SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_26psu_3_S11_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: 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_R1_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 59.39 s (3 us/read; 17.35 M reads/minute). === Summary === Total reads processed: 17,175,482 Reads with adapters: 14,848,929 (86.5%) Reads written (passing filters): 17,175,482 (100.0%) Total basepairs processed: 2,576,322,300 bp Quality-trimmed: 5,047,974 bp (0.2%) Total written (filtered): 1,818,633,191 bp (70.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14848929 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.8% C: 14.0% G: 22.1% T: 35.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1338924 4293870.5 0 1338924 2 219387 1073467.6 0 219387 3 135027 268366.9 0 135027 4 85370 67091.7 0 85370 5 77474 16772.9 0 77474 6 77037 4193.2 0 77037 7 61988 1048.3 0 61988 8 79862 262.1 0 79862 9 79304 65.5 0 78415 889 10 74894 16.4 1 70380 4514 11 85385 4.1 1 78459 6926 12 81941 1.0 1 76091 5850 13 85904 0.3 1 79720 6184 14 83830 0.3 1 77435 6395 15 91251 0.3 1 84448 6803 16 87362 0.3 1 80132 7230 17 108027 0.3 1 98268 9759 18 97765 0.3 1 91194 6571 19 79668 0.3 1 74013 5655 20 98415 0.3 1 91325 7090 21 108861 0.3 1 100754 8107 22 92432 0.3 1 86497 5935 23 109093 0.3 1 101170 7923 24 102961 0.3 1 94241 8720 25 110529 0.3 1 102334 8195 26 102489 0.3 1 95783 6706 27 115669 0.3 1 106602 9067 28 113524 0.3 1 105254 8270 29 122345 0.3 1 111712 10633 30 129585 0.3 1 121424 8161 31 102733 0.3 1 95540 7193 32 124071 0.3 1 115107 8964 33 119235 0.3 1 110316 8919 34 135312 0.3 1 123053 12259 35 144848 0.3 1 135072 9776 36 111252 0.3 1 103350 7902 37 137690 0.3 1 126540 11150 38 183318 0.3 1 172054 11264 39 89425 0.3 1 80789 8636 40 143455 0.3 1 132529 10926 41 167032 0.3 1 153468 13564 42 121530 0.3 1 111758 9772 43 226339 0.3 1 213169 13170 44 63952 0.3 1 57726 6226 45 153236 0.3 1 142659 10577 46 145389 0.3 1 135235 10154 47 153266 0.3 1 143025 10241 48 152876 0.3 1 141831 11045 49 168461 0.3 1 156017 12444 50 143668 0.3 1 134304 9364 51 158306 0.3 1 147182 11124 52 165500 0.3 1 153119 12381 53 177823 0.3 1 165831 11992 54 142891 0.3 1 133186 9705 55 170342 0.3 1 158433 11909 56 212493 0.3 1 198685 13808 57 130099 0.3 1 120181 9918 58 177795 0.3 1 167072 10723 59 156878 0.3 1 145935 10943 60 169887 0.3 1 158157 11730 61 170084 0.3 1 159037 11047 62 189821 0.3 1 177611 12210 63 149110 0.3 1 138396 10714 64 169980 0.3 1 159400 10580 65 190750 0.3 1 178067 12683 66 196470 0.3 1 183447 13023 67 212313 0.3 1 195505 16808 68 400251 0.3 1 379902 20349 69 75488 0.3 1 68954 6534 70 29970 0.3 1 25043 4927 71 114346 0.3 1 107216 7130 72 155823 0.3 1 146728 9095 73 164934 0.3 1 154662 10272 74 163683 0.3 1 153217 10466 75 161985 0.3 1 151549 10436 76 161854 0.3 1 151132 10722 77 161503 0.3 1 151032 10471 78 154856 0.3 1 144180 10676 79 152863 0.3 1 142631 10232 80 150353 0.3 1 140171 10182 81 150454 0.3 1 140509 9945 82 145676 0.3 1 135805 9871 83 141824 0.3 1 132558 9266 84 137190 0.3 1 128021 9169 85 134663 0.3 1 125634 9029 86 130352 0.3 1 121592 8760 87 125876 0.3 1 117794 8082 88 125030 0.3 1 116803 8227 89 117792 0.3 1 109945 7847 90 117830 0.3 1 110051 7779 91 112910 0.3 1 105546 7364 92 106310 0.3 1 99476 6834 93 100338 0.3 1 93657 6681 94 97374 0.3 1 90887 6487 95 91711 0.3 1 85495 6216 96 86651 0.3 1 80705 5946 97 81512 0.3 1 76160 5352 98 75813 0.3 1 70557 5256 99 73615 0.3 1 68470 5145 100 67314 0.3 1 62734 4580 101 63335 0.3 1 58922 4413 102 58250 0.3 1 54144 4106 103 54120 0.3 1 50374 3746 104 50265 0.3 1 46857 3408 105 44626 0.3 1 41570 3056 106 40793 0.3 1 37936 2857 107 37321 0.3 1 34670 2651 108 34705 0.3 1 32091 2614 109 31002 0.3 1 28677 2325 110 27578 0.3 1 25574 2004 111 24603 0.3 1 22785 1818 112 21972 0.3 1 20247 1725 113 18720 0.3 1 17311 1409 114 16688 0.3 1 15435 1253 115 14432 0.3 1 13232 1200 116 12245 0.3 1 11232 1013 117 10552 0.3 1 9672 880 118 8984 0.3 1 8244 740 119 7381 0.3 1 6703 678 120 6463 0.3 1 5860 603 121 5515 0.3 1 4963 552 122 4409 0.3 1 4006 403 123 3731 0.3 1 3377 354 124 3097 0.3 1 2824 273 125 2558 0.3 1 2286 272 126 2102 0.3 1 1889 213 127 1729 0.3 1 1530 199 128 1388 0.3 1 1248 140 129 1146 0.3 1 1007 139 130 884 0.3 1 785 99 131 740 0.3 1 651 89 132 734 0.3 1 647 87 133 973 0.3 1 886 87 134 1537 0.3 1 1449 88 135 609 0.3 1 551 58 136 234 0.3 1 208 26 137 157 0.3 1 138 19 138 104 0.3 1 87 17 139 80 0.3 1 60 20 140 68 0.3 1 51 17 141 33 0.3 1 25 8 142 34 0.3 1 26 8 143 16 0.3 1 16 144 16 0.3 1 14 2 145 39 0.3 1 27 12 146 32 0.3 1 26 6 147 85 0.3 1 77 8 148 60 0.3 1 51 9 149 55 0.3 1 49 6 150 652 0.3 1 552 100 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_26psu_3_S11_L002_R1_001.fastq.gz ============================================= 17175482 sequences processed in total