SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_32psu_3_S3_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: 655761). 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_32psu_3_S3_L002_R2_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 51.99 s (4 us/read; 15.78 M reads/minute). === Summary === Total reads processed: 13,670,957 Reads with adapters: 11,550,197 (84.5%) Reads written (passing filters): 13,670,957 (100.0%) Total basepairs processed: 2,050,643,550 bp Quality-trimmed: 11,580,867 bp (0.6%) Total written (filtered): 1,468,475,211 bp (71.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11550197 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.6% C: 12.3% G: 24.9% T: 34.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1212421 3417739.2 0 1212421 2 191566 854434.8 0 191566 3 121338 213608.7 0 121338 4 68246 53402.2 0 68246 5 66256 13350.5 0 66256 6 60146 3337.6 0 60146 7 46826 834.4 0 46826 8 69191 208.6 0 69191 9 54203 52.2 0 54035 168 10 59001 13.0 1 54514 4487 11 64399 3.3 1 58784 5615 12 63560 0.8 1 57831 5729 13 73714 0.2 1 67412 6302 14 69969 0.2 1 63352 6617 15 54986 0.2 1 50399 4587 16 83002 0.2 1 75869 7133 17 70639 0.2 1 64421 6218 18 61266 0.2 1 56207 5059 19 82751 0.2 1 75847 6904 20 76799 0.2 1 70584 6215 21 67039 0.2 1 61694 5345 22 77648 0.2 1 71294 6354 23 82616 0.2 1 75896 6720 24 82091 0.2 1 75051 7040 25 94761 0.2 1 87866 6895 26 78379 0.2 1 71576 6803 27 86685 0.2 1 79069 7616 28 79766 0.2 1 74088 5678 29 88958 0.2 1 82020 6938 30 87347 0.2 1 80721 6626 31 96436 0.2 1 89116 7320 32 84184 0.2 1 78013 6171 33 99064 0.2 1 91212 7852 34 126286 0.2 1 116784 9502 35 70478 0.2 1 65263 5215 36 102056 0.2 1 93957 8099 37 106427 0.2 1 98476 7951 38 101342 0.2 1 94365 6977 39 95863 0.2 1 89455 6408 40 111287 0.2 1 103069 8218 41 109099 0.2 1 101498 7601 42 114117 0.2 1 106148 7969 43 100632 0.2 1 93666 6966 44 121370 0.2 1 112650 8720 45 132112 0.2 1 122836 9276 46 87481 0.2 1 81280 6201 47 117137 0.2 1 109733 7404 48 116770 0.2 1 109144 7626 49 122930 0.2 1 114503 8427 50 118230 0.2 1 110078 8152 51 151502 0.2 1 141327 10175 52 106392 0.2 1 99321 7071 53 132940 0.2 1 125179 7761 54 95060 0.2 1 89153 5907 55 129755 0.2 1 121823 7932 56 133247 0.2 1 124572 8675 57 128656 0.2 1 121414 7242 58 125177 0.2 1 117960 7217 59 125701 0.2 1 118073 7628 60 133212 0.2 1 125145 8067 61 136943 0.2 1 128912 8031 62 152161 0.2 1 142895 9266 63 197608 0.2 1 187217 10391 64 170164 0.2 1 162758 7406 65 108925 0.2 1 102718 6207 66 119060 0.2 1 112190 6870 67 118638 0.2 1 111538 7100 68 122066 0.2 1 114957 7109 69 121361 0.2 1 113998 7363 70 127330 0.2 1 119753 7577 71 132672 0.2 1 124891 7781 72 129459 0.2 1 121850 7609 73 134714 0.2 1 127048 7666 74 126025 0.2 1 118830 7195 75 121497 0.2 1 114268 7229 76 117925 0.2 1 110905 7020 77 118215 0.2 1 111150 7065 78 114702 0.2 1 108059 6643 79 111977 0.2 1 105512 6465 80 111238 0.2 1 104912 6326 81 110074 0.2 1 103870 6204 82 104747 0.2 1 98712 6035 83 102994 0.2 1 97190 5804 84 97939 0.2 1 92413 5526 85 98027 0.2 1 92612 5415 86 97975 0.2 1 92622 5353 87 99113 0.2 1 93888 5225 88 97377 0.2 1 92204 5173 89 87121 0.2 1 82286 4835 90 84514 0.2 1 79963 4551 91 79415 0.2 1 75190 4225 92 74774 0.2 1 70849 3925 93 72752 0.2 1 68819 3933 94 70292 0.2 1 66493 3799 95 66513 0.2 1 62910 3603 96 64556 0.2 1 61082 3474 97 60915 0.2 1 57800 3115 98 57473 0.2 1 54587 2886 99 57713 0.2 1 54715 2998 100 49481 0.2 1 46774 2707 101 45740 0.2 1 43384 2356 102 41586 0.2 1 39421 2165 103 38173 0.2 1 36099 2074 104 36449 0.2 1 34460 1989 105 32790 0.2 1 31067 1723 106 30381 0.2 1 28796 1585 107 27663 0.2 1 26191 1472 108 25091 0.2 1 23805 1286 109 22776 0.2 1 21667 1109 110 20493 0.2 1 19406 1087 111 19435 0.2 1 18473 962 112 16596 0.2 1 15727 869 113 14532 0.2 1 13752 780 114 12824 0.2 1 12122 702 115 10619 0.2 1 10098 521 116 9188 0.2 1 8686 502 117 7612 0.2 1 7172 440 118 6805 0.2 1 6447 358 119 5613 0.2 1 5287 326 120 4455 0.2 1 4215 240 121 3795 0.2 1 3594 201 122 3385 0.2 1 3227 158 123 2919 0.2 1 2743 176 124 2401 0.2 1 2252 149 125 1949 0.2 1 1858 91 126 1662 0.2 1 1556 106 127 1275 0.2 1 1189 86 128 1017 0.2 1 960 57 129 911 0.2 1 861 50 130 712 0.2 1 666 46 131 583 0.2 1 553 30 132 498 0.2 1 473 25 133 459 0.2 1 441 18 134 540 0.2 1 495 45 135 343 0.2 1 318 25 136 185 0.2 1 166 19 137 142 0.2 1 134 8 138 102 0.2 1 96 6 139 72 0.2 1 71 1 140 56 0.2 1 51 5 141 30 0.2 1 27 3 142 45 0.2 1 39 6 143 48 0.2 1 43 5 144 33 0.2 1 32 1 145 35 0.2 1 32 3 146 81 0.2 1 79 2 147 221 0.2 1 208 13 148 193 0.2 1 178 15 149 78 0.2 1 71 7 150 649 0.2 1 611 38 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_32psu_3_S3_L002_R2_001.fastq.gz ============================================= 13670957 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 13670957 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 172676 (1.26%)