SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_32psu_3_S7_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: 622739). 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/8C_32psu_3_S7_L002_R1_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 51.43 s (4 us/read; 16.47 M reads/minute). === Summary === Total reads processed: 14,120,008 Reads with adapters: 11,800,625 (83.6%) Reads written (passing filters): 14,120,008 (100.0%) Total basepairs processed: 2,118,001,200 bp Quality-trimmed: 4,373,755 bp (0.2%) Total written (filtered): 1,553,898,462 bp (73.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11800625 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.0% C: 15.1% G: 21.0% T: 34.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1368833 3530002.0 0 1368833 2 213297 882500.5 0 213297 3 129961 220625.1 0 129961 4 79035 55156.3 0 79035 5 69573 13789.1 0 69573 6 67663 3447.3 0 67663 7 54249 861.8 0 54249 8 69306 215.5 0 69306 9 69302 53.9 0 68512 790 10 64667 13.5 1 60704 3963 11 73696 3.4 1 67523 6173 12 69675 0.8 1 64547 5128 13 71952 0.2 1 66511 5441 14 73593 0.2 1 67472 6121 15 76996 0.2 1 70887 6109 16 75526 0.2 1 69104 6422 17 93355 0.2 1 84545 8810 18 79593 0.2 1 73933 5660 19 68124 0.2 1 63039 5085 20 82749 0.2 1 76505 6244 21 92275 0.2 1 85139 7136 22 77618 0.2 1 72438 5180 23 92025 0.2 1 84966 7059 24 85340 0.2 1 77863 7477 25 92374 0.2 1 85186 7188 26 84405 0.2 1 78632 5773 27 95395 0.2 1 87567 7828 28 93111 0.2 1 85941 7170 29 103004 0.2 1 93769 9235 30 106080 0.2 1 99144 6936 31 80431 0.2 1 74401 6030 32 102254 0.2 1 94262 7992 33 95806 0.2 1 88463 7343 34 106075 0.2 1 96928 9147 35 108269 0.2 1 99389 8880 36 112253 0.2 1 102783 9470 37 99044 0.2 1 92235 6809 38 121329 0.2 1 110516 10813 39 100947 0.2 1 93251 7696 40 114342 0.2 1 105610 8732 41 128592 0.2 1 117446 11146 42 100668 0.2 1 92131 8537 43 169999 0.2 1 159204 10795 44 56249 0.2 1 50770 5479 45 119775 0.2 1 111031 8744 46 112063 0.2 1 103816 8247 47 119122 0.2 1 110508 8614 48 118788 0.2 1 109597 9191 49 131198 0.2 1 120814 10384 50 109980 0.2 1 102619 7361 51 122763 0.2 1 113852 8911 52 127644 0.2 1 117521 10123 53 136952 0.2 1 127680 9272 54 107784 0.2 1 99974 7810 55 130694 0.2 1 121255 9439 56 158527 0.2 1 147787 10740 57 103844 0.2 1 95331 8513 58 132382 0.2 1 124247 8135 59 116544 0.2 1 107902 8642 60 129622 0.2 1 120349 9273 61 128569 0.2 1 119774 8795 62 140522 0.2 1 130790 9732 63 114632 0.2 1 105994 8638 64 124792 0.2 1 116366 8426 65 140416 0.2 1 130644 9772 66 145932 0.2 1 135671 10261 67 159891 0.2 1 146767 13124 68 288595 0.2 1 272910 15685 69 63057 0.2 1 57575 5482 70 26024 0.2 1 21992 4032 71 79266 0.2 1 73983 5283 72 112824 0.2 1 105728 7096 73 119835 0.2 1 111892 7943 74 119611 0.2 1 111533 8078 75 117923 0.2 1 109788 8135 76 117731 0.2 1 109296 8435 77 118271 0.2 1 109919 8352 78 111566 0.2 1 103610 7956 79 111519 0.2 1 103611 7908 80 109197 0.2 1 101453 7744 81 107570 0.2 1 99856 7714 82 104569 0.2 1 97118 7451 83 102383 0.2 1 95228 7155 84 99102 0.2 1 92021 7081 85 96000 0.2 1 89098 6902 86 93524 0.2 1 86838 6686 87 89373 0.2 1 83285 6088 88 88917 0.2 1 82644 6273 89 84001 0.2 1 77961 6040 90 83693 0.2 1 77869 5824 91 80101 0.2 1 74574 5527 92 76032 0.2 1 70730 5302 93 71132 0.2 1 66158 4974 94 68649 0.2 1 63740 4909 95 64070 0.2 1 59484 4586 96 60750 0.2 1 56444 4306 97 57341 0.2 1 53268 4073 98 53260 0.2 1 49347 3913 99 52636 0.2 1 48599 4037 100 46791 0.2 1 43393 3398 101 44342 0.2 1 41093 3249 102 40590 0.2 1 37587 3003 103 37417 0.2 1 34694 2723 104 34470 0.2 1 31943 2527 105 30930 0.2 1 28658 2272 106 28279 0.2 1 26119 2160 107 25736 0.2 1 23845 1891 108 23849 0.2 1 22042 1807 109 21192 0.2 1 19537 1655 110 19116 0.2 1 17675 1441 111 17231 0.2 1 15808 1423 112 14798 0.2 1 13558 1240 113 12618 0.2 1 11582 1036 114 11317 0.2 1 10327 990 115 9619 0.2 1 8804 815 116 8405 0.2 1 7688 717 117 7048 0.2 1 6428 620 118 6316 0.2 1 5766 550 119 5076 0.2 1 4600 476 120 4250 0.2 1 3802 448 121 3670 0.2 1 3303 367 122 3096 0.2 1 2757 339 123 2589 0.2 1 2312 277 124 2201 0.2 1 1979 222 125 1708 0.2 1 1510 198 126 1570 0.2 1 1383 187 127 1266 0.2 1 1112 154 128 926 0.2 1 821 105 129 844 0.2 1 748 96 130 568 0.2 1 488 80 131 507 0.2 1 451 56 132 422 0.2 1 368 54 133 416 0.2 1 358 58 134 449 0.2 1 401 48 135 219 0.2 1 188 31 136 167 0.2 1 147 20 137 91 0.2 1 79 12 138 80 0.2 1 64 16 139 47 0.2 1 42 5 140 27 0.2 1 21 6 141 27 0.2 1 23 4 142 18 0.2 1 10 8 143 22 0.2 1 11 11 144 14 0.2 1 10 4 145 18 0.2 1 16 2 146 18 0.2 1 14 4 147 32 0.2 1 28 4 148 19 0.2 1 17 2 149 14 0.2 1 10 4 150 202 0.2 1 177 25 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_32psu_3_S7_L002_R1_001.fastq.gz ============================================= 14120008 sequences processed in total