SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/CTRL_16C_26psu_2_S21_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: 689591). 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_L002_R2_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 50.13 s (4 us/read; 16.05 M reads/minute). === Summary === Total reads processed: 13,408,232 Reads with adapters: 11,603,960 (86.5%) Reads written (passing filters): 13,408,232 (100.0%) Total basepairs processed: 2,011,234,800 bp Quality-trimmed: 8,433,724 bp (0.4%) Total written (filtered): 1,430,263,611 bp (71.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11603960 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.1% C: 11.7% G: 26.2% T: 34.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1017131 3352058.0 0 1017131 2 177058 838014.5 0 177058 3 112787 209503.6 0 112787 4 67003 52375.9 0 67003 5 66504 13094.0 0 66504 6 60966 3273.5 0 60966 7 50684 818.4 0 50684 8 71309 204.6 0 71309 9 56145 51.1 0 55917 228 10 61633 12.8 1 57525 4108 11 66766 3.2 1 61633 5133 12 66970 0.8 1 61817 5153 13 77136 0.2 1 71259 5877 14 74020 0.2 1 67910 6110 15 60571 0.2 1 56229 4342 16 86270 0.2 1 79871 6399 17 75982 0.2 1 70248 5734 18 65820 0.2 1 61090 4730 19 87582 0.2 1 81169 6413 20 81347 0.2 1 75534 5813 21 71738 0.2 1 66607 5131 22 82571 0.2 1 76726 5845 23 87855 0.2 1 81586 6269 24 88796 0.2 1 82344 6452 25 99857 0.2 1 93510 6347 26 83385 0.2 1 77300 6085 27 93625 0.2 1 86769 6856 28 85817 0.2 1 80874 4943 29 96248 0.2 1 90002 6246 30 93727 0.2 1 88168 5559 31 103646 0.2 1 97099 6547 32 90867 0.2 1 85391 5476 33 105892 0.2 1 98959 6933 34 137038 0.2 1 128489 8549 35 77044 0.2 1 72414 4630 36 105552 0.2 1 98517 7035 37 112682 0.2 1 105690 6992 38 106873 0.2 1 100867 6006 39 102355 0.2 1 96889 5466 40 117602 0.2 1 110487 7115 41 116162 0.2 1 109429 6733 42 121108 0.2 1 114095 7013 43 109639 0.2 1 103525 6114 44 129653 0.2 1 122002 7651 45 138376 0.2 1 130424 7952 46 97190 0.2 1 91779 5411 47 124803 0.2 1 118327 6476 48 124244 0.2 1 117667 6577 49 131343 0.2 1 123780 7563 50 128654 0.2 1 121411 7243 51 160151 0.2 1 151381 8770 52 116727 0.2 1 110469 6258 53 144929 0.2 1 137769 7160 54 104645 0.2 1 99281 5364 55 138649 0.2 1 131848 6801 56 142696 0.2 1 134983 7713 57 141410 0.2 1 134925 6485 58 134726 0.2 1 128298 6428 59 134797 0.2 1 128190 6607 60 140631 0.2 1 133581 7050 61 142568 0.2 1 135579 6989 62 160172 0.2 1 152064 8108 63 209874 0.2 1 200586 9288 64 163821 0.2 1 157603 6218 65 114086 0.2 1 108681 5405 66 126793 0.2 1 120700 6093 67 126587 0.2 1 120373 6214 68 128999 0.2 1 122868 6131 69 127101 0.2 1 121101 6000 70 133367 0.2 1 126848 6519 71 137940 0.2 1 131348 6592 72 133744 0.2 1 127253 6491 73 140847 0.2 1 134101 6746 74 131039 0.2 1 124610 6429 75 123648 0.2 1 117677 5971 76 121797 0.2 1 115805 5992 77 120668 0.2 1 114606 6062 78 116805 0.2 1 111027 5778 79 111250 0.2 1 105828 5422 80 110955 0.2 1 105751 5204 81 109348 0.2 1 104246 5102 82 103784 0.2 1 98831 4953 83 101052 0.2 1 96319 4733 84 98311 0.2 1 93628 4683 85 96878 0.2 1 92456 4422 86 95996 0.2 1 91571 4425 87 96605 0.2 1 92256 4349 88 93536 0.2 1 89501 4035 89 83632 0.2 1 79805 3827 90 80377 0.2 1 76751 3626 91 75608 0.2 1 72292 3316 92 71253 0.2 1 68176 3077 93 68064 0.2 1 65127 2937 94 65349 0.2 1 62356 2993 95 61296 0.2 1 58482 2814 96 57547 0.2 1 54961 2586 97 53666 0.2 1 51329 2337 98 50699 0.2 1 48576 2123 99 48177 0.2 1 46098 2079 100 43932 0.2 1 42005 1927 101 39615 0.2 1 37850 1765 102 35478 0.2 1 33828 1650 103 32345 0.2 1 30762 1583 104 30580 0.2 1 29207 1373 105 27062 0.2 1 25870 1192 106 24593 0.2 1 23539 1054 107 21633 0.2 1 20641 992 108 19150 0.2 1 18297 853 109 17101 0.2 1 16306 795 110 15550 0.2 1 14882 668 111 14159 0.2 1 13496 663 112 12046 0.2 1 11497 549 113 10553 0.2 1 10087 466 114 9330 0.2 1 8879 451 115 7323 0.2 1 7020 303 116 6173 0.2 1 5878 295 117 5159 0.2 1 4924 235 118 4546 0.2 1 4310 236 119 3676 0.2 1 3456 220 120 3075 0.2 1 2912 163 121 2608 0.2 1 2451 157 122 2115 0.2 1 1990 125 123 1712 0.2 1 1620 92 124 1534 0.2 1 1451 83 125 1259 0.2 1 1192 67 126 1123 0.2 1 1061 62 127 965 0.2 1 910 55 128 708 0.2 1 665 43 129 619 0.2 1 586 33 130 674 0.2 1 630 44 131 895 0.2 1 850 45 132 923 0.2 1 873 50 133 1446 0.2 1 1396 50 134 1648 0.2 1 1601 47 135 705 0.2 1 677 28 136 204 0.2 1 192 12 137 151 0.2 1 142 9 138 69 0.2 1 59 10 139 62 0.2 1 53 9 140 50 0.2 1 43 7 141 28 0.2 1 22 6 142 25 0.2 1 22 3 143 20 0.2 1 20 144 13 0.2 1 12 1 145 39 0.2 1 35 4 146 44 0.2 1 41 3 147 178 0.2 1 162 16 148 92 0.2 1 79 13 149 44 0.2 1 42 2 150 302 0.2 1 273 29 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/CTRL_16C_26psu_2_S21_L002_R2_001.fastq.gz ============================================= 13408232 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 13408232 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 132581 (0.99%)