SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_32psu_4_S4_L001_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: 436688). Second best hit was Nextera (count: 1) 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/16C_32psu_4_S4_L001_R2_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 66.35 s (4 us/read; 14.20 M reads/minute). === Summary === Total reads processed: 15,706,000 Reads with adapters: 11,248,615 (71.6%) Reads written (passing filters): 15,706,000 (100.0%) Total basepairs processed: 2,355,900,000 bp Quality-trimmed: 9,159,976 bp (0.4%) Total written (filtered): 1,968,243,578 bp (83.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11248615 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.1% C: 12.2% G: 21.7% T: 36.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2742334 3926500.0 0 2742334 2 376488 981625.0 0 376488 3 202415 245406.2 0 202415 4 115660 61351.6 0 115660 5 96934 15337.9 0 96934 6 82183 3834.5 0 82183 7 66579 958.6 0 66579 8 95001 239.7 0 95001 9 75363 59.9 0 75125 238 10 81209 15.0 1 77351 3858 11 85598 3.7 1 80376 5222 12 86515 0.9 1 81221 5294 13 96527 0.2 1 91069 5458 14 89686 0.2 1 83554 6132 15 72806 0.2 1 68412 4394 16 105343 0.2 1 99018 6325 17 82599 0.2 1 77199 5400 18 79503 0.2 1 74873 4630 19 100299 0.2 1 94044 6255 20 93401 0.2 1 87924 5477 21 81559 0.2 1 76639 4920 22 92216 0.2 1 86910 5306 23 94734 0.2 1 89009 5725 24 95149 0.2 1 89373 5776 25 105782 0.2 1 99776 6006 26 87770 0.2 1 82449 5321 27 95338 0.2 1 88893 6445 28 90298 0.2 1 85892 4406 29 95418 0.2 1 89790 5628 30 93873 0.2 1 89134 4739 31 100963 0.2 1 95205 5758 32 90423 0.2 1 85945 4478 33 99633 0.2 1 93789 5844 34 126170 0.2 1 118899 7271 35 71917 0.2 1 68415 3502 36 98752 0.2 1 93147 5605 37 104121 0.2 1 98203 5918 38 97206 0.2 1 92554 4652 39 94225 0.2 1 89765 4460 40 104186 0.2 1 98424 5762 41 99925 0.2 1 94861 5064 42 102480 0.2 1 97343 5137 43 92586 0.2 1 87878 4708 44 105897 0.2 1 100306 5591 45 112588 0.2 1 106743 5845 46 80544 0.2 1 76510 4034 47 101141 0.2 1 96374 4767 48 98066 0.2 1 93549 4517 49 101791 0.2 1 96776 5015 50 97034 0.2 1 92147 4887 51 120282 0.2 1 114381 5901 52 84235 0.2 1 80401 3834 53 102171 0.2 1 97747 4424 54 76841 0.2 1 73430 3411 55 99264 0.2 1 95032 4232 56 101316 0.2 1 96570 4746 57 94879 0.2 1 90678 4201 58 90444 0.2 1 86700 3744 59 92322 0.2 1 88235 4087 60 94688 0.2 1 90370 4318 61 97150 0.2 1 92685 4465 62 103718 0.2 1 98963 4755 63 136885 0.2 1 131195 5690 64 109397 0.2 1 105405 3992 65 71767 0.2 1 68765 3002 66 78028 0.2 1 74793 3235 67 77090 0.2 1 73810 3280 68 76844 0.2 1 73617 3227 69 75212 0.2 1 71969 3243 70 76863 0.2 1 73510 3353 71 80211 0.2 1 76869 3342 72 75920 0.2 1 72620 3300 73 78093 0.2 1 74948 3145 74 72443 0.2 1 69570 2873 75 68538 0.2 1 65762 2776 76 66619 0.2 1 63921 2698 77 66151 0.2 1 63438 2713 78 62817 0.2 1 60225 2592 79 60312 0.2 1 57778 2534 80 60163 0.2 1 57704 2459 81 57937 0.2 1 55639 2298 82 54845 0.2 1 52637 2208 83 53627 0.2 1 51399 2228 84 50792 0.2 1 48633 2159 85 49633 0.2 1 47523 2110 86 49264 0.2 1 47185 2079 87 49251 0.2 1 47314 1937 88 46501 0.2 1 44723 1778 89 41655 0.2 1 39945 1710 90 39420 0.2 1 37741 1679 91 37399 0.2 1 35859 1540 92 35077 0.2 1 33634 1443 93 32838 0.2 1 31397 1441 94 31873 0.2 1 30582 1291 95 29856 0.2 1 28661 1195 96 27831 0.2 1 26723 1108 97 25609 0.2 1 24584 1025 98 23598 0.2 1 22615 983 99 23296 0.2 1 22392 904 100 21689 0.2 1 20900 789 101 19855 0.2 1 19105 750 102 17867 0.2 1 17193 674 103 15691 0.2 1 15073 618 104 15000 0.2 1 14394 606 105 13326 0.2 1 12799 527 106 12111 0.2 1 11648 463 107 10556 0.2 1 10155 401 108 9460 0.2 1 9085 375 109 8474 0.2 1 8135 339 110 7655 0.2 1 7315 340 111 7041 0.2 1 6747 294 112 6163 0.2 1 5902 261 113 5337 0.2 1 5089 248 114 4565 0.2 1 4367 198 115 3763 0.2 1 3606 157 116 3164 0.2 1 2993 171 117 2789 0.2 1 2653 136 118 2380 0.2 1 2277 103 119 1999 0.2 1 1886 113 120 1562 0.2 1 1470 92 121 1457 0.2 1 1367 90 122 1103 0.2 1 1044 59 123 1029 0.2 1 972 57 124 896 0.2 1 845 51 125 678 0.2 1 637 41 126 611 0.2 1 570 41 127 481 0.2 1 451 30 128 387 0.2 1 354 33 129 379 0.2 1 356 23 130 249 0.2 1 234 15 131 280 0.2 1 263 17 132 196 0.2 1 186 10 133 279 0.2 1 264 15 134 375 0.2 1 361 14 135 138 0.2 1 127 11 136 76 0.2 1 71 5 137 48 0.2 1 43 5 138 41 0.2 1 37 4 139 18 0.2 1 17 1 140 14 0.2 1 12 2 141 8 0.2 1 8 142 12 0.2 1 8 4 143 10 0.2 1 6 4 144 13 0.2 1 11 2 145 15 0.2 1 13 2 146 12 0.2 1 10 2 147 37 0.2 1 35 2 148 25 0.2 1 24 1 149 9 0.2 1 6 3 150 99 0.2 1 92 7 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_32psu_4_S4_L001_R2_001.fastq.gz ============================================= 15706000 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 15706000 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 75350 (0.48%)