SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P13-ATCACG-READ1-Sequences.txt.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 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 15 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 15 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 4 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 4 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 /mnt/data/coral_RNAseq_2017/porites/20180415_trimmed/fastqc --threads 24 Output file will be GZIP compressed This is cutadapt 1.16 with Python 3.6.4 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P13-ATCACG-READ1-Sequences.txt.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 360.61 s (20 us/read; 2.95 M reads/minute). === Summary === Total reads processed: 17,735,907 Reads with adapters: 6,770,690 (38.2%) Reads written (passing filters): 17,735,907 (100.0%) Total basepairs processed: 1,773,590,700 bp Quality-trimmed: 7,228,061 bp (0.4%) Total written (filtered): 1,718,415,065 bp (96.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 6770690 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 34.2% C: 26.2% G: 15.3% T: 18.4% none/other: 5.9% Overview of removed sequences length count expect max.err error counts 1 4836894 4433976.8 0 4836894 2 972166 1108494.2 0 972166 3 296994 277123.5 0 296994 4 76625 69280.9 0 76625 5 25029 17320.2 0 25029 6 13387 4330.1 0 13387 7 10968 1082.5 0 10968 8 9921 270.6 0 9921 9 9801 67.7 0 9621 180 10 10238 16.9 1 8124 2114 11 8593 4.2 1 8042 551 12 7477 1.1 1 7137 340 13 6881 0.3 1 6570 311 14 6757 0.3 1 6415 342 15 6097 0.3 1 5784 313 16 5942 0.3 1 5592 350 17 5393 0.3 1 5139 254 18 5333 0.3 1 5020 313 19 4602 0.3 1 4364 238 20 4158 0.3 1 3917 241 21 3771 0.3 1 3550 221 22 3115 0.3 1 2980 135 23 2913 0.3 1 2763 150 24 2839 0.3 1 2673 166 25 2645 0.3 1 2493 152 26 2304 0.3 1 2183 121 27 2154 0.3 1 2028 126 28 2011 0.3 1 1918 93 29 1870 0.3 1 1753 117 30 1747 0.3 1 1657 90 31 1606 0.3 1 1515 91 32 1348 0.3 1 1276 72 33 1373 0.3 1 1278 95 34 1231 0.3 1 1167 64 35 1078 0.3 1 1003 75 36 1014 0.3 1 951 63 37 917 0.3 1 860 57 38 871 0.3 1 791 80 39 921 0.3 1 795 126 40 714 0.3 1 648 66 41 1028 0.3 1 959 69 42 213 0.3 1 195 18 43 323 0.3 1 293 30 44 405 0.3 1 370 35 45 346 0.3 1 318 28 46 360 0.3 1 332 28 47 312 0.3 1 285 27 48 351 0.3 1 316 35 49 355 0.3 1 308 47 50 301 0.3 1 273 28 51 323 0.3 1 282 41 52 217 0.3 1 191 26 53 254 0.3 1 228 26 54 155 0.3 1 128 27 55 168 0.3 1 150 18 56 139 0.3 1 120 19 57 120 0.3 1 102 18 58 151 0.3 1 105 46 59 89 0.3 1 73 16 60 113 0.3 1 79 34 61 132 0.3 1 111 21 62 112 0.3 1 82 30 63 135 0.3 1 74 61 64 96 0.3 1 63 33 65 92 0.3 1 58 34 66 110 0.3 1 80 30 67 108 0.3 1 70 38 68 110 0.3 1 48 62 69 308 0.3 1 183 125 70 284 0.3 1 67 217 71 404 0.3 1 79 325 72 1001 0.3 1 48 953 73 14137 0.3 1 123 14014 74 18277 0.3 1 204 18073 75 15920 0.3 1 459 15461 76 12229 0.3 1 176 12053 77 10273 0.3 1 191 10082 78 9393 0.3 1 167 9226 79 7658 0.3 1 205 7453 80 7446 0.3 1 162 7284 81 6415 0.3 1 128 6287 82 5508 0.3 1 138 5370 83 5347 0.3 1 143 5204 84 5052 0.3 1 121 4931 85 4394 0.3 1 117 4277 86 4125 0.3 1 101 4024 87 4001 0.3 1 150 3851 88 3733 0.3 1 98 3635 89 3627 0.3 1 83 3544 90 3531 0.3 1 68 3463 91 3503 0.3 1 84 3419 92 3333 0.3 1 59 3274 93 3864 0.3 1 42 3822 94 4529 0.3 1 47 4482 95 4736 0.3 1 57 4679 96 6120 0.3 1 53 6067 97 8095 0.3 1 96 7999 98 10574 0.3 1 56 10518 99 27067 0.3 1 48 27019 100 189490 0.3 1 106 189384 RUN STATISTICS FOR INPUT FILE: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P13-ATCACG-READ1-Sequences.txt.gz ============================================= 17735907 sequences processed in total