SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_26psu_2_S10_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: 573873). 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_2_S10_L001_R2_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 71.70 s (4 us/read; 15.47 M reads/minute). === Summary === Total reads processed: 18,482,577 Reads with adapters: 14,753,598 (79.8%) Reads written (passing filters): 18,482,577 (100.0%) Total basepairs processed: 2,772,386,550 bp Quality-trimmed: 14,899,580 bp (0.5%) Total written (filtered): 2,113,888,686 bp (76.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14753598 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.7% C: 12.5% G: 24.2% T: 34.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2286581 4620644.2 0 2286581 2 330310 1155161.1 0 330310 3 190033 288790.3 0 190033 4 111417 72197.6 0 111417 5 101556 18049.4 0 101556 6 87150 4512.3 0 87150 7 71559 1128.1 0 71559 8 101450 282.0 0 101450 9 81706 70.5 0 81446 260 10 88967 17.6 1 84555 4412 11 93801 4.4 1 88117 5684 12 95662 1.1 1 89704 5958 13 105924 0.3 1 99758 6166 14 100634 0.3 1 93826 6808 15 81502 0.3 1 76286 5216 16 118419 0.3 1 111030 7389 17 95042 0.3 1 88712 6330 18 90615 0.3 1 85225 5390 19 115837 0.3 1 108486 7351 20 108535 0.3 1 102151 6384 21 96158 0.3 1 90241 5917 22 109681 0.3 1 102998 6683 23 113064 0.3 1 106255 6809 24 112402 0.3 1 105369 7033 25 127609 0.3 1 120247 7362 26 106198 0.3 1 99534 6664 27 117379 0.3 1 109394 7985 28 111310 0.3 1 105607 5703 29 119257 0.3 1 111876 7381 30 117422 0.3 1 111230 6192 31 127799 0.3 1 120363 7436 32 115547 0.3 1 109515 6032 33 127479 0.3 1 119672 7807 34 163653 0.3 1 154089 9564 35 93410 0.3 1 88452 4958 36 129603 0.3 1 121811 7792 37 138172 0.3 1 130055 8117 38 129571 0.3 1 123089 6482 39 126899 0.3 1 120584 6315 40 141131 0.3 1 133007 8124 41 136856 0.3 1 129602 7254 42 140475 0.3 1 133264 7211 43 128682 0.3 1 121911 6771 44 148231 0.3 1 140352 7879 45 152393 0.3 1 144497 7896 46 120446 0.3 1 114128 6318 47 146135 0.3 1 138949 7186 48 143271 0.3 1 136268 7003 49 150045 0.3 1 142543 7502 50 141618 0.3 1 134295 7323 51 177184 0.3 1 168273 8911 52 127868 0.3 1 121986 5882 53 154234 0.3 1 147269 6965 54 117590 0.3 1 112052 5538 55 152743 0.3 1 146054 6689 56 157680 0.3 1 150094 7586 57 149551 0.3 1 143020 6531 58 143483 0.3 1 137470 6013 59 145998 0.3 1 139352 6646 60 151232 0.3 1 144310 6922 61 157550 0.3 1 150162 7388 62 169489 0.3 1 161516 7973 63 228128 0.3 1 218668 9460 64 191978 0.3 1 184960 7018 65 121739 0.3 1 116395 5344 66 132352 0.3 1 126524 5828 67 131028 0.3 1 125146 5882 68 132829 0.3 1 127004 5825 69 131726 0.3 1 125866 5860 70 137789 0.3 1 131635 6154 71 147946 0.3 1 141769 6177 72 139415 0.3 1 133242 6173 73 148725 0.3 1 142498 6227 74 135207 0.3 1 129643 5564 75 128520 0.3 1 123034 5486 76 126065 0.3 1 120765 5300 77 126228 0.3 1 120717 5511 78 120120 0.3 1 114978 5142 79 115495 0.3 1 110595 4900 80 116213 0.3 1 111348 4865 81 114795 0.3 1 109987 4808 82 110451 0.3 1 105814 4637 83 106907 0.3 1 102515 4392 84 102431 0.3 1 98006 4425 85 101678 0.3 1 97283 4395 86 102018 0.3 1 97662 4356 87 102379 0.3 1 98265 4114 88 100269 0.3 1 95923 4346 89 89766 0.3 1 85935 3831 90 86353 0.3 1 82825 3528 91 80857 0.3 1 77356 3501 92 76306 0.3 1 73107 3199 93 73595 0.3 1 70492 3103 94 71587 0.3 1 68546 3041 95 68110 0.3 1 65320 2790 96 64867 0.3 1 62264 2603 97 59245 0.3 1 56835 2410 98 55305 0.3 1 52942 2363 99 53891 0.3 1 51732 2159 100 50005 0.3 1 47952 2053 101 45894 0.3 1 44011 1883 102 43298 0.3 1 41576 1722 103 39322 0.3 1 37781 1541 104 38059 0.3 1 36523 1536 105 33918 0.3 1 32538 1380 106 31438 0.3 1 30241 1197 107 28204 0.3 1 27113 1091 108 26258 0.3 1 25170 1088 109 23534 0.3 1 22556 978 110 21525 0.3 1 20673 852 111 20335 0.3 1 19508 827 112 17540 0.3 1 16818 722 113 15580 0.3 1 14966 614 114 13626 0.3 1 13076 550 115 11545 0.3 1 11044 501 116 9893 0.3 1 9487 406 117 8220 0.3 1 7857 363 118 7416 0.3 1 7106 310 119 6364 0.3 1 6067 297 120 5214 0.3 1 4965 249 121 4800 0.3 1 4601 199 122 3856 0.3 1 3683 173 123 3424 0.3 1 3271 153 124 2951 0.3 1 2795 156 125 2462 0.3 1 2355 107 126 2026 0.3 1 1922 104 127 1586 0.3 1 1509 77 128 1233 0.3 1 1162 71 129 1142 0.3 1 1091 51 130 841 0.3 1 788 53 131 705 0.3 1 671 34 132 609 0.3 1 572 37 133 673 0.3 1 638 35 134 1003 0.3 1 960 43 135 407 0.3 1 396 11 136 221 0.3 1 202 19 137 162 0.3 1 156 6 138 117 0.3 1 109 8 139 71 0.3 1 63 8 140 67 0.3 1 63 4 141 48 0.3 1 47 1 142 50 0.3 1 49 1 143 41 0.3 1 37 4 144 23 0.3 1 20 3 145 62 0.3 1 59 3 146 126 0.3 1 123 3 147 381 0.3 1 366 15 148 234 0.3 1 226 8 149 166 0.3 1 155 11 150 1412 0.3 1 1344 68 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_26psu_2_S10_L001_R2_001.fastq.gz ============================================= 18482577 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 18482577 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 200326 (1.08%)