SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_26psu_3_S11_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: 677373). 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_26psu_3_S11_L002_R2_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 62.11 s (4 us/read; 16.59 M reads/minute). === Summary === Total reads processed: 17,175,482 Reads with adapters: 14,720,565 (85.7%) Reads written (passing filters): 17,175,482 (100.0%) Total basepairs processed: 2,576,322,300 bp Quality-trimmed: 12,927,719 bp (0.5%) Total written (filtered): 1,825,809,518 bp (70.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14720565 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 27.4% C: 12.3% G: 25.7% T: 34.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1394679 4293870.5 0 1394679 2 231063 1073467.6 0 231063 3 146836 268366.9 0 146836 4 85160 67091.7 0 85160 5 83607 16772.9 0 83607 6 75270 4193.2 0 75270 7 59401 1048.3 0 59401 8 87249 262.1 0 87249 9 68581 65.5 0 68364 217 10 75306 16.4 1 69907 5399 11 81844 4.1 1 75220 6624 12 81567 1.0 1 74921 6646 13 94550 0.3 1 87043 7507 14 88612 0.3 1 80763 7849 15 71080 0.3 1 65748 5332 16 104508 0.3 1 96265 8243 17 90450 0.3 1 83158 7292 18 79309 0.3 1 73193 6116 19 106248 0.3 1 97745 8503 20 97943 0.3 1 90478 7465 21 87195 0.3 1 80598 6597 22 99625 0.3 1 92109 7516 23 105941 0.3 1 98004 7937 24 105924 0.3 1 97524 8400 25 120959 0.3 1 112658 8301 26 100855 0.3 1 92739 8116 27 111349 0.3 1 102191 9158 28 103794 0.3 1 97081 6713 29 115018 0.3 1 106647 8371 30 112098 0.3 1 104443 7655 31 125293 0.3 1 116600 8693 32 108268 0.3 1 101076 7192 33 127668 0.3 1 118305 9363 34 163116 0.3 1 151740 11376 35 90695 0.3 1 84564 6131 36 130252 0.3 1 120794 9458 37 137508 0.3 1 128167 9341 38 131385 0.3 1 123153 8232 39 125429 0.3 1 117971 7458 40 144394 0.3 1 134617 9777 41 142244 0.3 1 133129 9115 42 146211 0.3 1 136886 9325 43 130656 0.3 1 122570 8086 44 158062 0.3 1 147788 10274 45 169410 0.3 1 158451 10959 46 116471 0.3 1 109140 7331 47 153771 0.3 1 145129 8642 48 151126 0.3 1 142022 9104 49 158775 0.3 1 148794 9981 50 155083 0.3 1 145500 9583 51 193098 0.3 1 181154 11944 52 138930 0.3 1 130761 8169 53 172888 0.3 1 163380 9508 54 126226 0.3 1 118962 7264 55 168553 0.3 1 159300 9253 56 174469 0.3 1 163938 10531 57 166262 0.3 1 157805 8457 58 161940 0.3 1 153447 8493 59 163516 0.3 1 154551 8965 60 171750 0.3 1 162391 9359 61 176379 0.3 1 166983 9396 62 194831 0.3 1 183858 10973 63 257381 0.3 1 244702 12679 64 218615 0.3 1 209942 8673 65 141285 0.3 1 134011 7274 66 154574 0.3 1 146600 7974 67 155286 0.3 1 146846 8440 68 158519 0.3 1 150042 8477 69 156924 0.3 1 148115 8809 70 167343 0.3 1 158462 8881 71 174948 0.3 1 165808 9140 72 168193 0.3 1 159291 8902 73 175743 0.3 1 166626 9117 74 163090 0.3 1 154296 8794 75 155077 0.3 1 146999 8078 76 152837 0.3 1 144700 8137 77 152701 0.3 1 144644 8057 78 148868 0.3 1 140946 7922 79 143248 0.3 1 135788 7460 80 143729 0.3 1 136194 7535 81 142811 0.3 1 135360 7451 82 135758 0.3 1 128640 7118 83 132076 0.3 1 125333 6743 84 127993 0.3 1 121417 6576 85 127663 0.3 1 121292 6371 86 126712 0.3 1 120456 6256 87 127809 0.3 1 121761 6048 88 125518 0.3 1 119426 6092 89 112440 0.3 1 106917 5523 90 109295 0.3 1 103850 5445 91 103669 0.3 1 98616 5053 92 96386 0.3 1 91748 4638 93 94174 0.3 1 89557 4617 94 91197 0.3 1 86759 4438 95 86770 0.3 1 82553 4217 96 83121 0.3 1 79129 3992 97 76650 0.3 1 72963 3687 98 72211 0.3 1 68803 3408 99 70867 0.3 1 67509 3358 100 63540 0.3 1 60596 2944 101 60139 0.3 1 57240 2899 102 55801 0.3 1 53158 2643 103 50487 0.3 1 47969 2518 104 48235 0.3 1 45902 2333 105 42853 0.3 1 40742 2111 106 39140 0.3 1 37246 1894 107 35386 0.3 1 33624 1762 108 31865 0.3 1 30331 1534 109 29026 0.3 1 27576 1450 110 25978 0.3 1 24750 1228 111 24137 0.3 1 23015 1122 112 21305 0.3 1 20312 993 113 18391 0.3 1 17493 898 114 16197 0.3 1 15347 850 115 13468 0.3 1 12821 647 116 11291 0.3 1 10728 563 117 9599 0.3 1 9121 478 118 8211 0.3 1 7795 416 119 6772 0.3 1 6417 355 120 5885 0.3 1 5586 299 121 5082 0.3 1 4799 283 122 4085 0.3 1 3891 194 123 3540 0.3 1 3373 167 124 2933 0.3 1 2771 162 125 2424 0.3 1 2286 138 126 1979 0.3 1 1877 102 127 1585 0.3 1 1504 81 128 1307 0.3 1 1233 74 129 1065 0.3 1 999 66 130 818 0.3 1 765 53 131 695 0.3 1 661 34 132 692 0.3 1 651 41 133 1029 0.3 1 991 38 134 1555 0.3 1 1499 56 135 581 0.3 1 564 17 136 217 0.3 1 210 7 137 148 0.3 1 133 15 138 96 0.3 1 87 9 139 66 0.3 1 63 3 140 62 0.3 1 58 4 141 31 0.3 1 28 3 142 29 0.3 1 25 4 143 15 0.3 1 15 144 16 0.3 1 16 145 37 0.3 1 37 146 31 0.3 1 30 1 147 76 0.3 1 72 4 148 44 0.3 1 40 4 149 38 0.3 1 34 4 150 422 0.3 1 392 30 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_26psu_3_S11_L002_R2_001.fastq.gz ============================================= 17175482 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 17175482 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 212097 (1.23%)