SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_32psu_4_S4_L001_R1_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_R1_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 63.66 s (4 us/read; 14.80 M reads/minute). === Summary === Total reads processed: 15,706,000 Reads with adapters: 11,318,033 (72.1%) Reads written (passing filters): 15,706,000 (100.0%) Total basepairs processed: 2,355,900,000 bp Quality-trimmed: 7,618,669 bp (0.3%) Total written (filtered): 1,966,841,132 bp (83.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11318033 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 31.8% C: 13.1% G: 19.5% T: 35.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2758722 3926500.0 0 2758722 2 358574 981625.0 0 358574 3 190965 245406.2 0 190965 4 113114 61351.6 0 113114 5 86888 15337.9 0 86888 6 85123 3834.5 0 85123 7 70336 958.6 0 70336 8 85928 239.7 0 85928 9 87066 59.9 0 86195 871 10 79602 15.0 1 75862 3740 11 88089 3.7 1 81938 6151 12 85321 0.9 1 80325 4996 13 84763 0.2 1 79667 5096 14 88305 0.2 1 82326 5979 15 88981 0.2 1 83685 5296 16 88786 0.2 1 82621 6165 17 106554 0.2 1 98505 8049 18 89122 0.2 1 84209 4913 19 77746 0.2 1 73215 4531 20 92038 0.2 1 86658 5380 21 99609 0.2 1 93006 6603 22 85867 0.2 1 81408 4459 23 100095 0.2 1 93955 6140 24 90779 0.2 1 83874 6905 25 97845 0.2 1 91593 6252 26 88800 0.2 1 83917 4883 27 97906 0.2 1 90971 6935 28 105510 0.2 1 98167 7343 29 95263 0.2 1 88170 7093 30 108904 0.2 1 103370 5534 31 79085 0.2 1 74523 4562 32 103105 0.2 1 96799 6306 33 92937 0.2 1 86945 5992 34 100117 0.2 1 93522 6595 35 106537 0.2 1 100062 6475 36 91203 0.2 1 86381 4822 37 99865 0.2 1 93587 6278 38 105531 0.2 1 98508 7023 39 105906 0.2 1 99469 6437 40 104183 0.2 1 97213 6970 41 116528 0.2 1 106559 9969 42 93606 0.2 1 87149 6457 43 153884 0.2 1 145422 8462 44 48528 0.2 1 44473 4055 45 107110 0.2 1 99279 7831 46 172499 0.2 1 161736 10763 47 116179 0.2 1 109492 6687 48 80709 0.2 1 73983 6726 49 159482 0.2 1 150516 8966 50 64228 0.2 1 59915 4313 51 90888 0.2 1 84987 5901 52 193279 0.2 1 183371 9908 53 141743 0.2 1 135721 6022 54 59956 0.2 1 56077 3879 55 102925 0.2 1 98274 4651 56 66784 0.2 1 62498 4286 57 123279 0.2 1 118108 5171 58 43777 0.2 1 41446 2331 59 39827 0.2 1 36676 3151 60 113430 0.2 1 108052 5378 61 89200 0.2 1 85501 3699 62 44869 0.2 1 41907 2962 63 85974 0.2 1 81524 4450 64 74880 0.2 1 71341 3539 65 59793 0.2 1 56240 3553 66 87755 0.2 1 82874 4881 67 100481 0.2 1 94117 6364 68 167488 0.2 1 159452 8036 69 79463 0.2 1 74811 4652 70 27878 0.2 1 25310 2568 71 23051 0.2 1 21160 1891 72 60528 0.2 1 57268 3260 73 72149 0.2 1 68285 3864 74 73360 0.2 1 69333 4027 75 71612 0.2 1 67692 3920 76 70649 0.2 1 66797 3852 77 70150 0.2 1 66254 3896 78 65804 0.2 1 62003 3801 79 64610 0.2 1 60969 3641 80 63497 0.2 1 60035 3462 81 61317 0.2 1 58042 3275 82 58860 0.2 1 55659 3201 83 57047 0.2 1 53828 3219 84 54423 0.2 1 51371 3052 85 52481 0.2 1 49574 2907 86 50571 0.2 1 47688 2883 87 48288 0.2 1 45567 2721 88 45981 0.2 1 43442 2539 89 43761 0.2 1 41217 2544 90 42661 0.2 1 40245 2416 91 40737 0.2 1 38345 2392 92 38688 0.2 1 36453 2235 93 34947 0.2 1 32894 2053 94 34299 0.2 1 32291 2008 95 31760 0.2 1 29854 1906 96 29525 0.2 1 27743 1782 97 27419 0.2 1 25829 1590 98 24938 0.2 1 23465 1473 99 24209 0.2 1 22665 1544 100 21792 0.2 1 20438 1354 101 20393 0.2 1 19119 1274 102 18597 0.2 1 17433 1164 103 16893 0.2 1 15821 1072 104 15643 0.2 1 14642 1001 105 14032 0.2 1 13104 928 106 12725 0.2 1 11896 829 107 11164 0.2 1 10388 776 108 10327 0.2 1 9611 716 109 9052 0.2 1 8399 653 110 8194 0.2 1 7576 618 111 7205 0.2 1 6690 515 112 6374 0.2 1 5898 476 113 5432 0.2 1 5054 378 114 4742 0.2 1 4349 393 115 4031 0.2 1 3736 295 116 3440 0.2 1 3126 314 117 3047 0.2 1 2793 254 118 2620 0.2 1 2385 235 119 2131 0.2 1 1953 178 120 1732 0.2 1 1592 140 121 1562 0.2 1 1390 172 122 1210 0.2 1 1094 116 123 1050 0.2 1 947 103 124 965 0.2 1 849 116 125 722 0.2 1 635 87 126 663 0.2 1 591 72 127 539 0.2 1 460 79 128 435 0.2 1 362 73 129 406 0.2 1 358 48 130 274 0.2 1 240 34 131 291 0.2 1 261 30 132 213 0.2 1 190 23 133 259 0.2 1 233 26 134 361 0.2 1 342 19 135 151 0.2 1 128 23 136 85 0.2 1 68 17 137 53 0.2 1 45 8 138 43 0.2 1 37 6 139 17 0.2 1 15 2 140 21 0.2 1 18 3 141 17 0.2 1 15 2 142 9 0.2 1 8 1 143 9 0.2 1 7 2 144 15 0.2 1 10 5 145 12 0.2 1 10 2 146 12 0.2 1 10 2 147 49 0.2 1 45 4 148 35 0.2 1 30 5 149 12 0.2 1 11 1 150 163 0.2 1 152 11 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_32psu_4_S4_L001_R1_001.fastq.gz ============================================= 15706000 sequences processed in total