SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_26psu_4_S12_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: 401336). Second best hit was Nextera (count: 1) 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_4_S12_L002_R2_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 52.95 s (4 us/read; 14.15 M reads/minute). === Summary === Total reads processed: 12,486,748 Reads with adapters: 8,772,809 (70.3%) Reads written (passing filters): 12,486,748 (100.0%) Total basepairs processed: 1,873,012,200 bp Quality-trimmed: 12,376,106 bp (0.7%) Total written (filtered): 1,558,147,987 bp (83.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 8772809 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.4% C: 12.6% G: 20.8% T: 36.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2358875 3121687.0 0 2358875 2 288344 780421.8 0 288344 3 173054 195105.4 0 173054 4 87112 48776.4 0 87112 5 64247 12194.1 0 64247 6 55212 3048.5 0 55212 7 41727 762.1 0 41727 8 62151 190.5 0 62151 9 50342 47.6 0 50157 185 10 52158 11.9 1 48148 4010 11 57855 3.0 1 52397 5458 12 56897 0.7 1 51566 5331 13 64575 0.2 1 58979 5596 14 59154 0.2 1 53315 5839 15 47002 0.2 1 42866 4136 16 69658 0.2 1 63405 6253 17 57386 0.2 1 52045 5341 18 51929 0.2 1 47327 4602 19 66863 0.2 1 60907 5956 20 62288 0.2 1 57071 5217 21 55272 0.2 1 50547 4725 22 61984 0.2 1 56766 5218 23 65026 0.2 1 59587 5439 24 63838 0.2 1 58214 5624 25 72434 0.2 1 66848 5586 26 60587 0.2 1 55112 5475 27 67754 0.2 1 61588 6166 28 59366 0.2 1 54979 4387 29 67701 0.2 1 62118 5583 30 62432 0.2 1 57688 4744 31 72162 0.2 1 66403 5759 32 60976 0.2 1 56497 4479 33 69840 0.2 1 64116 5724 34 91102 0.2 1 84079 7023 35 47382 0.2 1 43590 3792 36 69435 0.2 1 63655 5780 37 74003 0.2 1 67997 6006 38 68560 0.2 1 63793 4767 39 65708 0.2 1 61286 4422 40 74240 0.2 1 68710 5530 41 72214 0.2 1 67124 5090 42 72980 0.2 1 67853 5127 43 66699 0.2 1 62062 4637 44 76923 0.2 1 71373 5550 45 80740 0.2 1 74874 5866 46 58943 0.2 1 54854 4089 47 73645 0.2 1 68927 4718 48 72329 0.2 1 67389 4940 49 74646 0.2 1 69490 5156 50 70816 0.2 1 65987 4829 51 86746 0.2 1 80793 5953 52 63282 0.2 1 59102 4180 53 76728 0.2 1 71964 4764 54 55670 0.2 1 52124 3546 55 73350 0.2 1 68943 4407 56 76024 0.2 1 70858 5166 57 71982 0.2 1 67849 4133 58 68868 0.2 1 64881 3987 59 68360 0.2 1 64151 4209 60 71518 0.2 1 67054 4464 61 73466 0.2 1 69155 4311 62 79595 0.2 1 74642 4953 63 103748 0.2 1 97894 5854 64 85376 0.2 1 81260 4116 65 55857 0.2 1 52588 3269 66 61954 0.2 1 58405 3549 67 59930 0.2 1 56159 3771 68 60490 0.2 1 56878 3612 69 60452 0.2 1 56708 3744 70 61904 0.2 1 58197 3707 71 65599 0.2 1 61887 3712 72 62591 0.2 1 58936 3655 73 64906 0.2 1 61091 3815 74 60780 0.2 1 57167 3613 75 57385 0.2 1 53955 3430 76 55285 0.2 1 51973 3312 77 55087 0.2 1 51740 3347 78 52962 0.2 1 49812 3150 79 51023 0.2 1 48174 2849 80 50358 0.2 1 47516 2842 81 49364 0.2 1 46484 2880 82 47242 0.2 1 44529 2713 83 45686 0.2 1 43106 2580 84 44410 0.2 1 41863 2547 85 43592 0.2 1 41103 2489 86 43331 0.2 1 40952 2379 87 42675 0.2 1 40428 2247 88 42372 0.2 1 40023 2349 89 37747 0.2 1 35602 2145 90 37018 0.2 1 34943 2075 91 33562 0.2 1 31712 1850 92 31899 0.2 1 30215 1684 93 30547 0.2 1 28874 1673 94 30566 0.2 1 28886 1680 95 28277 0.2 1 26704 1573 96 27180 0.2 1 25709 1471 97 24703 0.2 1 23381 1322 98 23174 0.2 1 21893 1281 99 21741 0.2 1 20527 1214 100 19732 0.2 1 18608 1124 101 17665 0.2 1 16698 967 102 16908 0.2 1 15954 954 103 15998 0.2 1 15059 939 104 15634 0.2 1 14747 887 105 13889 0.2 1 13156 733 106 12626 0.2 1 11933 693 107 11469 0.2 1 10791 678 108 10122 0.2 1 9581 541 109 9139 0.2 1 8610 529 110 8759 0.2 1 8236 523 111 8023 0.2 1 7545 478 112 7113 0.2 1 6705 408 113 6235 0.2 1 5883 352 114 5409 0.2 1 5057 352 115 4485 0.2 1 4203 282 116 3795 0.2 1 3556 239 117 3367 0.2 1 3120 247 118 2891 0.2 1 2702 189 119 2519 0.2 1 2367 152 120 2120 0.2 1 1963 157 121 1866 0.2 1 1743 123 122 1561 0.2 1 1440 121 123 1426 0.2 1 1322 104 124 1196 0.2 1 1106 90 125 1010 0.2 1 943 67 126 988 0.2 1 920 68 127 903 0.2 1 840 63 128 611 0.2 1 560 51 129 510 0.2 1 470 40 130 453 0.2 1 423 30 131 514 0.2 1 467 47 132 553 0.2 1 529 24 133 1090 0.2 1 1032 58 134 2641 0.2 1 2566 75 135 828 0.2 1 794 34 136 185 0.2 1 169 16 137 110 0.2 1 95 15 138 79 0.2 1 73 6 139 44 0.2 1 40 4 140 39 0.2 1 36 3 141 22 0.2 1 17 5 142 20 0.2 1 14 6 143 16 0.2 1 15 1 144 54 0.2 1 47 7 145 219 0.2 1 204 15 146 229 0.2 1 213 16 147 1254 0.2 1 1201 53 148 756 0.2 1 716 40 149 417 0.2 1 400 17 150 2389 0.2 1 2234 155 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_26psu_4_S12_L002_R2_001.fastq.gz ============================================= 12486748 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 12486748 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 108309 (0.87%)