SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_26psu_3_S15_L002_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: 474456). 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/16C_26psu_3_S15_L002_R1_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 56.53 s (4 us/read; 15.52 M reads/minute). === Summary === Total reads processed: 14,622,552 Reads with adapters: 11,026,853 (75.4%) Reads written (passing filters): 14,622,552 (100.0%) Total basepairs processed: 2,193,382,800 bp Quality-trimmed: 5,795,035 bp (0.3%) Total written (filtered): 1,756,312,964 bp (80.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11026853 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.2% C: 18.2% G: 19.4% T: 32.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2255035 3655638.0 0 2255035 2 341709 913909.5 0 341709 3 202869 228477.4 0 202869 4 99930 57119.3 0 99930 5 74502 14279.8 0 74502 6 72604 3570.0 0 72604 7 55151 892.5 0 55151 8 72986 223.1 0 72986 9 72897 55.8 0 71832 1065 10 66371 13.9 1 61637 4734 11 77738 3.5 1 70168 7570 12 72088 0.9 1 66222 5866 13 72584 0.2 1 66413 6171 14 75037 0.2 1 68093 6944 15 77546 0.2 1 70821 6725 16 76138 0.2 1 68711 7427 17 96440 0.2 1 86428 10012 18 77278 0.2 1 71237 6041 19 65884 0.2 1 60354 5530 20 80966 0.2 1 74091 6875 21 91593 0.2 1 83562 8031 22 72795 0.2 1 67343 5452 23 89502 0.2 1 81872 7630 24 80431 0.2 1 72300 8131 25 87978 0.2 1 80303 7675 26 79303 0.2 1 73214 6089 27 90256 0.2 1 81812 8444 28 88151 0.2 1 80669 7482 29 90769 0.2 1 81855 8914 30 100156 0.2 1 92655 7501 31 70749 0.2 1 65028 5721 32 94056 0.2 1 86125 7931 33 85223 0.2 1 77723 7500 34 93938 0.2 1 85684 8254 35 95264 0.2 1 85673 9591 36 98487 0.2 1 89904 8583 37 91367 0.2 1 84496 6871 38 91067 0.2 1 83299 7768 39 98566 0.2 1 90240 8326 40 98669 0.2 1 89677 8992 41 109128 0.2 1 98383 10745 42 90124 0.2 1 81722 8402 43 141587 0.2 1 131681 9906 44 48458 0.2 1 43335 5123 45 101474 0.2 1 92754 8720 46 96951 0.2 1 88935 8016 47 101587 0.2 1 93762 7825 48 93451 0.2 1 85286 8165 49 109864 0.2 1 100369 9495 50 86419 0.2 1 80081 6338 51 97144 0.2 1 89290 7854 52 106661 0.2 1 96904 9757 53 115583 0.2 1 107526 8057 54 81720 0.2 1 74951 6769 55 103125 0.2 1 94975 8150 56 119342 0.2 1 110505 8837 57 94296 0.2 1 86511 7785 58 95906 0.2 1 89537 6369 59 78497 0.2 1 71935 6562 60 103672 0.2 1 95850 7822 61 99103 0.2 1 91989 7114 62 98519 0.2 1 91357 7162 63 92047 0.2 1 85069 6978 64 87141 0.2 1 80859 6282 65 98035 0.2 1 90511 7524 66 104856 0.2 1 96876 7980 67 112499 0.2 1 102554 9945 68 203504 0.2 1 191009 12495 69 62594 0.2 1 57415 5179 70 23252 0.2 1 19824 3428 71 45182 0.2 1 41443 3739 72 77078 0.2 1 71850 5228 73 85031 0.2 1 79046 5985 74 84254 0.2 1 78257 5997 75 83996 0.2 1 77711 6285 76 82731 0.2 1 76446 6285 77 82380 0.2 1 76363 6017 78 77279 0.2 1 71312 5967 79 77209 0.2 1 71223 5986 80 74817 0.2 1 69029 5788 81 73406 0.2 1 67839 5567 82 72738 0.2 1 67207 5531 83 69208 0.2 1 64025 5183 84 68393 0.2 1 63216 5177 85 66034 0.2 1 60887 5147 86 63919 0.2 1 59135 4784 87 60801 0.2 1 56313 4488 88 60788 0.2 1 56093 4695 89 57692 0.2 1 53269 4423 90 56584 0.2 1 52478 4106 91 53589 0.2 1 49546 4043 92 51833 0.2 1 47890 3943 93 48199 0.2 1 44575 3624 94 46944 0.2 1 43278 3666 95 43653 0.2 1 40307 3346 96 41698 0.2 1 38443 3255 97 38960 0.2 1 36083 2877 98 36779 0.2 1 33843 2936 99 34473 0.2 1 31757 2716 100 32693 0.2 1 30095 2598 101 30447 0.2 1 28045 2402 102 27845 0.2 1 25608 2237 103 26414 0.2 1 24289 2125 104 24929 0.2 1 23050 1879 105 21773 0.2 1 20195 1578 106 20226 0.2 1 18586 1640 107 18400 0.2 1 16897 1503 108 17326 0.2 1 15891 1435 109 15645 0.2 1 14342 1303 110 14020 0.2 1 12816 1204 111 12849 0.2 1 11744 1105 112 11234 0.2 1 10286 948 113 9985 0.2 1 9120 865 114 8637 0.2 1 7820 817 115 7857 0.2 1 7138 719 116 6705 0.2 1 6073 632 117 6037 0.2 1 5491 546 118 5126 0.2 1 4659 467 119 4476 0.2 1 4067 409 120 3856 0.2 1 3446 410 121 3506 0.2 1 3100 406 122 2914 0.2 1 2611 303 123 2582 0.2 1 2308 274 124 2250 0.2 1 1996 254 125 1869 0.2 1 1644 225 126 1660 0.2 1 1451 209 127 1486 0.2 1 1318 168 128 1135 0.2 1 1016 119 129 1048 0.2 1 958 90 130 730 0.2 1 642 88 131 781 0.2 1 698 83 132 769 0.2 1 708 61 133 1082 0.2 1 1006 76 134 1977 0.2 1 1867 110 135 796 0.2 1 751 45 136 320 0.2 1 290 30 137 204 0.2 1 187 17 138 179 0.2 1 161 18 139 112 0.2 1 104 8 140 111 0.2 1 94 17 141 71 0.2 1 68 3 142 79 0.2 1 67 12 143 106 0.2 1 93 13 144 63 0.2 1 61 2 145 233 0.2 1 213 20 146 995 0.2 1 960 35 147 4990 0.2 1 4774 216 148 3265 0.2 1 3135 130 149 1955 0.2 1 1846 109 150 16845 0.2 1 15820 1025 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_26psu_3_S15_L002_R1_001.fastq.gz ============================================= 14622552 sequences processed in total