SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_26psu_4_S12_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: 414349). 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/8C_26psu_4_S12_L001_R1_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 47.96 s (4 us/read; 15.75 M reads/minute). === Summary === Total reads processed: 12,592,704 Reads with adapters: 8,958,992 (71.1%) Reads written (passing filters): 12,592,704 (100.0%) Total basepairs processed: 1,888,905,600 bp Quality-trimmed: 4,951,530 bp (0.3%) Total written (filtered): 1,571,128,982 bp (83.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 8958992 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 31.4% C: 15.5% G: 17.3% T: 35.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2360389 3148176.0 0 2360389 2 294874 787044.0 0 294874 3 161693 196761.0 0 161693 4 87416 49190.2 0 87416 5 59722 12297.6 0 59722 6 57196 3074.4 0 57196 7 45727 768.6 0 45727 8 58159 192.1 0 58159 9 58762 48.0 0 57759 1003 10 54824 12.0 1 51199 3625 11 61143 3.0 1 55667 5476 12 58318 0.8 1 53717 4601 13 56920 0.2 1 52502 4418 14 60297 0.2 1 55050 5247 15 60573 0.2 1 55708 4865 16 61479 0.2 1 55954 5525 17 74409 0.2 1 67438 6971 18 61009 0.2 1 56681 4328 19 53089 0.2 1 48849 4240 20 63972 0.2 1 58870 5102 21 70043 0.2 1 64287 5756 22 58590 0.2 1 54441 4149 23 68150 0.2 1 62728 5422 24 64229 0.2 1 58023 6206 25 68130 0.2 1 62567 5563 26 62420 0.2 1 57820 4600 27 69993 0.2 1 63874 6119 28 67875 0.2 1 62387 5488 29 71196 0.2 1 64376 6820 30 75799 0.2 1 70433 5366 31 59056 0.2 1 54472 4584 32 73671 0.2 1 68075 5596 33 63947 0.2 1 58700 5247 34 74583 0.2 1 67925 6658 35 70104 0.2 1 64152 5952 36 77250 0.2 1 71393 5857 37 68309 0.2 1 62839 5470 38 72505 0.2 1 67371 5134 39 75409 0.2 1 69866 5543 40 72478 0.2 1 66543 5935 41 78235 0.2 1 70876 7359 42 73557 0.2 1 66866 6691 43 105788 0.2 1 99220 6568 44 39203 0.2 1 34910 4293 45 75980 0.2 1 70161 5819 46 74377 0.2 1 68346 6031 47 78776 0.2 1 72951 5825 48 70677 0.2 1 64756 5921 49 81336 0.2 1 74410 6926 50 66909 0.2 1 62092 4817 51 72737 0.2 1 67212 5525 52 78934 0.2 1 71865 7069 53 86579 0.2 1 80550 6029 54 62022 0.2 1 57173 4849 55 75974 0.2 1 70348 5626 56 85877 0.2 1 79807 6070 57 71505 0.2 1 65936 5569 58 69856 0.2 1 65606 4250 59 57167 0.2 1 52447 4720 60 78076 0.2 1 72356 5720 61 73472 0.2 1 68201 5271 62 71844 0.2 1 66745 5099 63 67131 0.2 1 62070 5061 64 65598 0.2 1 60901 4697 65 70779 0.2 1 65435 5344 66 77405 0.2 1 71580 5825 67 84608 0.2 1 76761 7847 68 150617 0.2 1 142058 8559 69 37132 0.2 1 33982 3150 70 13103 0.2 1 10914 2189 71 35026 0.2 1 32099 2927 72 57779 0.2 1 53691 4088 73 61230 0.2 1 56931 4299 74 61166 0.2 1 56777 4389 75 60302 0.2 1 55958 4344 76 59928 0.2 1 55484 4444 77 59440 0.2 1 54970 4470 78 56149 0.2 1 51928 4221 79 55286 0.2 1 51002 4284 80 53792 0.2 1 49846 3946 81 52637 0.2 1 48756 3881 82 51226 0.2 1 47353 3873 83 49579 0.2 1 45690 3889 84 48468 0.2 1 44896 3572 85 45867 0.2 1 42408 3459 86 44887 0.2 1 41555 3332 87 42251 0.2 1 38964 3287 88 42216 0.2 1 39029 3187 89 40149 0.2 1 37066 3083 90 40387 0.2 1 37102 3285 91 37214 0.2 1 34343 2871 92 35614 0.2 1 32860 2754 93 33363 0.2 1 30676 2687 94 32052 0.2 1 29598 2454 95 29858 0.2 1 27450 2408 96 28594 0.2 1 26301 2293 97 26730 0.2 1 24584 2146 98 25261 0.2 1 23132 2129 99 24232 0.2 1 22120 2112 100 22159 0.2 1 20358 1801 101 20488 0.2 1 18713 1775 102 19117 0.2 1 17450 1667 103 17468 0.2 1 15984 1484 104 16181 0.2 1 14728 1453 105 14521 0.2 1 13231 1290 106 13349 0.2 1 12105 1244 107 12159 0.2 1 11005 1154 108 11376 0.2 1 10302 1074 109 10099 0.2 1 9151 948 110 9379 0.2 1 8450 929 111 8577 0.2 1 7720 857 112 7623 0.2 1 6797 826 113 6486 0.2 1 5771 715 114 5676 0.2 1 5112 564 115 5089 0.2 1 4501 588 116 4254 0.2 1 3781 473 117 3599 0.2 1 3183 416 118 3110 0.2 1 2758 352 119 2723 0.2 1 2363 360 120 2307 0.2 1 1995 312 121 2051 0.2 1 1780 271 122 1835 0.2 1 1588 247 123 1508 0.2 1 1291 217 124 1263 0.2 1 1083 180 125 1119 0.2 1 966 153 126 1055 0.2 1 916 139 127 900 0.2 1 780 120 128 681 0.2 1 568 113 129 550 0.2 1 468 82 130 520 0.2 1 423 97 131 523 0.2 1 467 56 132 590 0.2 1 526 64 133 974 0.2 1 878 96 134 2631 0.2 1 2466 165 135 822 0.2 1 768 54 136 169 0.2 1 154 15 137 111 0.2 1 90 21 138 83 0.2 1 75 8 139 53 0.2 1 41 12 140 56 0.2 1 43 13 141 26 0.2 1 20 6 142 15 0.2 1 12 3 143 20 0.2 1 16 4 144 56 0.2 1 47 9 145 231 0.2 1 197 34 146 229 0.2 1 199 30 147 1212 0.2 1 1078 134 148 767 0.2 1 701 66 149 472 0.2 1 430 42 150 3085 0.2 1 2595 490 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_26psu_4_S12_L001_R1_001.fastq.gz ============================================= 12592704 sequences processed in total