SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_32psu_1_S5_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: 749024). Second best hit was Nextera (count: 0) 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_1_S5_L001_R2_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 49.16 s (4 us/read; 17.09 M reads/minute). === Summary === Total reads processed: 14,000,021 Reads with adapters: 12,482,400 (89.2%) Reads written (passing filters): 14,000,021 (100.0%) Total basepairs processed: 2,100,003,150 bp Quality-trimmed: 11,507,684 bp (0.5%) Total written (filtered): 1,389,836,957 bp (66.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 12482400 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 26.9% C: 13.5% G: 25.9% T: 33.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 842057 3500005.2 0 842057 2 142966 875001.3 0 142966 3 90255 218750.3 0 90255 4 55571 54687.6 0 55571 5 57545 13671.9 0 57545 6 49671 3418.0 0 49671 7 41298 854.5 0 41298 8 59001 213.6 0 59001 9 47476 53.4 0 47315 161 10 53026 13.4 1 50683 2343 11 55985 3.3 1 52789 3196 12 57070 0.8 1 53792 3278 13 64601 0.2 1 61294 3307 14 62201 0.2 1 58283 3918 15 50727 0.2 1 47889 2838 16 74265 0.2 1 70212 4053 17 60248 0.2 1 56657 3591 18 57873 0.2 1 54797 3076 19 74512 0.2 1 70251 4261 20 70260 0.2 1 66610 3650 21 62230 0.2 1 58933 3297 22 72026 0.2 1 68190 3836 23 75580 0.2 1 71483 4097 24 76103 0.2 1 71906 4197 25 87020 0.2 1 82705 4315 26 72653 0.2 1 68640 4013 27 81722 0.2 1 76658 5064 28 76893 0.2 1 73629 3264 29 84223 0.2 1 79742 4481 30 83568 0.2 1 79746 3822 31 92428 0.2 1 87765 4663 32 83785 0.2 1 79986 3799 33 94083 0.2 1 89299 4784 34 124234 0.2 1 117883 6351 35 70662 0.2 1 67495 3167 36 97571 0.2 1 92509 5062 37 105963 0.2 1 100553 5410 38 100112 0.2 1 95880 4232 39 98883 0.2 1 94704 4179 40 111592 0.2 1 106078 5514 41 108482 0.2 1 103543 4939 42 113048 0.2 1 108097 4951 43 104564 0.2 1 100168 4396 44 122044 0.2 1 116433 5611 45 132901 0.2 1 126882 6019 46 96495 0.2 1 92302 4193 47 123777 0.2 1 118653 5124 48 123419 0.2 1 118253 5166 49 130090 0.2 1 124494 5596 50 124769 0.2 1 119306 5463 51 159790 0.2 1 152747 7043 52 114726 0.2 1 110175 4551 53 140573 0.2 1 135310 5263 54 107631 0.2 1 103512 4119 55 142110 0.2 1 137013 5097 56 148511 0.2 1 142711 5800 57 141596 0.2 1 136449 5147 58 138299 0.2 1 133566 4733 59 142121 0.2 1 137002 5119 60 148830 0.2 1 143312 5518 61 154735 0.2 1 148878 5857 62 170128 0.2 1 163868 6260 63 234733 0.2 1 226789 7944 64 212296 0.2 1 206143 6153 65 126771 0.2 1 122389 4382 66 138120 0.2 1 133306 4814 67 139286 0.2 1 134193 5093 68 141731 0.2 1 136845 4886 69 141571 0.2 1 136513 5058 70 151101 0.2 1 145752 5349 71 165000 0.2 1 159543 5457 72 156137 0.2 1 150635 5502 73 168957 0.2 1 163425 5532 74 155346 0.2 1 150282 5064 75 149711 0.2 1 144684 5027 76 146688 0.2 1 141765 4923 77 148035 0.2 1 142983 5052 78 144141 0.2 1 139293 4848 79 140116 0.2 1 135357 4759 80 139815 0.2 1 135255 4560 81 140275 0.2 1 135701 4574 82 136237 0.2 1 131702 4535 83 133248 0.2 1 128960 4288 84 130802 0.2 1 126388 4414 85 131118 0.2 1 126640 4478 86 132538 0.2 1 128154 4384 87 134528 0.2 1 130166 4362 88 132145 0.2 1 127913 4232 89 119589 0.2 1 115716 3873 90 116381 0.2 1 112493 3888 91 109945 0.2 1 106186 3759 92 104899 0.2 1 101501 3398 93 102752 0.2 1 99467 3285 94 100398 0.2 1 97258 3140 95 96752 0.2 1 93687 3065 96 92474 0.2 1 89641 2833 97 85160 0.2 1 82565 2595 98 81057 0.2 1 78431 2626 99 79148 0.2 1 76636 2512 100 72036 0.2 1 69758 2278 101 69452 0.2 1 67404 2048 102 66047 0.2 1 64053 1994 103 62024 0.2 1 60217 1807 104 59709 0.2 1 57936 1773 105 53244 0.2 1 51636 1608 106 48557 0.2 1 47145 1412 107 44301 0.2 1 42956 1345 108 40672 0.2 1 39383 1289 109 36835 0.2 1 35717 1118 110 34356 0.2 1 33352 1004 111 32280 0.2 1 31328 952 112 28083 0.2 1 27306 777 113 24882 0.2 1 24139 743 114 22038 0.2 1 21386 652 115 18554 0.2 1 17942 612 116 16085 0.2 1 15523 562 117 13238 0.2 1 12820 418 118 11657 0.2 1 11269 388 119 10199 0.2 1 9853 346 120 8562 0.2 1 8250 312 121 7440 0.2 1 7187 253 122 5970 0.2 1 5758 212 123 5287 0.2 1 5099 188 124 4439 0.2 1 4276 163 125 3716 0.2 1 3583 133 126 2906 0.2 1 2772 134 127 2521 0.2 1 2432 89 128 1926 0.2 1 1855 71 129 1631 0.2 1 1564 67 130 1264 0.2 1 1221 43 131 1080 0.2 1 1044 36 132 1051 0.2 1 1017 34 133 1128 0.2 1 1088 40 134 1229 0.2 1 1204 25 135 567 0.2 1 545 22 136 312 0.2 1 296 16 137 233 0.2 1 225 8 138 145 0.2 1 135 10 139 105 0.2 1 99 6 140 127 0.2 1 124 3 141 54 0.2 1 50 4 142 42 0.2 1 36 6 143 34 0.2 1 31 3 144 35 0.2 1 32 3 145 45 0.2 1 43 2 146 40 0.2 1 38 2 147 105 0.2 1 96 9 148 62 0.2 1 59 3 149 54 0.2 1 50 4 150 462 0.2 1 437 25 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_32psu_1_S5_L001_R2_001.fastq.gz ============================================= 14000021 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 14000021 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 274173 (1.96%)