SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P04-GTCCGC-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-P04-GTCCGC-READ1-Sequences.txt.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 466.14 s (20 us/read; 2.95 M reads/minute). === Summary === Total reads processed: 22,919,563 Reads with adapters: 8,662,070 (37.8%) Reads written (passing filters): 22,919,563 (100.0%) Total basepairs processed: 2,291,956,300 bp Quality-trimmed: 11,887,894 bp (0.5%) Total written (filtered): 2,233,341,045 bp (97.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 8662070 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 34.7% C: 26.7% G: 16.2% T: 18.5% none/other: 3.9% Overview of removed sequences length count expect max.err error counts 1 6057249 5729890.8 0 6057249 2 1350476 1432472.7 0 1350476 3 401413 358118.2 0 401413 4 110413 89529.5 0 110413 5 44565 22382.4 0 44565 6 25971 5595.6 0 25971 7 23216 1398.9 0 23216 8 20554 349.7 0 20554 9 19437 87.4 0 19108 329 10 20458 21.9 1 17702 2756 11 16357 5.5 1 15457 900 12 15655 1.4 1 14905 750 13 14516 0.3 1 13873 643 14 13675 0.3 1 13024 651 15 13036 0.3 1 12404 632 16 12080 0.3 1 11519 561 17 11870 0.3 1 11350 520 18 11003 0.3 1 10430 573 19 9853 0.3 1 9418 435 20 8799 0.3 1 8380 419 21 7992 0.3 1 7576 416 22 7360 0.3 1 6980 380 23 6398 0.3 1 6079 319 24 6098 0.3 1 5790 308 25 5605 0.3 1 5310 295 26 5103 0.3 1 4892 211 27 5058 0.3 1 4797 261 28 4732 0.3 1 4476 256 29 4441 0.3 1 4209 232 30 4224 0.3 1 4002 222 31 3862 0.3 1 3630 232 32 3655 0.3 1 3465 190 33 3359 0.3 1 3184 175 34 3072 0.3 1 2914 158 35 2946 0.3 1 2795 151 36 2851 0.3 1 2690 161 37 2733 0.3 1 2549 184 38 2292 0.3 1 2138 154 39 2236 0.3 1 2079 157 40 2058 0.3 1 1932 126 41 1689 0.3 1 1597 92 42 1605 0.3 1 1500 105 43 2012 0.3 1 1891 121 44 759 0.3 1 695 64 45 1043 0.3 1 974 69 46 1209 0.3 1 1130 79 47 1158 0.3 1 1054 104 48 1274 0.3 1 1203 71 49 1199 0.3 1 1113 86 50 1084 0.3 1 1002 82 51 1033 0.3 1 955 78 52 976 0.3 1 898 78 53 917 0.3 1 814 103 54 833 0.3 1 760 73 55 787 0.3 1 714 73 56 508 0.3 1 460 48 57 541 0.3 1 474 67 58 483 0.3 1 448 35 59 448 0.3 1 404 44 60 422 0.3 1 391 31 61 414 0.3 1 375 39 62 345 0.3 1 302 43 63 361 0.3 1 319 42 64 321 0.3 1 292 29 65 377 0.3 1 296 81 66 353 0.3 1 300 53 67 333 0.3 1 273 60 68 383 0.3 1 306 77 69 420 0.3 1 320 100 70 474 0.3 1 332 142 71 465 0.3 1 279 186 72 619 0.3 1 300 319 73 1032 0.3 1 322 710 74 2398 0.3 1 343 2055 75 35876 0.3 1 593 35283 76 52294 0.3 1 1314 50980 77 47044 0.3 1 1967 45077 78 36303 0.3 1 1245 35058 79 21851 0.3 1 959 20892 80 14792 0.3 1 694 14098 81 9725 0.3 1 409 9316 82 6405 0.3 1 321 6084 83 3876 0.3 1 270 3606 84 2573 0.3 1 241 2332 85 2112 0.3 1 197 1915 86 1669 0.3 1 137 1532 87 1295 0.3 1 177 1118 88 1097 0.3 1 150 947 89 927 0.3 1 103 824 90 835 0.3 1 121 714 91 847 0.3 1 142 705 92 761 0.3 1 77 684 93 759 0.3 1 70 689 94 908 0.3 1 63 845 95 999 0.3 1 83 916 96 1478 0.3 1 76 1402 97 2171 0.3 1 167 2004 98 2803 0.3 1 93 2710 99 10194 0.3 1 44 10150 100 87530 0.3 1 102 87428 RUN STATISTICS FOR INPUT FILE: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P04-GTCCGC-READ1-Sequences.txt.gz ============================================= 22919563 sequences processed in total