SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/CTRL_16C_26psu_2_S21_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: 698110). 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_2_S21_L001_R1_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 47.95 s (4 us/read; 16.81 M reads/minute). === Summary === Total reads processed: 13,433,110 Reads with adapters: 11,700,096 (87.1%) Reads written (passing filters): 13,433,110 (100.0%) Total basepairs processed: 2,014,966,500 bp Quality-trimmed: 3,988,642 bp (0.2%) Total written (filtered): 1,426,352,975 bp (70.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11700096 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.8% C: 12.5% G: 23.6% T: 35.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 952009 3358277.5 0 952009 2 175701 839569.4 0 175701 3 106315 209892.3 0 106315 4 68924 52473.1 0 68924 5 62282 13118.3 0 62282 6 61633 3279.6 0 61633 7 52554 819.9 0 52554 8 65132 205.0 0 65132 9 65306 51.2 0 64521 785 10 61900 12.8 1 58796 3104 11 68989 3.2 1 63880 5109 12 67245 0.8 1 63248 3997 13 69213 0.2 1 64859 4354 14 71768 0.2 1 66846 4922 15 75062 0.2 1 70553 4509 16 74514 0.2 1 69133 5381 17 90491 0.2 1 83695 6796 18 77417 0.2 1 72980 4437 19 68949 0.2 1 64670 4279 20 81015 0.2 1 76032 4983 21 89626 0.2 1 83646 5980 22 77941 0.2 1 73613 4328 23 90688 0.2 1 84959 5729 24 86332 0.2 1 79509 6823 25 91755 0.2 1 85888 5867 26 86085 0.2 1 81297 4788 27 95329 0.2 1 88851 6478 28 95528 0.2 1 89551 5977 29 99349 0.2 1 92034 7315 30 106567 0.2 1 101023 5544 31 85587 0.2 1 80666 4921 32 103697 0.2 1 97691 6006 33 99669 0.2 1 93324 6345 34 119451 0.2 1 111551 7900 35 94360 0.2 1 88955 5405 36 108596 0.2 1 102097 6499 37 113594 0.2 1 106631 6963 38 108790 0.2 1 101383 7407 39 126706 0.2 1 119375 7331 40 103711 0.2 1 97817 5894 41 130432 0.2 1 122153 8279 42 110139 0.2 1 101991 8148 43 183261 0.2 1 174857 8404 44 57830 0.2 1 53254 4576 45 123796 0.2 1 116975 6821 46 119988 0.2 1 113024 6964 47 130141 0.2 1 122976 7165 48 120988 0.2 1 113912 7076 49 138463 0.2 1 129394 9069 50 122247 0.2 1 115770 6477 51 132587 0.2 1 124814 7773 52 139338 0.2 1 129873 9465 53 153954 0.2 1 145822 8132 54 118275 0.2 1 111358 6917 55 139368 0.2 1 131390 7978 56 164199 0.2 1 155690 8509 57 126552 0.2 1 118427 8125 58 144214 0.2 1 137457 6757 59 116278 0.2 1 109533 6745 60 144971 0.2 1 136747 8224 61 139800 0.2 1 132274 7526 62 147932 0.2 1 140286 7646 63 129438 0.2 1 121520 7918 64 136148 0.2 1 129121 7027 65 148136 0.2 1 139981 8155 66 158867 0.2 1 150035 8832 67 172296 0.2 1 160373 11923 68 325502 0.2 1 311428 14074 69 62909 0.2 1 58208 4701 70 23526 0.2 1 20186 3340 71 82740 0.2 1 78158 4582 72 124178 0.2 1 117785 6393 73 132921 0.2 1 125940 6981 74 131071 0.2 1 124071 7000 75 128974 0.2 1 122028 6946 76 128069 0.2 1 121139 6930 77 126522 0.2 1 119822 6700 78 120502 0.2 1 113788 6714 79 118821 0.2 1 112166 6655 80 115866 0.2 1 109547 6319 81 115264 0.2 1 108988 6276 82 110755 0.2 1 104576 6179 83 107566 0.2 1 101669 5897 84 105597 0.2 1 99846 5751 85 102751 0.2 1 97220 5531 86 97615 0.2 1 92219 5396 87 92989 0.2 1 87786 5203 88 92437 0.2 1 87288 5149 89 88099 0.2 1 83258 4841 90 86764 0.2 1 81847 4917 91 81829 0.2 1 77279 4550 92 77590 0.2 1 73265 4325 93 73175 0.2 1 69095 4080 94 69476 0.2 1 65477 3999 95 65431 0.2 1 61622 3809 96 61527 0.2 1 57946 3581 97 57358 0.2 1 54065 3293 98 53633 0.2 1 50498 3135 99 51351 0.2 1 48285 3066 100 46130 0.2 1 43457 2673 101 43563 0.2 1 40904 2659 102 39390 0.2 1 37016 2374 103 35867 0.2 1 33682 2185 104 32606 0.2 1 30634 1972 105 28646 0.2 1 26808 1838 106 26227 0.2 1 24640 1587 107 23172 0.2 1 21743 1429 108 21298 0.2 1 19891 1407 109 18913 0.2 1 17580 1333 110 16998 0.2 1 15871 1127 111 15038 0.2 1 14044 994 112 12635 0.2 1 11815 820 113 11352 0.2 1 10604 748 114 9838 0.2 1 9171 667 115 8151 0.2 1 7529 622 116 7025 0.2 1 6508 517 117 5831 0.2 1 5406 425 118 5154 0.2 1 4783 371 119 4064 0.2 1 3743 321 120 3640 0.2 1 3365 275 121 2769 0.2 1 2540 229 122 2341 0.2 1 2118 223 123 2056 0.2 1 1883 173 124 1687 0.2 1 1543 144 125 1340 0.2 1 1233 107 126 1317 0.2 1 1201 116 127 1059 0.2 1 975 84 128 810 0.2 1 740 70 129 681 0.2 1 600 81 130 748 0.2 1 679 69 131 837 0.2 1 795 42 132 954 0.2 1 903 51 133 1339 0.2 1 1266 73 134 1750 0.2 1 1667 83 135 759 0.2 1 718 41 136 229 0.2 1 209 20 137 121 0.2 1 104 17 138 84 0.2 1 73 11 139 75 0.2 1 63 12 140 73 0.2 1 58 15 141 35 0.2 1 32 3 142 38 0.2 1 35 3 143 19 0.2 1 15 4 144 19 0.2 1 11 8 145 22 0.2 1 21 1 146 64 0.2 1 59 5 147 278 0.2 1 250 28 148 168 0.2 1 142 26 149 83 0.2 1 70 13 150 577 0.2 1 506 71 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/CTRL_16C_26psu_2_S21_L001_R1_001.fastq.gz ============================================= 13433110 sequences processed in total