SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_26psu_1_S13_L001_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: 538094). Second best hit was smallRNA (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_1_S13_L001_R2_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 84.20 s (4 us/read; 15.79 M reads/minute). === Summary === Total reads processed: 22,159,935 Reads with adapters: 17,263,070 (77.9%) Reads written (passing filters): 22,159,935 (100.0%) Total basepairs processed: 3,323,990,250 bp Quality-trimmed: 16,760,179 bp (0.5%) Total written (filtered): 2,603,569,143 bp (78.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 17263070 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.6% C: 12.4% G: 23.7% T: 35.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2980698 5539983.8 0 2980698 2 434290 1384995.9 0 434290 3 244115 346249.0 0 244115 4 143736 86562.2 0 143736 5 130207 21640.6 0 130207 6 112454 5410.1 0 112454 7 91383 1352.5 0 91383 8 130413 338.1 0 130413 9 102897 84.5 0 102495 402 10 113241 21.1 1 107719 5522 11 119188 5.3 1 111572 7616 12 120663 1.3 1 112735 7928 13 133942 0.3 1 125965 7977 14 126547 0.3 1 117452 9095 15 102830 0.3 1 96138 6692 16 149163 0.3 1 139761 9402 17 119889 0.3 1 111631 8258 18 113552 0.3 1 106594 6958 19 144826 0.3 1 135202 9624 20 135016 0.3 1 126722 8294 21 118040 0.3 1 110327 7713 22 135122 0.3 1 126795 8327 23 139623 0.3 1 130868 8755 24 139327 0.3 1 130312 9015 25 156486 0.3 1 147346 9140 26 131367 0.3 1 122873 8494 27 144343 0.3 1 134126 10217 28 135732 0.3 1 128445 7287 29 144460 0.3 1 135341 9119 30 143460 0.3 1 135475 7985 31 154935 0.3 1 145507 9428 32 140211 0.3 1 132501 7710 33 154714 0.3 1 145023 9691 34 197197 0.3 1 185506 11691 35 114069 0.3 1 107701 6368 36 154713 0.3 1 145095 9618 37 166945 0.3 1 157027 9918 38 155394 0.3 1 147358 8036 39 151879 0.3 1 143914 7965 40 168764 0.3 1 158797 9967 41 162964 0.3 1 154146 8818 42 166211 0.3 1 157158 9053 43 152395 0.3 1 144005 8390 44 174656 0.3 1 164812 9844 45 186871 0.3 1 176811 10060 46 135036 0.3 1 127666 7370 47 168636 0.3 1 159853 8783 48 166288 0.3 1 157802 8486 49 174530 0.3 1 165351 9179 50 164769 0.3 1 155907 8862 51 207765 0.3 1 197011 10754 52 147151 0.3 1 139795 7356 53 177051 0.3 1 168817 8234 54 133625 0.3 1 126900 6725 55 174567 0.3 1 166338 8229 56 178950 0.3 1 169886 9064 57 168945 0.3 1 161037 7908 58 161931 0.3 1 154618 7313 59 165789 0.3 1 157874 7915 60 171736 0.3 1 163328 8408 61 175826 0.3 1 167046 8780 62 192123 0.3 1 182534 9589 63 252743 0.3 1 241513 11230 64 207112 0.3 1 199124 7988 65 135660 0.3 1 129354 6306 66 145866 0.3 1 139110 6756 67 145748 0.3 1 138731 7017 68 146161 0.3 1 139522 6639 69 144487 0.3 1 137768 6719 70 154292 0.3 1 147160 7132 71 158353 0.3 1 151327 7026 72 150227 0.3 1 143181 7046 73 157376 0.3 1 150704 6672 74 144388 0.3 1 138042 6346 75 137234 0.3 1 131094 6140 76 133825 0.3 1 127901 5924 77 133664 0.3 1 127640 6024 78 127632 0.3 1 121889 5743 79 122934 0.3 1 117397 5537 80 122791 0.3 1 117317 5474 81 119094 0.3 1 113976 5118 82 115048 0.3 1 109953 5095 83 110957 0.3 1 106119 4838 84 107760 0.3 1 102959 4801 85 105919 0.3 1 100973 4946 86 104575 0.3 1 99936 4639 87 105119 0.3 1 100537 4582 88 102473 0.3 1 97892 4581 89 90861 0.3 1 86820 4041 90 87725 0.3 1 83791 3934 91 82796 0.3 1 79052 3744 92 76768 0.3 1 73386 3382 93 74497 0.3 1 71224 3273 94 71670 0.3 1 68502 3168 95 67300 0.3 1 64357 2943 96 63751 0.3 1 61088 2663 97 58781 0.3 1 56250 2531 98 54871 0.3 1 52462 2409 99 53000 0.3 1 50773 2227 100 48407 0.3 1 46381 2026 101 45093 0.3 1 43177 1916 102 40752 0.3 1 38996 1756 103 37584 0.3 1 35906 1678 104 35749 0.3 1 34226 1523 105 31850 0.3 1 30464 1386 106 29282 0.3 1 28064 1218 107 26084 0.3 1 24956 1128 108 23726 0.3 1 22669 1057 109 21646 0.3 1 20704 942 110 19323 0.3 1 18515 808 111 18235 0.3 1 17436 799 112 15797 0.3 1 15095 702 113 13713 0.3 1 13089 624 114 11968 0.3 1 11416 552 115 10124 0.3 1 9656 468 116 8777 0.3 1 8354 423 117 7339 0.3 1 6995 344 118 6452 0.3 1 6137 315 119 5422 0.3 1 5101 321 120 4499 0.3 1 4281 218 121 3883 0.3 1 3680 203 122 3313 0.3 1 3156 157 123 2807 0.3 1 2669 138 124 2400 0.3 1 2285 115 125 2022 0.3 1 1907 115 126 1650 0.3 1 1555 95 127 1434 0.3 1 1346 88 128 1129 0.3 1 1055 74 129 969 0.3 1 902 67 130 682 0.3 1 644 38 131 587 0.3 1 552 35 132 523 0.3 1 500 23 133 524 0.3 1 494 30 134 633 0.3 1 604 29 135 337 0.3 1 318 19 136 197 0.3 1 186 11 137 147 0.3 1 133 14 138 92 0.3 1 88 4 139 79 0.3 1 71 8 140 57 0.3 1 52 5 141 37 0.3 1 35 2 142 37 0.3 1 35 2 143 25 0.3 1 20 5 144 20 0.3 1 20 145 26 0.3 1 25 1 146 24 0.3 1 23 1 147 85 0.3 1 85 148 61 0.3 1 59 2 149 39 0.3 1 36 3 150 325 0.3 1 310 15 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_26psu_1_S13_L001_R2_001.fastq.gz ============================================= 22159935 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 22159935 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 183151 (0.83%)