Starting /dee2/code/volunteer_pipeline.sh SRR12670117 current disk space = 3057213075456 free memory = 1580077348 SRR12670117 SRAfilesize 278d93fcb001ed2ccff82f102093a57c SRR12670117.sra SRR12670117.sra file validated SRR12670117 is paired end SRR12670117 is conventional basespace SRR12670117 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670117_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.5965 37.0 37.0 37.0 37.0 37.0 2 36.41525 37.0 37.0 37.0 37.0 37.0 3 36.5965 37.0 37.0 37.0 37.0 37.0 4 36.668 37.0 37.0 37.0 37.0 37.0 5 36.6925 37.0 37.0 37.0 37.0 37.0 6 36.6205 37.0 37.0 37.0 37.0 37.0 7 36.515 37.0 37.0 37.0 37.0 37.0 8 36.65 37.0 37.0 37.0 37.0 37.0 9 36.641 37.0 37.0 37.0 37.0 37.0 10-14 36.614599999999996 37.0 37.0 37.0 37.0 37.0 15-19 36.5792 37.0 37.0 37.0 37.0 37.0 20-24 36.5616 37.0 37.0 37.0 37.0 37.0 25-29 36.508399999999995 37.0 37.0 37.0 37.0 37.0 30-34 36.524899999999995 37.0 37.0 37.0 37.0 37.0 35-39 36.4894 37.0 37.0 37.0 37.0 37.0 40-44 36.475199999999994 37.0 37.0 37.0 37.0 37.0 45-49 36.459700000000005 37.0 37.0 37.0 37.0 37.0 50-54 36.4562 37.0 37.0 37.0 37.0 37.0 55-59 36.3895 37.0 37.0 37.0 37.0 37.0 60-64 36.4131 37.0 37.0 37.0 37.0 37.0 65-69 36.3537 37.0 37.0 37.0 37.0 37.0 70-74 36.312599999999996 37.0 37.0 37.0 37.0 37.0 75-79 36.358900000000006 37.0 37.0 37.0 37.0 37.0 80-84 36.3375 37.0 37.0 37.0 37.0 37.0 85-89 36.3163 37.0 37.0 37.0 37.0 37.0 90-94 36.3537 37.0 37.0 37.0 37.0 37.0 95-99 36.2302 37.0 37.0 37.0 37.0 37.0 100-104 36.2803 37.0 37.0 37.0 37.0 37.0 105-109 36.236200000000004 37.0 37.0 37.0 37.0 37.0 110-114 36.17739999999999 37.0 37.0 37.0 37.0 37.0 115-119 36.2241 37.0 37.0 37.0 37.0 37.0 120-124 36.1499 37.0 37.0 37.0 37.0 37.0 125-129 36.0295 37.0 37.0 37.0 37.0 37.0 130-134 36.0058 37.0 37.0 37.0 37.0 37.0 135-139 35.930099999999996 37.0 37.0 37.0 37.0 37.0 140-144 35.7729 37.0 37.0 37.0 37.0 37.0 145-149 35.827999999999996 37.0 37.0 37.0 37.0 37.0 150-151 35.555499999999995 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 1.0 22 0.0 23 0.0 24 0.0 25 3.0 26 5.0 27 6.0 28 10.0 29 18.0 30 29.0 31 30.0 32 35.0 33 61.0 34 108.0 35 312.0 36 3002.0 37 380.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 34.375 11.575000000000001 6.525 47.525 2 16.821258460767112 12.484331912760089 38.55602907996992 32.13838054650288 3 15.875 15.275 28.025 40.825 4 21.675 21.825 25.025 31.474999999999998 5 23.474999999999998 31.1 24.425 21.0 6 20.724999999999998 32.475 23.799999999999997 23.0 7 16.25 26.075 40.375 17.299999999999997 8 16.950000000000003 26.400000000000002 32.15 24.5 9 16.825000000000003 23.974999999999998 36.4 22.8 10-14 19.86 29.360000000000003 27.715 23.064999999999998 15-19 19.715 27.450000000000003 28.425 24.41 20-24 20.25 27.355 28.03 24.365000000000002 25-29 20.28 27.644999999999996 28.139999999999997 23.935000000000002 30-34 19.75 27.58 27.62 25.05 35-39 20.48 27.534999999999997 27.77 24.215 40-44 20.24 27.935 28.08 23.745 45-49 20.27 28.110000000000003 27.435 24.185000000000002 50-54 19.85 28.194999999999997 27.265 24.69 55-59 20.22 27.54 28.16 24.08 60-64 20.125 27.98 27.975 23.919999999999998 65-69 20.285 28.15 28.425 23.14 70-74 20.685000000000002 28.494999999999997 26.895000000000003 23.925 75-79 20.525 28.310000000000002 27.744999999999997 23.419999999999998 80-84 21.005 28.15 27.35 23.494999999999997 85-89 20.225 28.055000000000003 27.224999999999998 24.495 90-94 20.62 27.525 27.36 24.495 95-99 21.605 28.749999999999996 26.685 22.96 100-104 20.979999999999997 28.939999999999998 26.005 24.075 105-109 21.759999999999998 27.375 26.87 23.995 110-114 22.075 28.205000000000002 26.179999999999996 23.54 115-119 21.615000000000002 28.360000000000003 26.279999999999998 23.745 120-124 21.98 27.465 26.72 23.835 125-129 22.35 28.255000000000003 25.330000000000002 24.065 130-134 22.21 28.08 24.98 24.73 135-139 21.805 27.96 26.075 24.16 140-144 22.355 27.755000000000003 25.705 24.185000000000002 145-149 22.425 27.305 25.990000000000002 24.279999999999998 150-151 22.45 26.700000000000003 26.05 24.8 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.5 23 0.5 24 1.0 25 1.0 26 0.5 27 6.0 28 8.0 29 7.0 30 12.5 31 15.5 32 25.5 33 37.0 34 52.5 35 66.5 36 87.0 37 110.0 38 125.0 39 148.0 40 175.0 41 190.0 42 226.0 43 269.0 44 266.5 45 265.0 46 247.5 47 236.0 48 239.5 49 221.0 50 199.0 51 164.0 52 123.5 53 99.5 54 82.5 55 68.0 56 64.0 57 44.5 58 27.5 59 25.0 60 20.0 61 13.5 62 9.0 63 7.0 64 2.0 65 2.0 66 4.5 67 3.5 68 0.5 69 0.0 70 0.0 71 0.5 72 0.5 73 0.0 74 0.0 75 0.0 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.27499999999999997 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 80.35 #Duplication Level Percentage of deduplicated Percentage of total 1 81.33167392657124 65.35 2 14.49906658369633 23.3 3 3.0491599253266957 7.35 4 0.8089607965152459 2.6 5 0.18668326073428748 0.75 6 0.06222775357809583 0.3 7 0.06222775357809583 0.35000000000000003 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences warn #Sequence Count Percentage Possible Source CACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACAC 7 0.17500000000000002 No Hit GCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGC 7 0.17500000000000002 No Hit AGTTGTAAGTCAATTCCAGAACAGTTGTCTCATATTCATCAGCATACCCC 6 0.15 No Hit GTCGCCAATATGGATTTATATATAGAACTGCACCTATTACTAGCAGCACC 6 0.15 No Hit CTTCAGGAGTGCAGCTTGATCAGGATCCTTTGCCAAGCCCAGTGGGTCAA 5 0.125 No Hit TTCCCAACGGACGCATGACCTCCAGCTTTGTACAATCAGACAGTATAAGC 5 0.125 No Hit CTGGATTCTTGCCAAAAGCACTTGTAATAATGAGGTAATTGGTGCCTATA 5 0.125 No Hit TCACCCTCTCCGGCGCCCCTTTCCAGGGGACTTGGGCCTGGTCCGCCGCT 5 0.125 No Hit ATCCGATCCACTCTTCACCTCAACAGCTTCAACGACACTGGAGTTGACAT 5 0.125 No Hit TTTTATGATCAACAATTTCATTATTTTCCTGTTCTTCGTATTCTTCCATT 5 0.125 No Hit >>END_MODULE >>Adapter Content fail #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.0625 0.0 0.0 0.0 0.0 58-59 0.075 0.0 0.0 0.0 0.0 60-61 0.125 0.0 0.0 0.0 0.0 62-63 0.15 0.0 0.0 0.0 0.0 64-65 0.16249999999999998 0.0 0.0 0.0 0.0 66-67 0.2625 0.0 0.0 0.0 0.0 68-69 0.2875 0.0 0.0 0.0 0.0 70-71 0.375 0.0 0.0 0.0 0.0 72-73 0.5125 0.0 0.0 0.0 0.0 74-75 0.675 0.0 0.0 0.0 0.0 76-77 0.75 0.0 0.0 0.0 0.0 78-79 0.825 0.0 0.0 0.0 0.0 80-81 0.9 0.0 0.0 0.0 0.0 82-83 1.0875 0.0 0.0 0.0 0.0 84-85 1.275 0.0 0.0 0.0 0.0 86-87 1.7625 0.0 0.0 0.0 0.0 88-89 2.35 0.0 0.0 0.0 0.0 90-91 2.7375 0.0 0.0 0.0 0.0 92-93 3.2249999999999996 0.0 0.0 0.0 0.0 94-95 3.9124999999999996 0.0 0.0 0.0 0.0 96-97 4.5875 0.0 0.0 0.0 0.0 98-99 5.3125 0.0 0.0 0.0 0.0 100-101 5.95 0.0 0.0 0.0 0.0 102-103 6.525 0.0 0.0 0.0 0.0 104-105 7.375 0.0 0.0 0.0 0.0 106-107 8.1125 0.0 0.0 0.0 0.0 108-109 8.95 0.0 0.0 0.0 0.0 110-111 9.774999999999999 0.0 0.0 0.0 0.0 112-113 10.75 0.0 0.0 0.0 0.0 114-115 11.7 0.0 0.0 0.0 0.0 116-117 12.8625 0.0 0.0 0.0 0.0 118-119 13.9875 0.0 0.0 0.0 0.0 120-121 15.0 0.0 0.0 0.0 0.0 122-123 16.275 0.0 0.0 0.0 0.0 124-125 17.387500000000003 0.0 0.0 0.0 0.0 126-127 18.3 0.0 0.0 0.0 0.0 128-129 19.200000000000003 0.0 0.0 0.0 0.0 130-131 19.85 0.0 0.0 0.0 0.0 132-133 20.9625 0.0 0.0 0.0 0.0 134-135 21.775 0.0 0.0 0.0 0.0 136-137 22.7875 0.0 0.0 0.0 0.0 138-139 23.85 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ACAAATT 10 0.006830828 145.0 2 AACTTCA 10 0.006830828 145.0 5 GACAAAT 10 0.006830828 145.0 1 GTTGTAG 10 0.006830828 145.0 5 >>END_MODULE SRR12670117 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670117_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.3445 37.0 37.0 37.0 37.0 37.0 2 36.2245 37.0 37.0 37.0 37.0 37.0 3 36.288 37.0 37.0 37.0 37.0 37.0 4 36.2255 37.0 37.0 37.0 37.0 37.0 5 36.446 37.0 37.0 37.0 37.0 37.0 6 36.2905 37.0 37.0 37.0 37.0 37.0 7 36.336 37.0 37.0 37.0 37.0 37.0 8 36.3345 37.0 37.0 37.0 37.0 37.0 9 36.275 37.0 37.0 37.0 37.0 37.0 10-14 36.31229999999999 37.0 37.0 37.0 37.0 37.0 15-19 36.3353 37.0 37.0 37.0 37.0 37.0 20-24 36.244 37.0 37.0 37.0 37.0 37.0 25-29 36.248799999999996 37.0 37.0 37.0 37.0 37.0 30-34 36.2045 37.0 37.0 37.0 37.0 37.0 35-39 36.135000000000005 37.0 37.0 37.0 37.0 37.0 40-44 36.144600000000004 37.0 37.0 37.0 37.0 37.0 45-49 36.108200000000004 37.0 37.0 37.0 37.0 37.0 50-54 36.002700000000004 37.0 37.0 37.0 37.0 37.0 55-59 36.066599999999994 37.0 37.0 37.0 37.0 37.0 60-64 36.01969999999999 37.0 37.0 37.0 37.0 37.0 65-69 36.0932 37.0 37.0 37.0 37.0 37.0 70-74 35.9723 37.0 37.0 37.0 37.0 37.0 75-79 36.015299999999996 37.0 37.0 37.0 37.0 37.0 80-84 35.9336 37.0 37.0 37.0 37.0 37.0 85-89 35.9674 37.0 37.0 37.0 37.0 37.0 90-94 35.9349 37.0 37.0 37.0 37.0 37.0 95-99 35.8842 37.0 37.0 37.0 37.0 37.0 100-104 35.824200000000005 37.0 37.0 37.0 37.0 37.0 105-109 35.703700000000005 37.0 37.0 37.0 37.0 37.0 110-114 35.730599999999995 37.0 37.0 37.0 37.0 37.0 115-119 35.7127 37.0 37.0 37.0 37.0 37.0 120-124 35.545 37.0 37.0 37.0 37.0 37.0 125-129 35.4766 37.0 37.0 37.0 37.0 37.0 130-134 35.215 37.0 37.0 37.0 34.6 37.0 135-139 35.039699999999996 37.0 37.0 37.0 27.4 37.0 140-144 34.918 37.0 37.0 37.0 25.0 37.0 145-149 34.4941 37.0 37.0 37.0 25.0 37.0 150-151 34.4405 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 1.0 13 5.0 14 7.0 15 3.0 16 2.0 17 0.0 18 1.0 19 2.0 20 0.0 21 2.0 22 1.0 23 7.0 24 5.0 25 8.0 26 4.0 27 15.0 28 10.0 29 12.0 30 23.0 31 51.0 32 57.0 33 122.0 34 213.0 35 566.0 36 2645.0 37 238.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 35.9 22.5 10.674999999999999 30.925000000000004 2 26.450000000000003 27.625 30.775000000000002 15.15 3 19.650000000000002 27.1 32.5 20.75 4 23.075000000000003 34.25 24.15 18.525 5 24.325 37.025000000000006 21.875 16.775000000000002 6 19.775000000000002 40.25 22.45 17.525 7 20.65 23.799999999999997 36.4 19.15 8 19.775000000000002 25.15 28.15 26.924999999999997 9 21.825 25.0 30.9 22.275 10-14 23.09 28.87 26.340000000000003 21.7 15-19 23.474999999999998 27.87 27.439999999999998 21.215 20-24 23.175 28.64 27.025 21.16 25-29 23.23 28.205000000000002 27.284999999999997 21.279999999999998 30-34 22.95 28.355000000000004 27.450000000000003 21.245 35-39 23.68 28.1 26.805 21.415 40-44 23.185 28.599999999999998 27.38 20.835 45-49 23.16 28.27 27.6 20.97 50-54 23.365 29.185 26.72 20.73 55-59 23.77 28.175 26.83 21.224999999999998 60-64 23.02 27.805000000000003 28.175 21.0 65-69 23.974999999999998 27.900000000000002 27.42 20.705000000000002 70-74 24.54 28.38 26.169999999999998 20.91 75-79 24.3 28.01 26.640000000000004 21.05 80-84 23.69 28.425 26.55 21.335 85-89 24.72 27.66 26.784999999999997 20.835 90-94 25.145 28.194999999999997 26.245 20.415 95-99 24.925 28.12 26.985 19.97 100-104 24.97 27.685 27.425 19.919999999999998 105-109 25.39 28.215 26.650000000000002 19.744999999999997 110-114 26.150000000000002 29.220000000000002 25.495 19.134999999999998 115-119 26.645000000000003 28.165000000000003 26.155 19.035 120-124 26.900000000000002 28.54 25.435000000000002 19.125 125-129 27.33 27.97 25.995 18.705 130-134 27.965 27.839999999999996 25.759999999999998 18.435000000000002 135-139 28.615000000000002 26.755000000000003 26.595000000000002 18.035 140-144 30.409999999999997 27.389999999999997 24.93 17.27 145-149 31.230000000000004 26.845000000000002 24.57 17.355 150-151 32.675 25.9875 24.525 16.8125 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.5 10 1.0 11 0.5 12 0.0 13 0.5 14 1.0 15 1.0 16 0.5 17 0.5 18 0.5 19 0.0 20 0.0 21 1.5 22 1.5 23 0.0 24 0.0 25 1.0 26 3.5 27 4.0 28 3.0 29 5.0 30 7.0 31 10.0 32 19.0 33 29.5 34 40.0 35 60.0 36 73.5 37 85.0 38 122.0 39 167.5 40 206.0 41 241.0 42 260.5 43 272.5 44 275.5 45 272.5 46 263.0 47 245.5 48 241.5 49 212.5 50 164.5 51 127.5 52 108.5 53 98.0 54 89.5 55 68.0 56 49.5 57 45.0 58 29.0 59 18.0 60 16.0 61 15.0 62 11.5 63 7.5 64 3.5 65 2.5 66 1.0 67 0.0 68 2.0 69 2.5 70 1.5 71 1.5 72 1.0 73 0.5 74 0.0 75 0.5 76 0.5 77 0.5 78 1.0 79 1.0 80 0.5 81 0.0 82 0.0 83 0.0 84 0.0 85 0.5 86 0.5 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.5 97 0.5 98 0.0 99 0.0 100 0.5 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 80.95 #Duplication Level Percentage of deduplicated Percentage of total 1 82.24212476837553 66.57499999999999 2 13.835701050030883 22.400000000000002 3 2.7486102532427426 6.675000000000001 4 0.8338480543545399 2.7 5 0.1852995676343422 0.75 6 0.0926497838171711 0.44999999999999996 7 0.030883261272390366 0.17500000000000002 8 0.0 0.0 9 0.0 0.0 >10 0.030883261272390366 0.27499999999999997 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences warn #Sequence Count Percentage Possible Source CAGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTA 11 0.27499999999999997 No Hit GGCGGGACTACCCGCTGAGTTTAAGCATATCAATAAGCGGAGGAAAAGAA 7 0.17500000000000002 No Hit GGAAGATTGATAGACCTGAGTACAAGTACACATTGGCCATGATGGGGTAT 6 0.15 No Hit CAATTTGCCACGTTTGATGAGAAGTGCTACAAGGACAACCCTTTTCTTTG 6 0.15 No Hit ATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATCAATCAAT 6 0.15 No Hit GAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAAT 5 0.125 No Hit ATCTAACCATATCTAGGCACGGAGGGTTGGAATTGCCAAGTTGGATGGTG 5 0.125 No Hit CACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATCAATC 5 0.125 No Hit GCCCTACTGTGCGTGCAAAACAAGCAGGAAAACACGCTTTCCCGATGACT 5 0.125 No Hit CCGACAGGTTTTTGATAAATGGATCAAGGGAGAATTAAGCAAGAAAACGA 5 0.125 No Hit GTCTGAGATCCCAGAATACTTGACTGGAGAAGTCCCTGGAGACTATGGTT 5 0.125 No Hit >>END_MODULE >>Adapter Content fail #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.0625 0.0 0.0 0.0 0.0 58-59 0.075 0.0 0.0 0.0 0.0 60-61 0.125 0.0 0.0 0.0 0.0 62-63 0.15 0.0 0.0 0.0 0.0 64-65 0.16249999999999998 0.0 0.0 0.0 0.0 66-67 0.2625 0.0 0.0 0.0 0.0 68-69 0.2875 0.0 0.0 0.0 0.0 70-71 0.375 0.0 0.0 0.0 0.0 72-73 0.5125 0.0 0.0 0.0 0.0 74-75 0.675 0.0 0.0 0.0 0.0 76-77 0.75 0.0 0.0 0.0 0.0 78-79 0.825 0.0 0.0 0.0 0.0 80-81 0.9 0.0 0.0 0.0 0.0 82-83 1.0875 0.0 0.0 0.0 0.0 84-85 1.275 0.0 0.0 0.0 0.0 86-87 1.7625 0.0 0.0 0.0 0.0 88-89 2.35 0.0 0.0 0.0 0.0 90-91 2.7375 0.0 0.0 0.0 0.0 92-93 3.2125 0.0 0.0 0.0 0.0 94-95 3.8875 0.0 0.0 0.0 0.0 96-97 4.550000000000001 0.0 0.0 0.0 0.0 98-99 5.2625 0.0 0.0 0.0 0.0 100-101 5.9 0.0 0.0 0.0 0.0 102-103 6.449999999999999 0.0 0.0 0.0 0.0 104-105 7.300000000000001 0.0 0.0 0.0 0.0 106-107 8.0625 0.0 0.0 0.0 0.0 108-109 8.899999999999999 0.0 0.0 0.0 0.0 110-111 9.725000000000001 0.0 0.0 0.0 0.0 112-113 10.7 0.0 0.0 0.0 0.0 114-115 11.675 0.0 0.0 0.0 0.0 116-117 12.875 0.0 0.0 0.0 0.0 118-119 14.0125 0.0 0.0 0.0 0.0 120-121 15.024999999999999 0.0 0.0 0.0 0.0 122-123 16.3 0.0 0.0 0.0 0.0 124-125 17.4125 0.0 0.0 0.0 0.0 126-127 18.35 0.0 0.0 0.0 0.0 128-129 19.2625 0.0 0.0 0.0 0.0 130-131 19.925 0.0 0.0 0.0 0.0 132-133 21.0375 0.0 0.0 0.0 0.0 134-135 21.887500000000003 0.0 0.0 0.0 0.0 136-137 22.8875 0.0 0.0 0.0 0.0 138-139 23.95 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GAGCCAA 10 0.006830828 145.0 5 GAGTTTT 10 0.006830828 145.0 4 AAGATTA 10 0.006830828 145.0 3 AAAGATT 10 0.006830828 145.0 2 >>END_MODULE Read 582400 spots for SRR12670117.sra Written 582400 spots for SRR12670117.sra Read 582400 spots for SRR12670117.sra Written 582400 spots for SRR12670117.sra Read 582400 spots for SRR12670117.sra Written 582400 spots for SRR12670117.sra Read 582400 spots for SRR12670117.sra Written 582400 spots for SRR12670117.sra Read 582400 spots for SRR12670117.sra Written 582400 spots for SRR12670117.sra Read 582400 spots for SRR12670117.sra Written 582400 spots for SRR12670117.sra Read 582400 spots for SRR12670117.sra Written 582400 spots for SRR12670117.sra Read 582400 spots for SRR12670117.sra Written 582400 spots for SRR12670117.sra Read 582400 spots for SRR12670117.sra Written 582400 spots for SRR12670117.sra Read 582400 spots for SRR12670117.sra Written 582400 spots for SRR12670117.sra Read 582400 spots for SRR12670117.sra Written 582400 spots for SRR12670117.sra Read 582400 spots for SRR12670117.sra Written 582400 spots for SRR12670117.sra Read 582400 spots for SRR12670117.sra Written 582400 spots for SRR12670117.sra Read 582400 spots for SRR12670117.sra Written 582400 spots for SRR12670117.sra Read 582400 spots for SRR12670117.sra Written 582400 spots for SRR12670117.sra Read 582400 spots for SRR12670117.sra Written 582400 spots for SRR12670117.sra Read 582400 spots for SRR12670117.sra Written 582400 spots for SRR12670117.sra Read 582400 spots for SRR12670117.sra Written 582400 spots for SRR12670117.sra Read 582405 spots for SRR12670117.sra Written 582405 spots for SRR12670117.sra Read 582400 spots for SRR12670117.sra Written 582400 spots for SRR12670117.sra SRR ids: ['SRR12670117.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_08_f4vdd SRR12670117.sra spots: 11648005 blocks: [[1, 582400], [582401, 1164800], [1164801, 1747200], [1747201, 2329600], [2329601, 2912000], [2912001, 3494400], [3494401, 4076800], [4076801, 4659200], [4659201, 5241600], [5241601, 5824000], [5824001, 6406400], [6406401, 6988800], [6988801, 7571200], [7571201, 8153600], [8153601, 8736000], [8736001, 9318400], [9318401, 9900800], [9900801, 10483200], [10483201, 11065600], [11065601, 11648005]] SRR12670117 file size 3936801 SRR12670117 completed basic pipeline successfully skewer v0.2.2 [April 4, 2016] COMMAND LINE: skewer -f sanger -l 18 -q 10 -k inf -t 20 -o SRR12670117 SRR12670117_1.fastq SRR12670117_2.fastq Input file: SRR12670117_1.fastq Paired file: SRR12670117_2.fastq trimmed: SRR12670117-trimmed-pair1.fastq, SRR12670117-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- paired 3' end adapter sequence (-y): AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- end quality threshold (-q): 10 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- number of concurrent threads (-t): 20 Tue Feb 11 00:35:16 2025 >> started Tue Feb 11 00:35:28 2025 >> done (12.595s) 11648005 read pairs processed; of these: 54 ( 0.00%) short read pairs filtered out after trimming by size control 2251 ( 0.02%) empty read pairs filtered out after trimming by size control 11645700 (99.98%) read pairs available; of these: 3436357 (29.51%) trimmed read pairs available after processing 8209343 (70.49%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 2 0.00% 19 0 0.00% 20 1 0.00% 21 9 0.00% 22 5 0.00% 23 10 0.00% 24 13 0.00% 25 13 0.00% 26 31 0.00% 27 26 0.00% 28 20 0.00% 29 49 0.00% 30 46 0.00% 31 48 0.00% 32 52 0.00% 33 66 0.00% 34 69 0.00% 35 81 0.00% 36 104 0.00% 37 78 0.00% 38 132 0.00% 39 142 0.00% 40 135 0.00% 41 176 0.00% 42 203 0.00% 43 147 0.00% 44 169 0.00% 45 211 0.00% 46 218 0.00% 47 299 0.00% 48 308 0.00% 49 408 0.00% 50 551 0.00% 51 605 0.01% 52 646 0.01% 53 687 0.01% 54 709 0.01% 55 793 0.01% 56 832 0.01% 57 974 0.01% 58 1202 0.01% 59 1305 0.01% 60 1534 0.01% 61 1820 0.02% 62 2169 0.02% 63 2355 0.02% 64 2499 0.02% 65 2789 0.02% 66 2916 0.03% 67 3345 0.03% 68 3704 0.03% 69 4141 0.04% 70 4788 0.04% 71 5572 0.05% 72 6415 0.06% 73 7223 0.06% 74 7837 0.07% 75 8440 0.07% 76 9145 0.08% 77 9887 0.08% 78 10798 0.09% 79 11810 0.10% 80 12815 0.11% 81 14443 0.12% 82 16114 0.14% 83 17216 0.15% 84 19500 0.17% 85 21017 0.18% 86 22338 0.19% 87 23023 0.20% 88 24695 0.21% 89 25334 0.22% 90 27407 0.24% 91 28761 0.25% 92 30148 0.26% 93 32723 0.28% 94 34772 0.30% 95 36829 0.32% 96 38098 0.33% 97 39166 0.34% 98 40300 0.35% 99 40403 0.35% 100 41873 0.36% 101 42227 0.36% 102 44217 0.38% 103 45024 0.39% 104 46923 0.40% 105 47746 0.41% 106 49506 0.43% 107 49951 0.43% 108 49930 0.43% 109 50531 0.43% 110 49979 0.43% 111 50941 0.44% 112 51465 0.44% 113 52189 0.45% 114 53610 0.46% 115 54793 0.47% 116 55090 0.47% 117 56081 0.48% 118 56743 0.49% 119 56174 0.48% 120 56935 0.49% 121 55956 0.48% 122 56618 0.49% 123 56919 0.49% 124 56728 0.49% 125 57247 0.49% 126 58237 0.50% 127 57510 0.49% 128 58200 0.50% 129 57286 0.49% 130 57816 0.50% 131 56686 0.49% 132 56667 0.49% 133 57077 0.49% 134 56444 0.48% 135 57163 0.49% 136 56718 0.49% 137 57012 0.49% 138 57045 0.49% 139 57825 0.50% 140 56959 0.49% 141 57610 0.49% 142 57037 0.49% 143 56249 0.48% 144 57367 0.49% 145 55980 0.48% 146 56420 0.48% 147 55509 0.48% 148 57182 0.49% 149 55905 0.48% 150 57193 0.49% 151 8209343 70.49% 11645700 reads passed initial QC criterion=sequence-density sequence-density=0.74 sequence-density-rank=1 fanout-score=1.98 fanout-score-rank=25 prefix-density=0.74 prefix-fanout=2.0 sequence=TGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGGAGTATGAATGTGTTCTCTGTGTA criterion=fanout-score sequence-density=0.02 sequence-density-rank=27 fanout-score=33.01 fanout-score-rank=1 prefix-density=0.11 prefix-fanout=5.6 sequence=ACCACACCAGAGGCCACAGACATGGCCAATACATAACAATGAAGAAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAG criterion=sequence-density sequence-density=1.39 sequence-density-rank=1 fanout-score=2.02 fanout-score-rank=29 prefix-density=1.38 prefix-fanout=2.0 sequence=CTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGGAGTGAACAAACAAAAGTGTCCGTGAGTGTCTTTATCTTTGTGTCTTCTTCATTGTTATGTATTGGCCATGTCTGTGGCCTCTGGTGTGGT criterion=fanout-score sequence-density=0.04 sequence-density-rank=32 fanout-score=13.66 fanout-score-rank=1 prefix-density=0.07 prefix-fanout=7.1 sequence=CTGAGCTTGAGTGCATTCTTCTAAGTAAAAGAAATCCCTTAATTTCATCA SRR12670117 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 00:36:08 Started mapping on | Feb 11 00:36:08 Finished on | Feb 11 00:37:23 Mapping speed, Million of reads per hour | 558.99 Number of input reads | 11645700 Average input read length | 282 UNIQUE READS: Uniquely mapped reads number | 10864664 Uniquely mapped reads % | 93.29% Average mapped length | 281.76 Number of splices: Total | 10404532 Number of splices: Annotated (sjdb) | 10167466 Number of splices: GT/AG | 10199657 Number of splices: GC/AG | 159781 Number of splices: AT/AC | 6886 Number of splices: Non-canonical | 38208 Mismatch rate per base, % | 0.35% Deletion rate per base | 0.03% Deletion average length | 2.85 Insertion rate per base | 0.02% Insertion average length | 2.46 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 270202 % of reads mapped to multiple loci | 2.32% Number of reads mapped to too many loci | 196308 % of reads mapped to too many loci | 1.69% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.40% % of reads unmapped: other | 0.30% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 510834 510834 510834 N_multimapping 270202 270202 270202 N_noFeature 442136 10675421 518049 N_ambiguous 173196 689 59454 UnstrandedReadsAssigned:10249332 PositiveStrandReadsAssigned:188554 NegativeStrandReadsAssigned:10287161 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=131 echo kmer=127 SRR12670117 Starting Kallisto paired end mapping to ensembl reference transcriptome [quant] fragment length distribution will be estimated from the data [index] k-mer length: 31 [index] number of targets: 52,400 [index] number of k-mers: 62,057,036 [index] number of equivalence classes: 130,681 [quant] running in paired-end mode [quant] will process pair 1: SRR12670117-trimmed-pair1.fastq SRR12670117-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 11,645,700 reads, 10,373,669 reads pseudoaligned [quant] estimated average fragment length: 202.96 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,030 rounds 52401 SRR12670117.ke.tsv 34699 SRR12670117.se.tsv 87100 total ==> SRR12670117.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1816.04 475 22.6355 Potri.005G024800.1.v4.1 1035 833.04 223 23.1665 Potri.004G059700.1.v4.1 961 759.117 2 0.228004 Potri.007G009000.2.v4.1 1416 1214.04 0 0 Potri.003G141000.2.v4.1 2943 2741.04 746 23.553 Potri.016G087400.1.v4.1 270 111.485 612 475.068 Potri.015G069301.1.v4.1 564 369.486 0 0 Potri.010G195200.1.v4.1 1773 1571.04 55 3.02968 Potri.012G127500.1.v4.1 977 775.066 52 5.80613 ==> SRR12670117.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 48 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 187 Potri.001G212900.v4.1 19 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 8 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 5 SRR12670117 completed mapping pipeline successfully