SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_32psu_4_S8_L002_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: 488601). 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_L002_R2_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 61.23 s (4 us/read; 14.31 M reads/minute). === Summary === Total reads processed: 14,607,942 Reads with adapters: 10,984,887 (75.2%) Reads written (passing filters): 14,607,942 (100.0%) Total basepairs processed: 2,191,191,300 bp Quality-trimmed: 8,040,292 bp (0.4%) Total written (filtered): 1,774,637,805 bp (81.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10984887 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.9% C: 11.2% G: 23.3% T: 36.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2154515 3651985.5 0 2154515 2 307769 912996.4 0 307769 3 171355 228249.1 0 171355 4 100114 57062.3 0 100114 5 89281 14265.6 0 89281 6 78941 3566.4 0 78941 7 64482 891.6 0 64482 8 90895 222.9 0 90895 9 71519 55.7 0 71259 260 10 77769 13.9 1 72602 5167 11 81991 3.5 1 75629 6362 12 81945 0.9 1 75457 6488 13 93276 0.2 1 85901 7375 14 86548 0.2 1 79069 7479 15 71575 0.2 1 66062 5513 16 101873 0.2 1 93937 7936 17 86756 0.2 1 79766 6990 18 75151 0.2 1 69487 5664 19 100031 0.2 1 92361 7670 20 92540 0.2 1 85573 6967 21 80563 0.2 1 74553 6010 22 91001 0.2 1 84166 6835 23 96186 0.2 1 88873 7313 24 95097 0.2 1 87831 7266 25 107490 0.2 1 100206 7284 26 89500 0.2 1 82469 7031 27 97464 0.2 1 89433 8031 28 89257 0.2 1 83469 5788 29 97776 0.2 1 90646 7130 30 94678 0.2 1 88320 6358 31 104562 0.2 1 97122 7440 32 90375 0.2 1 84247 6128 33 104255 0.2 1 96395 7860 34 131765 0.2 1 122731 9034 35 71827 0.2 1 67071 4756 36 101000 0.2 1 93594 7406 37 108384 0.2 1 100841 7543 38 100305 0.2 1 93893 6412 39 96265 0.2 1 90338 5927 40 108609 0.2 1 101413 7196 41 105469 0.2 1 98528 6941 42 108491 0.2 1 101465 7026 43 97504 0.2 1 91262 6242 44 114735 0.2 1 107039 7696 45 119691 0.2 1 111821 7870 46 85524 0.2 1 79914 5610 47 107169 0.2 1 100947 6222 48 104472 0.2 1 98077 6395 49 109888 0.2 1 102993 6895 50 104895 0.2 1 98149 6746 51 128024 0.2 1 120005 8019 52 92440 0.2 1 86601 5839 53 114005 0.2 1 107513 6492 54 82023 0.2 1 77215 4808 55 107798 0.2 1 101620 6178 56 110208 0.2 1 103344 6864 57 105022 0.2 1 99470 5552 58 100686 0.2 1 95258 5428 59 100045 0.2 1 94333 5712 60 103616 0.2 1 97757 5859 61 106446 0.2 1 100410 6036 62 115794 0.2 1 108819 6975 63 149726 0.2 1 142046 7680 64 116619 0.2 1 111405 5214 65 80564 0.2 1 76264 4300 66 87049 0.2 1 82185 4864 67 86779 0.2 1 81921 4858 68 87371 0.2 1 82619 4752 69 85219 0.2 1 80357 4862 70 93639 0.2 1 88366 5273 71 91437 0.2 1 86289 5148 72 86910 0.2 1 81943 4967 73 89655 0.2 1 84810 4845 74 82770 0.2 1 78094 4676 75 77878 0.2 1 73550 4328 76 75167 0.2 1 70959 4208 77 74827 0.2 1 70567 4260 78 71263 0.2 1 67257 4006 79 68082 0.2 1 64314 3768 80 66978 0.2 1 63430 3548 81 67480 0.2 1 63757 3723 82 63500 0.2 1 60093 3407 83 60414 0.2 1 57170 3244 84 57646 0.2 1 54576 3070 85 56216 0.2 1 53261 2955 86 55705 0.2 1 52806 2899 87 54555 0.2 1 51737 2818 88 52657 0.2 1 49839 2818 89 47083 0.2 1 44512 2571 90 45017 0.2 1 42539 2478 91 42292 0.2 1 40068 2224 92 39093 0.2 1 37073 2020 93 36824 0.2 1 34979 1845 94 35114 0.2 1 33278 1836 95 33006 0.2 1 31281 1725 96 30878 0.2 1 29246 1632 97 28202 0.2 1 26749 1453 98 25663 0.2 1 24339 1324 99 24079 0.2 1 22771 1308 100 21840 0.2 1 20690 1150 101 19586 0.2 1 18574 1012 102 18375 0.2 1 17447 928 103 16706 0.2 1 15871 835 104 15675 0.2 1 14815 860 105 13756 0.2 1 13047 709 106 12568 0.2 1 11946 622 107 10619 0.2 1 10045 574 108 9793 0.2 1 9277 516 109 8520 0.2 1 8082 438 110 7642 0.2 1 7254 388 111 7055 0.2 1 6693 362 112 5993 0.2 1 5692 301 113 5089 0.2 1 4789 300 114 4335 0.2 1 4087 248 115 3576 0.2 1 3383 193 116 2943 0.2 1 2759 184 117 2497 0.2 1 2342 155 118 2119 0.2 1 1989 130 119 1740 0.2 1 1643 97 120 1465 0.2 1 1354 111 121 1235 0.2 1 1152 83 122 1011 0.2 1 954 57 123 812 0.2 1 749 63 124 706 0.2 1 655 51 125 559 0.2 1 512 47 126 438 0.2 1 415 23 127 439 0.2 1 406 33 128 306 0.2 1 286 20 129 222 0.2 1 208 14 130 202 0.2 1 190 12 131 161 0.2 1 148 13 132 146 0.2 1 132 14 133 137 0.2 1 126 11 134 210 0.2 1 203 7 135 81 0.2 1 72 9 136 43 0.2 1 38 5 137 44 0.2 1 36 8 138 25 0.2 1 22 3 139 23 0.2 1 23 140 5 0.2 1 5 141 9 0.2 1 9 142 12 0.2 1 11 1 143 2 0.2 1 2 144 10 0.2 1 7 3 145 5 0.2 1 5 146 6 0.2 1 6 147 23 0.2 1 22 1 148 13 0.2 1 13 149 11 0.2 1 10 1 150 112 0.2 1 105 7 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_32psu_4_S8_L002_R2_001.fastq.gz ============================================= 14607942 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 14607942 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 65313 (0.45%)