 1 113314 7059 40 138522 0.3 1 128397 10125 41 158012 0.3 1 146728 11284 42 111371 0.3 1 103118 8253 43 217278 0.3 1 206218 11060 44 57407 0.3 1 51985 5422 45 143497 0.3 1 134258 9239 46 142849 0.3 1 133725 9124 47 147972 0.3 1 139076 8896 48 148858 0.3 1 138933 9925 49 163896 0.3 1 152740 11156 50 140197 0.3 1 131951 8246 51 154425 0.3 1 144692 9733 52 163399 0.3 1 151525 11874 53 181558 0.3 1 170911 10647 54 136765 0.3 1 128031 8734 55 172905 0.3 1 161877 11028 56 211987 0.3 1 200164 11823 57 138899 0.3 1 129027 9872 58 181048 0.3 1 171675 9373 59 152882 0.3 1 143208 9674 60 179132 0.3 1 167976 11156 61 179957 0.3 1 169292 10665 62 195431 0.3 1 184537 10894 63 158140 0.3 1 148011 10129 64 177885 0.3 1 167763 10122 65 200563 0.3 1 188662 11901 66 211859 0.3 1 199050 12809 67 228942 0.3 1 211658 17284 68 447452 0.3 1 426829 20623 69 83220 0.3 1 76361 6859 70 30543 0.3 1 25376 5167 71 119720 0.3 1 112578 7142 72 172151 0.3 1 162467 9684 73 185670 0.3 1 174903 10767 74 186107 0.3 1 175086 11021 75 187142 0.3 1 176040 11102 76 187583 0.3 1 176804 10779 77 190166 0.3 1 178927 11239 78 180337 0.3 1 169693 10644 79 182061 0.3 1 171352 10709 80 179279 0.3 1 168912 10367 81 180871 0.3 1 170399 10472 82 177227 0.3 1 166777 10450 83 175671 0.3 1 165379 10292 84 171899 0.3 1 161834 10065 85 167562 0.3 1 157917 9645 86 164690 0.3 1 155117 9573 87 159808 0.3 1 150364 9444 88 160575 0.3 1 151109 9466 89 154675 0.3 1 145660 9015 90 155657 0.3 1 146266 9391 91 151129 0.3 1 142165 8964 92 144841 0.3 1 136295 8546 93 137285 0.3 1 129298 7987 94 135380 0.3 1 127295 8085 95 127081 0.3 1 119343 7738 96 122579 0.3 1 115210 7369 97 117441 0.3 1 110330 7111 98 110426 0.3 1 103591 6835 99 109189 0.3 1 102159 7030 100 100853 0.3 1 94763 6090 101 96345 0.3 1 90423 5922 102 89845 0.3 1 84149 5696 103 85390 0.3 1 80150 5240 104 79941 0.3 1 74924 5017 105 72924 0.3 1 68266 4658 106 67356 0.3 1 63014 4342 107 62697 0.3 1 58614 4083 108 60572 0.3 1 56580 3992 109 54023 0.3 1 50378 3645 110 49550 0.3 1 46112 3438 111 45365 0.3 1 42247 3118 112 40518 0.3 1 37628 2890 113 35484 0.3 1 32846 2638 114 32042 0.3 1 29706 2336 115 28111 0.3 1 26004 2107 116 25248 0.3 1 23329 1919 117 21991 0.3 1 20192 1799 118 18981 0.3 1 17374 1607 119 16315 0.3 1 14943 1372 120 14190 0.3 1 13063 1127 121 12626 0.3 1 11644 982 122 10330 0.3 1 9443 887 123 9025 0.3 1 8218 807 124 7634 0.3 1 6995 639 125 6434 0.3 1 5834 600 126 5520 0.3 1 5002 518 127 4681 0.3 1 4249 432 128 3676 0.3 1 3257 419 129 3146 0.3 1 2839 307 130 2431 0.3 1 2189 242 131 2160 0.3 1 1904 256 132 1916 0.3 1 1719 197 133 2331 0.3 1 2120 211 134 4696 0.3 1 4441 255 135 1717 0.3 1 1602 115 136 624 0.3 1 562 62 137 434 0.3 1 390 44 138 279 0.3 1 239 40 139 193 0.3 1 171 22 140 139 0.3 1 121 18 141 116 0.3 1 101 15 142 99 0.3 1 87 12 143 71 0.3 1 56 15 144 68 0.3 1 49 19 145 142 0.3 1 121 21 146 149 0.3 1 136 13 147 732 0.3 1 658 74 148 489 0.3 1 451 38 149 276 0.3 1 251 25 150 3068 0.3 1 2637 431 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/CTRL_8C_26psu_2_S18_L001_R1_001.fastq.gz ============================================= 16982389 sequences processed in total