SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_32psu_2_S2_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: 626101). 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_32psu_2_S2_L001_R1_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 60.24 s (3 us/read; 17.66 M reads/minute). === Summary === Total reads processed: 17,734,461 Reads with adapters: 14,777,967 (83.3%) Reads written (passing filters): 17,734,461 (100.0%) Total basepairs processed: 2,660,169,150 bp Quality-trimmed: 5,148,925 bp (0.2%) Total written (filtered): 1,960,839,520 bp (73.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14777967 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.6% C: 12.9% G: 21.9% T: 35.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1738050 4433615.2 0 1738050 2 278207 1108403.8 0 278207 3 163757 277101.0 0 163757 4 100314 69275.2 0 100314 5 85611 17318.8 0 85611 6 82934 4329.7 0 82934 7 71901 1082.4 0 71901 8 92752 270.6 0 92752 9 83307 67.7 0 82257 1050 10 83535 16.9 1 78970 4565 11 92909 4.2 1 85625 7284 12 89396 1.1 1 83407 5989 13 91391 0.3 1 85129 6262 14 92986 0.3 1 86205 6781 15 95417 0.3 1 88994 6423 16 96485 0.3 1 89177 7308 17 117735 0.3 1 108243 9492 18 99811 0.3 1 93600 6211 19 87560 0.3 1 81823 5737 20 104404 0.3 1 97366 7038 21 115608 0.3 1 107491 8117 22 99044 0.3 1 93521 5523 23 114295 0.3 1 106563 7732 24 108405 0.3 1 99404 9001 25 115898 0.3 1 108064 7834 26 106400 0.3 1 100103 6297 27 119862 0.3 1 110913 8949 28 117009 0.3 1 108719 8290 29 126066 0.3 1 115846 10220 30 135672 0.3 1 127802 7870 31 103769 0.3 1 96862 6907 32 134576 0.3 1 125712 8864 33 115506 0.3 1 107678 7828 34 131922 0.3 1 122476 9446 35 139540 0.3 1 128729 10811 36 129944 0.3 1 121921 8023 37 155181 0.3 1 145058 10123 38 125033 0.3 1 115777 9256 39 137711 0.3 1 129241 8470 40 145763 0.3 1 136531 9232 41 145406 0.3 1 134994 10412 42 140227 0.3 1 129509 10718 43 213869 0.3 1 202923 10946 44 71935 0.3 1 65627 6308 45 151697 0.3 1 142261 9436 46 139466 0.3 1 130673 8793 47 151314 0.3 1 141909 9405 48 149772 0.3 1 140199 9573 49 163566 0.3 1 152198 11368 50 142863 0.3 1 134146 8717 51 154145 0.3 1 144042 10103 52 159345 0.3 1 148339 11006 53 168861 0.3 1 158401 10460 54 140944 0.3 1 132160 8784 55 163358 0.3 1 152729 10629 56 198374 0.3 1 186858 11516 57 129041 0.3 1 119923 9118 58 168939 0.3 1 159723 9216 59 149936 0.3 1 140432 9504 60 161773 0.3 1 151304 10469 61 159837 0.3 1 150130 9707 62 178889 0.3 1 168432 10457 63 140394 0.3 1 131036 9358 64 159197 0.3 1 149784 9413 65 178150 0.3 1 167258 10892 66 185093 0.3 1 173786 11307 67 199374 0.3 1 184232 15142 68 376952 0.3 1 359289 17663 69 53765 0.3 1 48910 4855 70 23496 0.3 1 19245 4251 71 105909 0.3 1 99682 6227 72 143025 0.3 1 134667 8358 73 150010 0.3 1 141153 8857 74 148858 0.3 1 139863 8995 75 147559 0.3 1 138722 8837 76 146256 0.3 1 137657 8599 77 146473 0.3 1 137642 8831 78 139439 0.3 1 130923 8516 79 138812 0.3 1 130392 8420 80 134925 0.3 1 126986 7939 81 132740 0.3 1 124849 7891 82 129707 0.3 1 121848 7859 83 125045 0.3 1 117720 7325 84 120955 0.3 1 113756 7199 85 117638 0.3 1 110705 6933 86 114999 0.3 1 108021 6978 87 110985 0.3 1 104322 6663 88 108344 0.3 1 101912 6432 89 103347 0.3 1 97100 6247 90 102084 0.3 1 95939 6145 91 97477 0.3 1 91376 6101 92 92174 0.3 1 86611 5563 93 86985 0.3 1 81755 5230 94 84316 0.3 1 79155 5161 95 78474 0.3 1 73684 4790 96 73594 0.3 1 68994 4600 97 68665 0.3 1 64422 4243 98 65130 0.3 1 60988 4142 99 62724 0.3 1 58428 4296 100 57069 0.3 1 53328 3741 101 53096 0.3 1 49656 3440 102 48453 0.3 1 45307 3146 103 44883 0.3 1 41855 3028 104 41860 0.3 1 39145 2715 105 37319 0.3 1 34804 2515 106 33117 0.3 1 30846 2271 107 30224 0.3 1 28086 2138 108 28577 0.3 1 26568 2009 109 24900 0.3 1 23148 1752 110 22182 0.3 1 20539 1643 111 19835 0.3 1 18458 1377 112 17455 0.3 1 16149 1306 113 15019 0.3 1 13793 1226 114 13036 0.3 1 12026 1010 115 11314 0.3 1 10380 934 116 9567 0.3 1 8809 758 117 8005 0.3 1 7289 716 118 6890 0.3 1 6310 580 119 5712 0.3 1 5183 529 120 4607 0.3 1 4200 407 121 4029 0.3 1 3642 387 122 3364 0.3 1 3030 334 123 2640 0.3 1 2382 258 124 2162 0.3 1 1941 221 125 1794 0.3 1 1596 198 126 1531 0.3 1 1353 178 127 1215 0.3 1 1098 117 128 1005 0.3 1 879 126 129 809 0.3 1 695 114 130 661 0.3 1 597 64 131 509 0.3 1 455 54 132 443 0.3 1 389 54 133 409 0.3 1 355 54 134 483 0.3 1 430 53 135 256 0.3 1 227 29 136 159 0.3 1 133 26 137 104 0.3 1 91 13 138 67 0.3 1 53 14 139 54 0.3 1 47 7 140 47 0.3 1 39 8 141 21 0.3 1 15 6 142 21 0.3 1 19 2 143 8 0.3 1 4 4 144 21 0.3 1 20 1 145 51 0.3 1 46 5 146 37 0.3 1 29 8 147 70 0.3 1 63 7 148 65 0.3 1 52 13 149 39 0.3 1 35 4 150 480 0.3 1 358 122 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_32psu_2_S2_L001_R1_001.fastq.gz ============================================= 17734461 sequences processed in total