SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_26psu_3_S15_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: 482987). Second best hit was smallRNA (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/16C_26psu_3_S15_L001_R2_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 58.48 s (4 us/read; 15.09 M reads/minute). === Summary === Total reads processed: 14,705,097 Reads with adapters: 10,980,117 (74.7%) Reads written (passing filters): 14,705,097 (100.0%) Total basepairs processed: 2,205,764,550 bp Quality-trimmed: 13,510,954 bp (0.6%) Total written (filtered): 1,769,417,806 bp (80.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10980117 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.1% C: 14.1% G: 23.8% T: 33.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2264307 3676274.2 0 2264307 2 373214 919068.6 0 373214 3 218063 229767.1 0 218063 4 104965 57441.8 0 104965 5 83066 14360.4 0 83066 6 70406 3590.1 0 70406 7 54672 897.5 0 54672 8 80609 224.4 0 80609 9 63967 56.1 0 63675 292 10 69384 14.0 1 65411 3973 11 74885 3.5 1 69453 5432 12 74890 0.9 1 69291 5599 13 82476 0.2 1 76999 5477 14 78491 0.2 1 72263 6228 15 61874 0.2 1 57566 4308 16 91303 0.2 1 84745 6558 17 72220 0.2 1 66746 5474 18 69582 0.2 1 64867 4715 19 88040 0.2 1 81744 6296 20 81620 0.2 1 76073 5547 21 72843 0.2 1 67713 5130 22 82391 0.2 1 76741 5650 23 83759 0.2 1 77887 5872 24 82590 0.2 1 76725 5865 25 94974 0.2 1 88688 6286 26 78108 0.2 1 72602 5506 27 87345 0.2 1 80708 6637 28 80301 0.2 1 75686 4615 29 86749 0.2 1 80805 5944 30 84969 0.2 1 79761 5208 31 91560 0.2 1 85496 6064 32 82472 0.2 1 77608 4864 33 91075 0.2 1 85011 6064 34 115701 0.2 1 108310 7391 35 65587 0.2 1 61631 3956 36 92396 0.2 1 86112 6284 37 97880 0.2 1 91450 6430 38 93812 0.2 1 88555 5257 39 89857 0.2 1 84658 5199 40 100686 0.2 1 94165 6521 41 95917 0.2 1 90320 5597 42 99426 0.2 1 93710 5716 43 89895 0.2 1 84632 5263 44 101978 0.2 1 95733 6245 45 107145 0.2 1 100731 6414 46 78559 0.2 1 74098 4461 47 99270 0.2 1 93634 5636 48 97566 0.2 1 92156 5410 49 101230 0.2 1 95394 5836 50 95465 0.2 1 89881 5584 51 119107 0.2 1 112449 6658 52 84719 0.2 1 80119 4600 53 101734 0.2 1 96544 5190 54 78783 0.2 1 74521 4262 55 102169 0.2 1 97154 5015 56 104926 0.2 1 99510 5416 57 97330 0.2 1 92599 4731 58 94743 0.2 1 90360 4383 59 96773 0.2 1 91767 5006 60 98229 0.2 1 93172 5057 61 101518 0.2 1 96208 5310 62 108759 0.2 1 103148 5611 63 145227 0.2 1 138420 6807 64 118502 0.2 1 113544 4958 65 77875 0.2 1 74180 3695 66 85279 0.2 1 81158 4121 67 82906 0.2 1 78696 4210 68 83568 0.2 1 79559 4009 69 83055 0.2 1 79009 4046 70 85605 0.2 1 81510 4095 71 91438 0.2 1 87015 4423 72 86608 0.2 1 82445 4163 73 91905 0.2 1 87632 4273 74 84442 0.2 1 80649 3793 75 80482 0.2 1 76627 3855 76 78424 0.2 1 74783 3641 77 78513 0.2 1 74716 3797 78 74066 0.2 1 70442 3624 79 70946 0.2 1 67597 3349 80 70802 0.2 1 67560 3242 81 69586 0.2 1 66414 3172 82 67330 0.2 1 64176 3154 83 64772 0.2 1 61853 2919 84 63911 0.2 1 60972 2939 85 62434 0.2 1 59365 3069 86 62539 0.2 1 59521 3018 87 61465 0.2 1 58594 2871 88 60482 0.2 1 57646 2836 89 54895 0.2 1 52333 2562 90 52052 0.2 1 49599 2453 91 49106 0.2 1 46822 2284 92 45843 0.2 1 43672 2171 93 44679 0.2 1 42566 2113 94 43439 0.2 1 41408 2031 95 41369 0.2 1 39446 1923 96 39301 0.2 1 37521 1780 97 36285 0.2 1 34613 1672 98 34034 0.2 1 32424 1610 99 33720 0.2 1 32265 1455 100 30495 0.2 1 29039 1456 101 27811 0.2 1 26487 1324 102 25647 0.2 1 24471 1176 103 23848 0.2 1 22756 1092 104 23030 0.2 1 22018 1012 105 20481 0.2 1 19504 977 106 19291 0.2 1 18417 874 107 17027 0.2 1 16232 795 108 15744 0.2 1 15015 729 109 13986 0.2 1 13295 691 110 13128 0.2 1 12523 605 111 12855 0.2 1 12274 581 112 11119 0.2 1 10542 577 113 9437 0.2 1 8968 469 114 8605 0.2 1 8220 385 115 7442 0.2 1 7067 375 116 6235 0.2 1 5927 308 117 5342 0.2 1 5066 276 118 4634 0.2 1 4366 268 119 4041 0.2 1 3836 205 120 3372 0.2 1 3167 205 121 3329 0.2 1 3149 180 122 2717 0.2 1 2578 139 123 2317 0.2 1 2172 145 124 2087 0.2 1 1969 118 125 1757 0.2 1 1630 127 126 1582 0.2 1 1504 78 127 1368 0.2 1 1287 81 128 1019 0.2 1 960 59 129 887 0.2 1 843 44 130 669 0.2 1 637 32 131 775 0.2 1 731 44 132 814 0.2 1 771 43 133 1245 0.2 1 1202 43 134 1982 0.2 1 1926 56 135 810 0.2 1 778 32 136 281 0.2 1 260 21 137 198 0.2 1 181 17 138 183 0.2 1 171 12 139 135 0.2 1 124 11 140 85 0.2 1 83 2 141 71 0.2 1 66 5 142 55 0.2 1 52 3 143 87 0.2 1 84 3 144 82 0.2 1 77 5 145 214 0.2 1 204 10 146 799 0.2 1 768 31 147 4799 0.2 1 4649 150 148 3222 0.2 1 3110 112 149 1903 0.2 1 1826 77 150 15860 0.2 1 15305 555 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_26psu_3_S15_L001_R2_001.fastq.gz ============================================= 14705097 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 14705097 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 172314 (1.17%)