SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_26psu_4_S16_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: 560031). Second best hit was smallRNA (count: 2) 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_4_S16_L001_R2_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 65.13 s (4 us/read; 15.91 M reads/minute). === Summary === Total reads processed: 17,274,454 Reads with adapters: 13,645,900 (79.0%) Reads written (passing filters): 17,274,454 (100.0%) Total basepairs processed: 2,591,168,100 bp Quality-trimmed: 13,876,099 bp (0.5%) Total written (filtered): 1,990,000,241 bp (76.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 13645900 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 27.8% C: 13.6% G: 24.3% T: 34.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2190701 4318613.5 0 2190701 2 333937 1079653.4 0 333937 3 193297 269913.3 0 193297 4 108228 67478.3 0 108228 5 96340 16869.6 0 96340 6 82360 4217.4 0 82360 7 66626 1054.3 0 66626 8 94895 263.6 0 94895 9 77384 65.9 0 77094 290 10 82708 16.5 1 78572 4136 11 89357 4.1 1 83568 5789 12 89625 1.0 1 83594 6031 13 99746 0.3 1 93650 6096 14 92613 0.3 1 86134 6479 15 76114 0.3 1 71248 4866 16 111173 0.3 1 104156 7017 17 86562 0.3 1 80610 5952 18 85573 0.3 1 80223 5350 19 106850 0.3 1 99751 7099 20 100367 0.3 1 94128 6239 21 90921 0.3 1 85159 5762 22 101235 0.3 1 95178 6057 23 104933 0.3 1 98391 6542 24 104547 0.3 1 97881 6666 25 118815 0.3 1 111628 7187 26 97285 0.3 1 91138 6147 27 109196 0.3 1 101511 7685 28 101869 0.3 1 96609 5260 29 109573 0.3 1 102802 6771 30 108062 0.3 1 102093 5969 31 117609 0.3 1 110646 6963 32 106258 0.3 1 100439 5819 33 117522 0.3 1 110451 7071 34 150731 0.3 1 141819 8912 35 85761 0.3 1 81040 4721 36 120033 0.3 1 112538 7495 37 128229 0.3 1 120721 7508 38 120207 0.3 1 114092 6115 39 117619 0.3 1 111621 5998 40 131723 0.3 1 123921 7802 41 124695 0.3 1 117864 6831 42 129575 0.3 1 122681 6894 43 116234 0.3 1 109884 6350 44 134420 0.3 1 127012 7408 45 140609 0.3 1 133114 7495 46 107286 0.3 1 101613 5673 47 132633 0.3 1 125745 6888 48 129386 0.3 1 122927 6459 49 135218 0.3 1 128159 7059 50 128960 0.3 1 121933 7027 51 158199 0.3 1 150290 7909 52 115635 0.3 1 110127 5508 53 138536 0.3 1 132192 6344 54 107841 0.3 1 102539 5302 55 138155 0.3 1 131891 6264 56 143145 0.3 1 136120 7025 57 134481 0.3 1 128427 6054 58 129238 0.3 1 123474 5764 59 132359 0.3 1 126122 6237 60 136774 0.3 1 130227 6547 61 140635 0.3 1 133777 6858 62 151391 0.3 1 144144 7247 63 203160 0.3 1 194409 8751 64 167385 0.3 1 160989 6396 65 109630 0.3 1 104767 4863 66 118791 0.3 1 113616 5175 67 117636 0.3 1 112066 5570 68 118814 0.3 1 113546 5268 69 118228 0.3 1 112812 5416 70 124633 0.3 1 118945 5688 71 132024 0.3 1 126339 5685 72 125001 0.3 1 119396 5605 73 132138 0.3 1 126543 5595 74 121069 0.3 1 115983 5086 75 115800 0.3 1 110816 4984 76 113271 0.3 1 108471 4800 77 113434 0.3 1 108479 4955 78 108048 0.3 1 103289 4759 79 104688 0.3 1 100095 4593 80 104276 0.3 1 99811 4465 81 103173 0.3 1 98658 4515 82 98745 0.3 1 94559 4186 83 96106 0.3 1 91915 4191 84 93144 0.3 1 88994 4150 85 92176 0.3 1 88129 4047 86 91669 0.3 1 87622 4047 87 92154 0.3 1 88295 3859 88 89148 0.3 1 85288 3860 89 81149 0.3 1 77666 3483 90 78174 0.3 1 74845 3329 91 73485 0.3 1 70395 3090 92 69397 0.3 1 66501 2896 93 66171 0.3 1 63215 2956 94 65063 0.3 1 62271 2792 95 61764 0.3 1 59094 2670 96 58368 0.3 1 55944 2424 97 55755 0.3 1 53423 2332 98 52903 0.3 1 50745 2158 99 53244 0.3 1 51088 2156 100 47728 0.3 1 45793 1935 101 43677 0.3 1 41891 1786 102 42206 0.3 1 40454 1752 103 39193 0.3 1 37641 1552 104 38151 0.3 1 36638 1513 105 33427 0.3 1 32096 1331 106 30687 0.3 1 29498 1189 107 27695 0.3 1 26647 1048 108 24686 0.3 1 23641 1045 109 22730 0.3 1 21817 913 110 20941 0.3 1 20113 828 111 19623 0.3 1 18797 826 112 17030 0.3 1 16327 703 113 14883 0.3 1 14295 588 114 13223 0.3 1 12713 510 115 11548 0.3 1 11042 506 116 9826 0.3 1 9358 468 117 8325 0.3 1 7930 395 118 7266 0.3 1 6933 333 119 6187 0.3 1 5890 297 120 5282 0.3 1 5029 253 121 4888 0.3 1 4641 247 122 4001 0.3 1 3828 173 123 3492 0.3 1 3320 172 124 2873 0.3 1 2729 144 125 2466 0.3 1 2331 135 126 2028 0.3 1 1925 103 127 1732 0.3 1 1662 70 128 1274 0.3 1 1214 60 129 1089 0.3 1 1028 61 130 827 0.3 1 782 45 131 699 0.3 1 652 47 132 657 0.3 1 618 39 133 790 0.3 1 750 40 134 1089 0.3 1 1048 41 135 486 0.3 1 468 18 136 232 0.3 1 220 12 137 137 0.3 1 130 7 138 117 0.3 1 101 16 139 79 0.3 1 72 7 140 58 0.3 1 53 5 141 42 0.3 1 40 2 142 42 0.3 1 37 5 143 28 0.3 1 25 3 144 19 0.3 1 18 1 145 43 0.3 1 41 2 146 41 0.3 1 36 5 147 80 0.3 1 71 9 148 57 0.3 1 57 149 45 0.3 1 41 4 150 372 0.3 1 355 17 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_26psu_4_S16_L001_R2_001.fastq.gz ============================================= 17274454 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 17274454 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 196568 (1.14%)