SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_32psu_4_S8_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: 498122). 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_32psu_4_S8_L001_R2_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 62.55 s (4 us/read; 14.09 M reads/minute). === Summary === Total reads processed: 14,686,084 Reads with adapters: 11,052,394 (75.3%) Reads written (passing filters): 14,686,084 (100.0%) Total basepairs processed: 2,202,912,600 bp Quality-trimmed: 8,170,892 bp (0.4%) Total written (filtered): 1,785,498,326 bp (81.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11052394 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.9% C: 11.2% G: 23.2% T: 36.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2172306 3671521.0 0 2172306 2 315945 917880.2 0 315945 3 169586 229470.1 0 169586 4 102198 57367.5 0 102198 5 92121 14341.9 0 92121 6 78915 3585.5 0 78915 7 65916 896.4 0 65916 8 91966 224.1 0 91966 9 73557 56.0 0 73312 245 10 79999 14.0 1 76173 3826 11 83777 3.5 1 78744 5033 12 84445 0.9 1 79272 5173 13 92865 0.2 1 87504 5361 14 88444 0.2 1 82453 5991 15 72972 0.2 1 68400 4572 16 103628 0.2 1 97383 6245 17 83622 0.2 1 78153 5469 18 78826 0.2 1 74157 4669 19 100647 0.2 1 94372 6275 20 93537 0.2 1 88067 5470 21 82005 0.2 1 77188 4817 22 92897 0.2 1 87543 5354 23 95873 0.2 1 90242 5631 24 96154 0.2 1 90197 5957 25 107344 0.2 1 101210 6134 26 88692 0.2 1 83193 5499 27 96620 0.2 1 90107 6513 28 92786 0.2 1 88163 4623 29 97544 0.2 1 91712 5832 30 97471 0.2 1 92326 5145 31 103994 0.2 1 98068 5926 32 93992 0.2 1 89009 4983 33 103947 0.2 1 97692 6255 34 130356 0.2 1 123003 7353 35 75888 0.2 1 71960 3928 36 101074 0.2 1 95184 5890 37 109064 0.2 1 102746 6318 38 100719 0.2 1 95809 4910 39 99097 0.2 1 94226 4871 40 108626 0.2 1 102518 6108 41 105593 0.2 1 100195 5398 42 108346 0.2 1 102605 5741 43 99135 0.2 1 93859 5276 44 112964 0.2 1 106912 6052 45 120273 0.2 1 114139 6134 46 86822 0.2 1 82356 4466 47 107964 0.2 1 102668 5296 48 105861 0.2 1 100664 5197 49 110040 0.2 1 104589 5451 50 103888 0.2 1 98336 5552 51 130541 0.2 1 123943 6598 52 92963 0.2 1 88623 4340 53 111922 0.2 1 106898 5024 54 84092 0.2 1 80032 4060 55 108967 0.2 1 104198 4769 56 110137 0.2 1 104842 5295 57 104380 0.2 1 99728 4652 58 100352 0.2 1 95962 4390 59 101272 0.2 1 96515 4757 60 103619 0.2 1 98712 4907 61 107020 0.2 1 101830 5190 62 116477 0.2 1 111010 5467 63 153560 0.2 1 147083 6477 64 118136 0.2 1 113593 4543 65 80776 0.2 1 77236 3540 66 87168 0.2 1 83301 3867 67 85836 0.2 1 81942 3894 68 86253 0.2 1 82443 3810 69 84506 0.2 1 80622 3884 70 92306 0.2 1 88038 4268 71 90825 0.2 1 86927 3898 72 86185 0.2 1 82424 3761 73 89325 0.2 1 85551 3774 74 82222 0.2 1 78765 3457 75 77552 0.2 1 74138 3414 76 75204 0.2 1 71865 3339 77 74674 0.2 1 71463 3211 78 71366 0.2 1 68191 3175 79 67543 0.2 1 64632 2911 80 67004 0.2 1 64137 2867 81 66579 0.2 1 63792 2787 82 63260 0.2 1 60623 2637 83 59885 0.2 1 57259 2626 84 57771 0.2 1 55217 2554 85 56672 0.2 1 54103 2569 86 55528 0.2 1 53139 2389 87 54690 0.2 1 52283 2407 88 52598 0.2 1 50360 2238 89 46378 0.2 1 44318 2060 90 44805 0.2 1 42852 1953 91 41839 0.2 1 39962 1877 92 38539 0.2 1 36849 1690 93 36522 0.2 1 35046 1476 94 35648 0.2 1 34150 1498 95 33020 0.2 1 31626 1394 96 31039 0.2 1 29760 1279 97 28162 0.2 1 26958 1204 98 25327 0.2 1 24248 1079 99 23909 0.2 1 22911 998 100 21397 0.2 1 20519 878 101 19468 0.2 1 18700 768 102 18321 0.2 1 17542 779 103 16795 0.2 1 16092 703 104 15607 0.2 1 14948 659 105 13615 0.2 1 13013 602 106 12134 0.2 1 11629 505 107 10718 0.2 1 10267 451 108 9677 0.2 1 9284 393 109 8561 0.2 1 8182 379 110 7592 0.2 1 7242 350 111 6810 0.2 1 6531 279 112 6017 0.2 1 5741 276 113 5139 0.2 1 4918 221 114 4338 0.2 1 4134 204 115 3645 0.2 1 3478 167 116 2960 0.2 1 2807 153 117 2433 0.2 1 2312 121 118 2180 0.2 1 2058 122 119 1702 0.2 1 1624 78 120 1461 0.2 1 1377 84 121 1230 0.2 1 1157 73 122 1031 0.2 1 968 63 123 857 0.2 1 808 49 124 756 0.2 1 706 50 125 617 0.2 1 580 37 126 477 0.2 1 448 29 127 390 0.2 1 359 31 128 303 0.2 1 291 12 129 226 0.2 1 207 19 130 179 0.2 1 161 18 131 150 0.2 1 142 8 132 131 0.2 1 123 8 133 129 0.2 1 118 11 134 199 0.2 1 187 12 135 112 0.2 1 107 5 136 50 0.2 1 48 2 137 54 0.2 1 49 5 138 38 0.2 1 37 1 139 28 0.2 1 24 4 140 20 0.2 1 18 2 141 13 0.2 1 12 1 142 11 0.2 1 10 1 143 8 0.2 1 7 1 144 5 0.2 1 3 2 145 4 0.2 1 3 1 146 7 0.2 1 3 4 147 20 0.2 1 18 2 148 18 0.2 1 17 1 149 13 0.2 1 11 2 150 93 0.2 1 85 8 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_32psu_4_S8_L001_R2_001.fastq.gz ============================================= 14686084 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 14686084 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 66696 (0.45%)