SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_32psu_2_S6_L002_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: 561352). 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/8C_32psu_2_S6_L002_R2_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 52.59 s (4 us/read; 14.68 M reads/minute). === Summary === Total reads processed: 12,868,767 Reads with adapters: 10,225,148 (79.5%) Reads written (passing filters): 12,868,767 (100.0%) Total basepairs processed: 1,930,315,050 bp Quality-trimmed: 8,911,212 bp (0.5%) Total written (filtered): 1,486,049,208 bp (77.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10225148 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.1% C: 13.1% G: 23.9% T: 34.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1581903 3217191.8 0 1581903 2 233784 804297.9 0 233784 3 139412 201074.5 0 139412 4 79292 50268.6 0 79292 5 72507 12567.2 0 72507 6 64695 3141.8 0 64695 7 50784 785.4 0 50784 8 73943 196.4 0 73943 9 59253 49.1 0 59073 180 10 62906 12.3 1 58824 4082 11 69220 3.1 1 63844 5376 12 67633 0.8 1 62443 5190 13 78337 0.2 1 72455 5882 14 72684 0.2 1 66542 6142 15 59253 0.2 1 54996 4257 16 85878 0.2 1 79407 6471 17 71616 0.2 1 66058 5558 18 64381 0.2 1 59775 4606 19 83620 0.2 1 77611 6009 20 78383 0.2 1 72906 5477 21 69471 0.2 1 64687 4784 22 78479 0.2 1 73016 5463 23 83210 0.2 1 77230 5980 24 82011 0.2 1 76117 5894 25 93094 0.2 1 87025 6069 26 77459 0.2 1 71634 5825 27 86527 0.2 1 79790 6737 28 77466 0.2 1 72862 4604 29 87078 0.2 1 81023 6055 30 83340 0.2 1 78135 5205 31 92587 0.2 1 86504 6083 32 80491 0.2 1 75656 4835 33 92967 0.2 1 86621 6346 34 120697 0.2 1 112803 7894 35 64048 0.2 1 59979 4069 36 95138 0.2 1 88610 6528 37 100610 0.2 1 93904 6706 38 93157 0.2 1 87717 5440 39 88669 0.2 1 83789 4880 40 101334 0.2 1 95182 6152 41 98089 0.2 1 92269 5820 42 100106 0.2 1 94212 5894 43 90866 0.2 1 85570 5296 44 106583 0.2 1 100029 6554 45 108549 0.2 1 101877 6672 46 84237 0.2 1 79394 4843 47 103605 0.2 1 98067 5538 48 100222 0.2 1 94797 5425 49 105528 0.2 1 99377 6151 50 101252 0.2 1 95306 5946 51 124662 0.2 1 117482 7180 52 89980 0.2 1 85108 4872 53 112122 0.2 1 106274 5848 54 81922 0.2 1 77760 4162 55 105894 0.2 1 100558 5336 56 109567 0.2 1 103471 6096 57 105084 0.2 1 100060 5024 58 101375 0.2 1 96453 4922 59 101412 0.2 1 96219 5193 60 106019 0.2 1 100584 5435 61 107866 0.2 1 102516 5350 62 117046 0.2 1 111012 6034 63 155210 0.2 1 148115 7095 64 127345 0.2 1 122328 5017 65 83662 0.2 1 79683 3979 66 91095 0.2 1 86676 4419 67 90432 0.2 1 85682 4750 68 91566 0.2 1 87021 4545 69 91038 0.2 1 86455 4583 70 97071 0.2 1 92328 4743 71 100160 0.2 1 95222 4938 72 95370 0.2 1 90793 4577 73 99146 0.2 1 94377 4769 74 90186 0.2 1 85699 4487 75 87292 0.2 1 82908 4384 76 84846 0.2 1 80550 4296 77 84110 0.2 1 79782 4328 78 80083 0.2 1 76044 4039 79 77641 0.2 1 73764 3877 80 76649 0.2 1 72933 3716 81 75643 0.2 1 71998 3645 82 72511 0.2 1 69001 3510 83 70456 0.2 1 67059 3397 84 67826 0.2 1 64473 3353 85 66652 0.2 1 63633 3019 86 65922 0.2 1 62797 3125 87 65939 0.2 1 62926 3013 88 64115 0.2 1 61226 2889 89 57559 0.2 1 54978 2581 90 55692 0.2 1 53148 2544 91 51986 0.2 1 49669 2317 92 49131 0.2 1 46914 2217 93 46886 0.2 1 44668 2218 94 45747 0.2 1 43801 1946 95 42950 0.2 1 40887 2063 96 40716 0.2 1 38860 1856 97 37404 0.2 1 35730 1674 98 34443 0.2 1 32843 1600 99 33264 0.2 1 31734 1530 100 30705 0.2 1 29262 1443 101 28943 0.2 1 27671 1272 102 27964 0.2 1 26691 1273 103 25366 0.2 1 24255 1111 104 24064 0.2 1 22990 1074 105 21070 0.2 1 20080 990 106 19078 0.2 1 18244 834 107 17343 0.2 1 16582 761 108 15238 0.2 1 14525 713 109 14062 0.2 1 13403 659 110 12670 0.2 1 12101 569 111 11892 0.2 1 11362 530 112 10243 0.2 1 9780 463 113 8834 0.2 1 8449 385 114 7653 0.2 1 7300 353 115 6468 0.2 1 6167 301 116 5767 0.2 1 5513 254 117 4744 0.2 1 4519 225 118 4267 0.2 1 4031 236 119 3534 0.2 1 3331 203 120 2971 0.2 1 2813 158 121 2616 0.2 1 2484 132 122 2300 0.2 1 2180 120 123 1889 0.2 1 1769 120 124 1591 0.2 1 1513 78 125 1198 0.2 1 1143 55 126 1107 0.2 1 1053 54 127 843 0.2 1 791 52 128 694 0.2 1 650 44 129 581 0.2 1 539 42 130 407 0.2 1 381 26 131 412 0.2 1 395 17 132 294 0.2 1 275 19 133 274 0.2 1 263 11 134 295 0.2 1 282 13 135 162 0.2 1 152 10 136 127 0.2 1 120 7 137 72 0.2 1 67 5 138 53 0.2 1 46 7 139 48 0.2 1 43 5 140 33 0.2 1 30 3 141 23 0.2 1 20 3 142 13 0.2 1 11 2 143 12 0.2 1 11 1 144 5 0.2 1 3 2 145 11 0.2 1 11 146 13 0.2 1 12 1 147 30 0.2 1 28 2 148 16 0.2 1 14 2 149 14 0.2 1 13 1 150 92 0.2 1 87 5 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_32psu_2_S6_L002_R2_001.fastq.gz ============================================= 12868767 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 12868767 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 111253 (0.86%)