SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P11-ACTTGA-READ2-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-P11-ACTTGA-READ2-Sequences.txt.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 458.47 s (21 us/read; 2.89 M reads/minute). === Summary === Total reads processed: 22,073,550 Reads with adapters: 8,546,750 (38.7%) Reads written (passing filters): 22,073,550 (100.0%) Total basepairs processed: 2,207,355,000 bp Quality-trimmed: 12,328,881 bp (0.6%) Total written (filtered): 2,174,060,281 bp (98.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 8546750 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 38.1% C: 23.9% G: 19.3% T: 18.0% none/other: 0.7% Overview of removed sequences length count expect max.err error counts 1 6062251 5518387.5 0 6062251 2 1555315 1379596.9 0 1555315 3 521554 344899.2 0 521554 4 128828 86224.8 0 128828 5 34979 21556.2 0 34979 6 14528 5389.1 0 14528 7 11013 1347.3 0 11013 8 9367 336.8 0 9367 9 9717 84.2 0 9037 680 10 9870 21.1 1 8339 1531 11 8114 5.3 1 7199 915 12 7712 1.3 1 7098 614 13 6545 0.3 1 6156 389 14 7336 0.3 1 6840 496 15 5222 0.3 1 4859 363 16 5471 0.3 1 5162 309 17 6452 0.3 1 6002 450 18 3743 0.3 1 3501 242 19 5064 0.3 1 4690 374 20 3573 0.3 1 3344 229 21 3797 0.3 1 3557 240 22 3463 0.3 1 3151 312 23 3239 0.3 1 2914 325 24 3191 0.3 1 2895 296 25 2607 0.3 1 2368 239 26 2618 0.3 1 2366 252 27 2480 0.3 1 2248 232 28 2392 0.3 1 2189 203 29 2165 0.3 1 1930 235 30 2545 0.3 1 2267 278 31 1611 0.3 1 1449 162 32 1816 0.3 1 1607 209 33 1603 0.3 1 1418 185 34 1651 0.3 1 1451 200 35 1567 0.3 1 1359 208 36 1604 0.3 1 1370 234 37 1365 0.3 1 1215 150 38 1230 0.3 1 1055 175 39 1103 0.3 1 942 161 40 976 0.3 1 841 135 41 950 0.3 1 794 156 42 1170 0.3 1 983 187 43 680 0.3 1 568 112 44 873 0.3 1 700 173 45 1018 0.3 1 822 196 46 660 0.3 1 558 102 47 669 0.3 1 541 128 48 741 0.3 1 605 136 49 662 0.3 1 542 120 50 568 0.3 1 468 100 51 820 0.3 1 659 161 52 494 0.3 1 392 102 53 557 0.3 1 457 100 54 449 0.3 1 370 79 55 410 0.3 1 325 85 56 392 0.3 1 292 100 57 357 0.3 1 288 69 58 353 0.3 1 254 99 59 355 0.3 1 252 103 60 318 0.3 1 253 65 61 406 0.3 1 302 104 62 331 0.3 1 234 97 63 317 0.3 1 228 89 64 353 0.3 1 275 78 65 339 0.3 1 241 98 66 428 0.3 1 264 164 67 3520 0.3 1 296 3224 68 6877 0.3 1 859 6018 69 6037 0.3 1 1138 4899 70 4921 0.3 1 942 3979 71 3163 0.3 1 676 2487 72 1949 0.3 1 482 1467 73 1172 0.3 1 319 853 74 695 0.3 1 189 506 75 569 0.3 1 191 378 76 332 0.3 1 119 213 77 312 0.3 1 126 186 78 298 0.3 1 111 187 79 283 0.3 1 131 152 80 229 0.3 1 99 130 81 219 0.3 1 96 123 82 190 0.3 1 99 91 83 229 0.3 1 104 125 84 229 0.3 1 114 115 85 252 0.3 1 139 113 86 242 0.3 1 116 126 87 232 0.3 1 107 125 88 245 0.3 1 118 127 89 195 0.3 1 50 145 90 214 0.3 1 49 165 91 308 0.3 1 96 212 92 214 0.3 1 60 154 93 280 0.3 1 42 238 94 410 0.3 1 38 372 95 590 0.3 1 41 549 96 901 0.3 1 57 844 97 1400 0.3 1 101 1299 98 1951 0.3 1 77 1874 99 4993 0.3 1 24 4969 100 28752 0.3 1 78 28674 RUN STATISTICS FOR INPUT FILE: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P11-ACTTGA-READ2-Sequences.txt.gz ============================================= 22073550 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 22073550 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 134382 (0.61%)