SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/CTRL_16C_26psu_2_S21_L002_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: 689591). 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/CTRL_16C_26psu_2_S21_L002_R1_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 47.47 s (4 us/read; 16.95 M reads/minute). === Summary === Total reads processed: 13,408,232 Reads with adapters: 11,662,676 (87.0%) Reads written (passing filters): 13,408,232 (100.0%) Total basepairs processed: 2,011,234,800 bp Quality-trimmed: 4,075,788 bp (0.2%) Total written (filtered): 1,423,488,059 bp (70.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11662676 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.8% C: 12.5% G: 23.6% T: 35.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 950454 3352058.0 0 950454 2 175107 838014.5 0 175107 3 106043 209503.6 0 106043 4 68134 52375.9 0 68134 5 61886 13094.0 0 61886 6 61175 3273.5 0 61175 7 51159 818.4 0 51159 8 64511 204.6 0 64511 9 64557 51.1 0 63785 772 10 60792 12.8 1 57082 3710 11 68970 3.2 1 63184 5786 12 66553 0.8 1 61883 4670 13 68274 0.2 1 63204 5070 14 71364 0.2 1 65643 5721 15 74174 0.2 1 68692 5482 16 73515 0.2 1 67346 6169 17 90659 0.2 1 82653 8006 18 76471 0.2 1 71237 5234 19 67430 0.2 1 62447 4983 20 80487 0.2 1 74742 5745 21 89676 0.2 1 82775 6901 22 76355 0.2 1 71205 5150 23 90468 0.2 1 83777 6691 24 85067 0.2 1 77644 7423 25 91076 0.2 1 84134 6942 26 84890 0.2 1 79317 5573 27 95709 0.2 1 88308 7401 28 95026 0.2 1 88099 6927 29 98118 0.2 1 89948 8170 30 107848 0.2 1 101119 6729 31 84062 0.2 1 78313 5749 32 103994 0.2 1 96660 7334 33 98133 0.2 1 90574 7559 34 120505 0.2 1 111057 9448 35 94055 0.2 1 87482 6573 36 107881 0.2 1 100206 7675 37 113227 0.2 1 104836 8391 38 107162 0.2 1 98615 8547 39 126650 0.2 1 117366 9284 40 101784 0.2 1 94417 7367 41 130084 0.2 1 120107 9977 42 108652 0.2 1 99173 9479 43 179621 0.2 1 169283 10338 44 59500 0.2 1 54067 5433 45 124819 0.2 1 116443 8376 46 119134 0.2 1 110810 8324 47 129268 0.2 1 120606 8662 48 119694 0.2 1 111395 8299 49 138243 0.2 1 127784 10459 50 121057 0.2 1 113597 7460 51 131350 0.2 1 122521 8829 52 138351 0.2 1 127802 10549 53 154024 0.2 1 144429 9595 54 116951 0.2 1 108870 8081 55 139783 0.2 1 130545 9238 56 165267 0.2 1 155186 10081 57 126758 0.2 1 117494 9264 58 142781 0.2 1 134977 7804 59 117589 0.2 1 109427 8162 60 144831 0.2 1 135423 9408 61 138318 0.2 1 129552 8766 62 148945 0.2 1 139636 9309 63 129691 0.2 1 120718 8973 64 134879 0.2 1 126688 8191 65 146410 0.2 1 137112 9298 66 156960 0.2 1 146744 10216 67 171283 0.2 1 158133 13150 68 312723 0.2 1 296738 15985 69 76525 0.2 1 70767 5758 70 28798 0.2 1 24712 4086 71 79564 0.2 1 74491 5073 72 122325 0.2 1 115172 7153 73 132393 0.2 1 124378 8015 74 131213 0.2 1 123087 8126 75 128592 0.2 1 120236 8356 76 128119 0.2 1 119430 8689 77 126752 0.2 1 118441 8311 78 121397 0.2 1 113322 8075 79 118367 0.2 1 110488 7879 80 116333 0.2 1 108557 7776 81 115083 0.2 1 107691 7392 82 111285 0.2 1 103893 7392 83 107858 0.2 1 100817 7041 84 105350 0.2 1 98390 6960 85 102602 0.2 1 95870 6732 86 97359 0.2 1 90922 6437 87 94015 0.2 1 87784 6231 88 92275 0.2 1 86366 5909 89 87740 0.2 1 82108 5632 90 86642 0.2 1 80943 5699 91 81958 0.2 1 76615 5343 92 78763 0.2 1 73589 5174 93 72932 0.2 1 68198 4734 94 70403 0.2 1 65851 4552 95 65162 0.2 1 60795 4367 96 61147 0.2 1 56990 4157 97 57845 0.2 1 54051 3794 98 54088 0.2 1 50353 3735 99 50912 0.2 1 47388 3524 100 46451 0.2 1 43306 3145 101 43581 0.2 1 40541 3040 102 39156 0.2 1 36546 2610 103 35574 0.2 1 33122 2452 104 32789 0.2 1 30678 2111 105 29034 0.2 1 27055 1979 106 26298 0.2 1 24343 1955 107 23552 0.2 1 21942 1610 108 21227 0.2 1 19666 1561 109 18723 0.2 1 17348 1375 110 16933 0.2 1 15728 1205 111 14813 0.2 1 13715 1098 112 12788 0.2 1 11763 1025 113 11310 0.2 1 10437 873 114 9920 0.2 1 9142 778 115 8131 0.2 1 7451 680 116 6933 0.2 1 6415 518 117 5884 0.2 1 5388 496 118 5136 0.2 1 4702 434 119 4097 0.2 1 3751 346 120 3546 0.2 1 3238 308 121 2947 0.2 1 2707 240 122 2422 0.2 1 2210 212 123 1924 0.2 1 1761 163 124 1733 0.2 1 1576 157 125 1418 0.2 1 1276 142 126 1305 0.2 1 1178 127 127 1104 0.2 1 1004 100 128 823 0.2 1 732 91 129 659 0.2 1 593 66 130 710 0.2 1 634 76 131 875 0.2 1 812 63 132 926 0.2 1 862 64 133 1378 0.2 1 1297 81 134 1693 0.2 1 1594 99 135 721 0.2 1 691 30 136 229 0.2 1 205 24 137 172 0.2 1 157 15 138 80 0.2 1 66 14 139 66 0.2 1 55 11 140 62 0.2 1 53 9 141 37 0.2 1 35 2 142 33 0.2 1 27 6 143 21 0.2 1 19 2 144 18 0.2 1 17 1 145 32 0.2 1 28 4 146 69 0.2 1 67 2 147 283 0.2 1 250 33 148 183 0.2 1 166 17 149 88 0.2 1 79 9 150 625 0.2 1 537 88 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/CTRL_16C_26psu_2_S21_L002_R1_001.fastq.gz ============================================= 13408232 sequences processed in total