SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_32psu_1_S5_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: 740292). 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_1_S5_L002_R1_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 46.27 s (3 us/read; 18.13 M reads/minute). === Summary === Total reads processed: 13,980,098 Reads with adapters: 12,547,273 (89.8%) Reads written (passing filters): 13,980,098 (100.0%) Total basepairs processed: 2,097,014,700 bp Quality-trimmed: 3,995,329 bp (0.2%) Total written (filtered): 1,381,322,734 bp (65.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 12547273 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.6% C: 15.4% G: 21.7% T: 34.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 797770 3495024.5 0 797770 2 136013 873756.1 0 136013 3 88578 218439.0 0 88578 4 54507 54609.8 0 54507 5 51433 13652.4 0 51433 6 50368 3413.1 0 50368 7 41781 853.3 0 41781 8 52923 213.3 0 52923 9 54051 53.3 0 53431 620 10 50288 13.3 1 47174 3114 11 58137 3.3 1 53328 4809 12 55530 0.8 1 51625 3905 13 56413 0.2 1 52378 4035 14 59004 0.2 1 54278 4726 15 60957 0.2 1 56359 4598 16 62617 0.2 1 57287 5330 17 77034 0.2 1 70041 6993 18 64851 0.2 1 60415 4436 19 55636 0.2 1 51675 3961 20 69068 0.2 1 64118 4950 21 78331 0.2 1 72354 5977 22 65036 0.2 1 60845 4191 23 77471 0.2 1 71757 5714 24 73017 0.2 1 66655 6362 25 80097 0.2 1 74072 6025 26 72725 0.2 1 67966 4759 27 83104 0.2 1 76594 6510 28 81931 0.2 1 75845 6086 29 90548 0.2 1 82404 8144 30 97688 0.2 1 91724 5964 31 71240 0.2 1 66196 5044 32 92668 0.2 1 85724 6944 33 88978 0.2 1 82032 6946 34 98712 0.2 1 91302 7410 35 92968 0.2 1 85787 7181 36 107083 0.2 1 98683 8400 37 102524 0.2 1 93933 8591 38 103053 0.2 1 96018 7035 39 106015 0.2 1 98258 7757 40 105210 0.2 1 97541 7669 41 121909 0.2 1 112224 9685 42 102833 0.2 1 93869 8964 43 167631 0.2 1 157548 10083 44 59347 0.2 1 53867 5480 45 119124 0.2 1 111193 7931 46 115006 0.2 1 106994 8012 47 123238 0.2 1 114804 8434 48 121882 0.2 1 113175 8707 49 136657 0.2 1 126388 10269 50 117352 0.2 1 109816 7536 51 128981 0.2 1 119944 9037 52 136441 0.2 1 126118 10323 53 146650 0.2 1 137000 9650 54 118855 0.2 1 110740 8115 55 142441 0.2 1 132669 9772 56 173419 0.2 1 162260 11159 57 115395 0.2 1 106550 8845 58 148737 0.2 1 140083 8654 59 131828 0.2 1 122332 9496 60 148604 0.2 1 138387 10217 61 147891 0.2 1 138429 9462 62 164090 0.2 1 153607 10483 63 134153 0.2 1 124429 9724 64 146788 0.2 1 137613 9175 65 167405 0.2 1 156219 11186 66 175152 0.2 1 163306 11846 67 193973 0.2 1 178444 15529 68 355893 0.2 1 337623 18270 69 77628 0.2 1 71288 6340 70 32194 0.2 1 27237 4957 71 98744 0.2 1 92367 6377 72 142722 0.2 1 134109 8613 73 153911 0.2 1 144323 9588 74 152982 0.2 1 143267 9715 75 155312 0.2 1 145139 10173 76 154296 0.2 1 143821 10475 77 156257 0.2 1 146141 10116 78 149276 0.2 1 139442 9834 79 150468 0.2 1 140290 10178 80 147626 0.2 1 137573 10053 81 147629 0.2 1 137952 9677 82 146000 0.2 1 136195 9805 83 142550 0.2 1 133188 9362 84 139878 0.2 1 130510 9368 85 136886 0.2 1 127696 9190 86 134793 0.2 1 125685 9108 87 130207 0.2 1 121771 8436 88 129730 0.2 1 121003 8727 89 125338 0.2 1 117059 8279 90 125920 0.2 1 117611 8309 91 120727 0.2 1 112765 7962 92 116230 0.2 1 108426 7804 93 110261 0.2 1 102836 7425 94 107731 0.2 1 100461 7270 95 101765 0.2 1 94845 6920 96 97730 0.2 1 91189 6541 97 92862 0.2 1 86658 6204 98 87553 0.2 1 81547 6006 99 87158 0.2 1 80825 6333 100 78638 0.2 1 73170 5468 101 74653 0.2 1 69508 5145 102 70275 0.2 1 65468 4807 103 65373 0.2 1 60911 4462 104 61766 0.2 1 57502 4264 105 55492 0.2 1 51811 3681 106 51179 0.2 1 47624 3555 107 46618 0.2 1 43293 3325 108 44553 0.2 1 41440 3113 109 39712 0.2 1 36840 2872 110 36630 0.2 1 33977 2653 111 32740 0.2 1 30268 2472 112 29144 0.2 1 26890 2254 113 25615 0.2 1 23550 2065 114 22855 0.2 1 21063 1792 115 19838 0.2 1 18299 1539 116 17636 0.2 1 16221 1415 117 14547 0.2 1 13334 1213 118 13235 0.2 1 12137 1098 119 10988 0.2 1 10016 972 120 9462 0.2 1 8648 814 121 7752 0.2 1 7051 701 122 6591 0.2 1 5988 603 123 5413 0.2 1 4917 496 124 4773 0.2 1 4290 483 125 3899 0.2 1 3520 379 126 3211 0.2 1 2920 291 127 2698 0.2 1 2418 280 128 2171 0.2 1 1932 239 129 1648 0.2 1 1461 187 130 1400 0.2 1 1257 143 131 1218 0.2 1 1094 124 132 1037 0.2 1 929 108 133 1169 0.2 1 1044 125 134 1204 0.2 1 1109 95 135 602 0.2 1 535 67 136 395 0.2 1 343 52 137 232 0.2 1 196 36 138 155 0.2 1 142 13 139 118 0.2 1 95 23 140 87 0.2 1 71 16 141 57 0.2 1 45 12 142 68 0.2 1 58 10 143 37 0.2 1 32 5 144 24 0.2 1 22 2 145 36 0.2 1 30 6 146 26 0.2 1 23 3 147 105 0.2 1 86 19 148 85 0.2 1 66 19 149 76 0.2 1 64 12 150 640 0.2 1 546 94 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_32psu_1_S5_L002_R1_001.fastq.gz ============================================= 13980098 sequences processed in total