Starting /dee2/code/volunteer_pipeline.sh SRR13695429 current disk space = 3049178247168 free memory = 1571541712 SRR13695429 SRAfilesize 273ed9a31d7c7bf57fd06d246f4835a5 SRR13695429.sra SRR13695429.sra file validated SRR13695429 is paired end SRR13695429 is conventional basespace SRR13695429 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR13695429_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 43 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.5785 37.0 37.0 37.0 37.0 37.0 2 36.18725 37.0 37.0 37.0 37.0 37.0 3 36.4435 37.0 37.0 37.0 37.0 37.0 4 36.544 37.0 37.0 37.0 37.0 37.0 5 36.599 37.0 37.0 37.0 37.0 37.0 6 36.53 37.0 37.0 37.0 37.0 37.0 7 36.4835 37.0 37.0 37.0 37.0 37.0 8 36.526 37.0 37.0 37.0 37.0 37.0 9 36.5335 37.0 37.0 37.0 37.0 37.0 10-14 36.542899999999996 37.0 37.0 37.0 37.0 37.0 15-19 36.507799999999996 37.0 37.0 37.0 37.0 37.0 20-24 36.448 37.0 37.0 37.0 37.0 37.0 25-29 36.4788 37.0 37.0 37.0 37.0 37.0 30-34 36.398700000000005 37.0 37.0 37.0 37.0 37.0 35-39 36.4 37.0 37.0 37.0 37.0 37.0 40-44 36.3942 37.0 37.0 37.0 37.0 37.0 45-49 36.3683 37.0 37.0 37.0 37.0 37.0 50-54 36.388 37.0 37.0 37.0 37.0 37.0 55-59 36.3721 37.0 37.0 37.0 37.0 37.0 60-64 36.347699999999996 37.0 37.0 37.0 37.0 37.0 65-69 36.313100000000006 37.0 37.0 37.0 37.0 37.0 70-74 36.3027 37.0 37.0 37.0 37.0 37.0 75-79 36.28959999999999 37.0 37.0 37.0 37.0 37.0 80-84 36.245900000000006 37.0 37.0 37.0 37.0 37.0 85-89 36.201 37.0 37.0 37.0 37.0 37.0 90-94 36.1262 37.0 37.0 37.0 37.0 37.0 95-99 36.1164 37.0 37.0 37.0 37.0 37.0 100-104 36.0727 37.0 37.0 37.0 37.0 37.0 105-109 36.0783 37.0 37.0 37.0 37.0 37.0 110-114 36.042699999999996 37.0 37.0 37.0 37.0 37.0 115-119 36.0651 37.0 37.0 37.0 37.0 37.0 120-124 35.9196 37.0 37.0 37.0 37.0 37.0 125-129 35.9367 37.0 37.0 37.0 37.0 37.0 130-134 35.8797 37.0 37.0 37.0 37.0 37.0 135-139 35.848800000000004 37.0 37.0 37.0 37.0 37.0 140-144 35.733799999999995 37.0 37.0 37.0 37.0 37.0 145-149 35.532 37.0 37.0 37.0 37.0 37.0 150-151 35.512 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 22 1.0 23 2.0 24 3.0 25 3.0 26 4.0 27 6.0 28 10.0 29 19.0 30 25.0 31 44.0 32 63.0 33 73.0 34 139.0 35 344.0 36 2943.0 37 321.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 34.075 11.35 8.85 45.725 2 18.09284818067754 14.40401505646173 38.82057716436638 28.682559598494358 3 18.8 16.2 27.150000000000002 37.85 4 21.75 24.125 23.625 30.5 5 22.95 31.4 24.65 21.0 6 17.150000000000002 37.35 24.9 20.599999999999998 7 15.475 27.1 40.849999999999994 16.575 8 18.224999999999998 26.25 33.074999999999996 22.45 9 16.625 23.549999999999997 34.25 25.575 10-14 19.67 29.134999999999998 28.475 22.720000000000002 15-19 19.48 28.34 28.02 24.16 20-24 20.085 28.685 27.834999999999997 23.395 25-29 19.45 28.970000000000002 27.87 23.71 30-34 19.43 28.860000000000003 27.58 24.13 35-39 19.985 28.285 27.79 23.94 40-44 20.044999999999998 28.005000000000003 27.92 24.03 45-49 20.41 28.79 27.515 23.285 50-54 19.615 29.255 28.12 23.01 55-59 19.615 28.854999999999997 28.01 23.52 60-64 19.205 28.71 28.075 24.01 65-69 20.23 28.48 27.77 23.52 70-74 20.080000000000002 29.020000000000003 27.284999999999997 23.615 75-79 18.845 28.26 28.675 24.22 80-84 20.23 28.63 27.38 23.76 85-89 20.085 28.689999999999998 27.725 23.5 90-94 20.525 28.285 28.005000000000003 23.185 95-99 20.435 28.084999999999997 28.294999999999998 23.185 100-104 20.185 28.975 27.875 22.965 105-109 20.315 28.42 27.83 23.435 110-114 20.59 27.894999999999996 27.755000000000003 23.76 115-119 21.105 29.189999999999998 27.560000000000002 22.145 120-124 21.11 28.854999999999997 27.450000000000003 22.585 125-129 20.94 28.28 27.915 22.865 130-134 20.244999999999997 28.449999999999996 27.935 23.369999999999997 135-139 21.035 28.64 27.165 23.16 140-144 21.295 29.060000000000002 26.095000000000002 23.549999999999997 145-149 21.34 28.52 27.325 22.814999999999998 150-151 20.925 29.525000000000002 25.137500000000003 24.4125 >>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 0.5 7 0.5 8 0.5 9 0.5 10 0.0 11 0.0 12 0.0 13 0.5 14 1.0 15 0.5 16 0.0 17 0.5 18 1.0 19 1.5 20 2.5 21 1.5 22 1.0 23 2.0 24 2.5 25 3.5 26 7.5 27 8.5 28 8.0 29 13.0 30 21.0 31 27.0 32 30.0 33 37.5 34 65.5 35 92.5 36 105.5 37 129.0 38 138.0 39 157.0 40 206.5 41 224.5 42 234.0 43 255.0 44 237.5 45 223.5 46 250.5 47 251.5 48 227.5 49 197.5 50 173.0 51 155.0 52 125.5 53 87.5 54 60.0 55 52.5 56 44.0 57 34.0 58 26.5 59 21.5 60 17.5 61 11.5 62 5.5 63 5.0 64 2.5 65 0.5 66 1.0 67 2.5 68 2.0 69 2.0 70 2.0 71 0.5 72 0.0 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 0.375 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 71.625 #Duplication Level Percentage of deduplicated Percentage of total 1 72.42582897033158 51.87500000000001 2 19.476439790575917 27.900000000000002 3 5.514834205933682 11.85 4 1.780104712041885 5.1 5 0.48865619546247824 1.7500000000000002 6 0.24432809773123912 1.05 7 0.0 0.0 8 0.034904013961605584 0.2 9 0.0 0.0 >10 0.034904013961605584 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 TGAGAAAGAGTACCAACATTTTGAGCAAGTTGATTGGATGACGGATCAGG 11 0.27499999999999997 No Hit CCAAATTCCAACTTTAATGTCCAAATGCACAAGTTCAATACTGTGACTAT 8 0.2 No Hit GCTCTCACAACATCAAGCATTGTAACTCCTAGAAGTCGCTTTGGATCATA 6 0.15 No Hit CTCATATATCCTTCAAGACTTGCAAAGACAGGTATTCTGAGTCCACTTTG 6 0.15 No Hit GCACCCTTGGTCACCTGACTGAATCAAACCAAATAGATGTAAATGTACAA 6 0.15 No Hit GCAAGAATCTTTTCATCCCCATTAGGGTAATAAATACCTTGGAAGAAAAA 6 0.15 No Hit CTGATAAATTGTCTTGAAGCCGGCGAGTTCCAGGGAATTTATGAGCTGAT 6 0.15 No Hit CTTTCTTGCTCCCTTGAACCATCTCTTGTCTCCAGCTTGTGCCTTGCAAA 6 0.15 No Hit CAACAATTCTCGCCCGATTCAGCATCCGAATCCAGAAGCTAAAAACAAAA 6 0.15 No Hit TGCTGGTTTTAGGAACAGAGTCCATCAGGGCTTCTCTCCCGTCATTCTTT 5 0.125 No Hit CTGAAAGGTCTCTTAAATCAGTCTCGGAAAAGGCTCTTGTCATTCTTTTA 5 0.125 No Hit CATGATTTGATTATGCAAAGCAATAAAGTGGATCCATACATTCATTAAGA 5 0.125 No Hit AGGGATGGGAGGAGGGAATTCATATGCTCAGGCATGGACTTCAAATTTGC 5 0.125 No Hit ACCTTCAGATGCAAAACTGCATACTCTACTGCTGCCCCAACTCCAGCGTA 5 0.125 No Hit ATCTGTGCTAAATACACAATTGCCCACATCATCCAGCAGCAGACTGTTGC 5 0.125 No Hit CGACTATGTGGTTGCCGCCAATGAAAACATTCGGCACGGTGCGTTGTCCA 5 0.125 No Hit TGGAGACTTGGATAAGGTGTTGTAGTATTGCTCTGCAAAGGCATTCCCCA 5 0.125 No Hit GTTGTACTCCTCGACCTCTTCTTTACTCTTCTGTCATCTGTGCCTGTGTC 5 0.125 No Hit GCAGAATACATACAGTTGGCGTTTCAACCATTGTAGATGCTTCAAATGTT 5 0.125 No Hit GCCTCCTGCCAGTTTCCTTGCCAATTGCAAGCTGATCCCCAGTAATCATC 5 0.125 No Hit GTTGCATATCCTCAATTTTACTCGCGGGAATATATTAAGCCTGCGTATCC 5 0.125 No Hit CCTTCCCTTCCTCTCCTCCTTCGACCTCCGAATCCGAGACTTCTTCCCTC 5 0.125 No Hit GACACTTGTAGCCTGGCATGAAATTCTCATTCCTCTCTCCTTTAACACCA 5 0.125 No Hit >>END_MODULE >>Adapter Content warn #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 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.025 0.0 0.0 0.0 0.0 72-73 0.05 0.0 0.0 0.0 0.0 74-75 0.075 0.0 0.0 0.0 0.0 76-77 0.1 0.0 0.0 0.0 0.0 78-79 0.15 0.0 0.0 0.0 0.0 80-81 0.1875 0.0 0.0 0.0 0.0 82-83 0.25 0.0 0.0 0.0 0.0 84-85 0.275 0.0 0.0 0.0 0.0 86-87 0.275 0.0 0.0 0.0 0.0 88-89 0.32499999999999996 0.0 0.0 0.0 0.0 90-91 0.35 0.0 0.0 0.0 0.0 92-93 0.375 0.0 0.0 0.0 0.0 94-95 0.4 0.0 0.0 0.0 0.0 96-97 0.475 0.0 0.0 0.0 0.0 98-99 0.6 0.0 0.0 0.0 0.0 100-101 0.875 0.0 0.0 0.0 0.0 102-103 1.0125 0.0 0.0 0.0 0.0 104-105 1.1124999999999998 0.0 0.0 0.0 0.0 106-107 1.25 0.0 0.0 0.0 0.0 108-109 1.425 0.0 0.0 0.0 0.0 110-111 1.525 0.0 0.0 0.0 0.0 112-113 1.7 0.0 0.0 0.0 0.0 114-115 1.875 0.0 0.0 0.0 0.0 116-117 2.0625 0.0 0.0 0.0 0.0 118-119 2.425 0.0 0.0 0.0 0.0 120-121 2.7625 0.0 0.0 0.0 0.0 122-123 3.0375 0.0 0.0 0.0 0.0 124-125 3.3499999999999996 0.0 0.0 0.0 0.0 126-127 3.7375 0.0 0.0 0.0 0.0 128-129 4.475 0.0 0.0 0.0 0.0 130-131 5.0875 0.0 0.0 0.0 0.0 132-133 5.3125 0.0 0.0 0.0 0.0 134-135 5.7375 0.0 0.0 0.0 0.0 136-137 6.262499999999999 0.0 0.0 0.0 0.0 138-139 6.862500000000001 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TATATTA 10 0.006830828 145.0 2 GATACGC 10 0.006830828 145.0 7 TTATTGA 10 0.006830828 145.0 6 CTCTCAC 10 0.006830828 145.0 2 TATTGAT 10 0.006830828 145.0 7 TGATACG 10 0.006830828 145.0 6 ATTATTG 10 0.006830828 145.0 5 ATACGCT 10 0.006830828 145.0 8 ATTGATA 10 0.006830828 145.0 8 TATTATT 10 0.006830828 145.0 4 GCTCTTG 10 0.006830828 145.0 1 GGTGCCA 10 0.006830828 145.0 8 GTTTCAA 25 4.977651E-4 29.0 35-39 >>END_MODULE SRR13695429 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR13695429_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 43 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.2735 37.0 37.0 37.0 37.0 37.0 2 36.1005 37.0 37.0 37.0 37.0 37.0 3 36.087 37.0 37.0 37.0 37.0 37.0 4 36.1415 37.0 37.0 37.0 37.0 37.0 5 36.2585 37.0 37.0 37.0 37.0 37.0 6 36.243 37.0 37.0 37.0 37.0 37.0 7 36.274 37.0 37.0 37.0 37.0 37.0 8 36.2835 37.0 37.0 37.0 37.0 37.0 9 36.263 37.0 37.0 37.0 37.0 37.0 10-14 36.2642 37.0 37.0 37.0 37.0 37.0 15-19 36.2487 37.0 37.0 37.0 37.0 37.0 20-24 36.208800000000004 37.0 37.0 37.0 37.0 37.0 25-29 36.1203 37.0 37.0 37.0 37.0 37.0 30-34 36.0861 37.0 37.0 37.0 37.0 37.0 35-39 36.0484 37.0 37.0 37.0 37.0 37.0 40-44 36.06965 37.0 37.0 37.0 37.0 37.0 45-49 36.0972 37.0 37.0 37.0 37.0 37.0 50-54 35.93495 37.0 37.0 37.0 37.0 37.0 55-59 35.9656 37.0 37.0 37.0 37.0 37.0 60-64 35.9122 37.0 37.0 37.0 37.0 37.0 65-69 35.9491 37.0 37.0 37.0 37.0 37.0 70-74 35.865199999999994 37.0 37.0 37.0 37.0 37.0 75-79 35.9254 37.0 37.0 37.0 37.0 37.0 80-84 35.8863 37.0 37.0 37.0 37.0 37.0 85-89 35.809400000000004 37.0 37.0 37.0 37.0 37.0 90-94 35.801300000000005 37.0 37.0 37.0 37.0 37.0 95-99 35.7723 37.0 37.0 37.0 37.0 37.0 100-104 35.7097 37.0 37.0 37.0 37.0 37.0 105-109 35.708000000000006 37.0 37.0 37.0 37.0 37.0 110-114 35.606100000000005 37.0 37.0 37.0 37.0 37.0 115-119 35.5714 37.0 37.0 37.0 37.0 37.0 120-124 35.558899999999994 37.0 37.0 37.0 37.0 37.0 125-129 35.51825 37.0 37.0 37.0 37.0 37.0 130-134 35.5004 37.0 37.0 37.0 37.0 37.0 135-139 35.4238 37.0 37.0 37.0 37.0 37.0 140-144 35.3103 37.0 37.0 37.0 32.2 37.0 145-149 35.20399999999999 37.0 37.0 37.0 32.2 37.0 150-151 34.935500000000005 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 14 2.0 15 1.0 16 1.0 17 0.0 18 1.0 19 2.0 20 1.0 21 4.0 22 2.0 23 3.0 24 2.0 25 4.0 26 18.0 27 15.0 28 10.0 29 27.0 30 30.0 31 46.0 32 66.0 33 111.0 34 222.0 35 617.0 36 2610.0 37 205.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 34.69438877755511 20.741482965931866 13.126252505010019 31.437875751503007 2 27.425 25.124999999999996 32.15 15.299999999999999 3 19.2 27.224999999999998 31.775 21.8 4 21.224999999999998 35.725 23.625 19.425 5 25.224999999999998 36.95 23.674999999999997 14.149999999999999 6 19.3 39.4 24.6 16.7 7 20.4 22.475 38.95 18.175 8 21.2 23.775 30.0 25.025 9 20.674999999999997 24.075 30.95 24.3 10-14 22.27 29.79 27.27 20.669999999999998 15-19 22.655 28.32 28.04 20.985 20-24 22.207220722072208 29.4029402940294 27.852785278527854 20.537053705370536 25-29 22.341170585292648 28.74937468734367 28.81940970485243 20.090045022511255 30-34 22.494498899779956 29.05081016203241 28.175635127025405 20.279055811162234 35-39 22.642264226422643 28.422842284228423 27.707770777077705 21.227122712271225 40-44 22.440610152538135 27.961990497624406 28.402100525131285 21.195298824706178 45-49 21.734346869373873 28.650730146029208 28.480696139227845 21.134226845369074 50-54 21.52607630381519 28.73143657182859 28.186409320466023 21.556077803890194 55-59 21.975987993997 27.70885442721361 29.244622311155577 21.070535267633815 60-64 22.417241724172417 27.63776377637764 28.38783878387839 21.557155715571557 65-69 21.98 28.23 28.42 21.37 70-74 22.236118059029515 28.29414707353677 27.668834417208604 21.800900450225114 75-79 22.28668600580174 28.573572071621488 27.888366509952984 21.251375412623787 80-84 23.185 28.42 27.325 21.07 85-89 22.984193677470987 27.766106442577033 28.321328531412565 20.928371348539414 90-94 22.177217721772177 28.757875787578758 27.9027902790279 21.16211621162116 95-99 22.78 28.185 27.77 21.265 100-104 23.491745872936466 27.85892946473237 27.56378189094547 21.085542771385693 105-109 22.458983593437377 29.39675870348139 27.85114045618247 20.29311724689876 110-114 22.682268226822682 28.842884288428845 27.847784778477845 20.627062706270628 115-119 23.22696809042713 28.283485045513657 27.86335900770231 20.626187856356907 120-124 23.741870935467734 28.119059529764883 27.48874437218609 20.65032516258129 125-129 23.658280398139347 28.089831441004353 27.474616115640476 20.777272045215824 130-134 23.781890945472735 27.808904452226113 27.48874437218609 20.920460230115058 135-139 24.15207603801901 28.094047023511752 28.044022011005502 19.70985492746373 140-144 24.61746174617462 27.457745774577457 27.447744774477446 20.477047704770477 145-149 25.047523761880942 28.119059529764883 26.643321660830416 20.190095047523762 150-151 25.42521260630315 28.38919459729865 26.688344172086044 19.497248624312157 >>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 1.0 7 1.0 8 1.0 9 1.5 10 0.5 11 0.5 12 0.5 13 0.0 14 1.5 15 1.5 16 1.0 17 1.5 18 0.5 19 0.0 20 0.5 21 1.5 22 1.5 23 1.0 24 1.5 25 4.0 26 9.0 27 12.5 28 15.5 29 19.0 30 23.5 31 28.0 32 33.5 33 45.5 34 54.5 35 73.0 36 109.5 37 130.0 38 146.0 39 174.5 40 206.5 41 239.5 42 277.5 43 285.5 44 269.5 45 250.0 46 239.5 47 227.5 48 193.0 49 179.5 50 151.5 51 126.5 52 101.0 53 71.5 54 66.0 55 56.0 56 45.5 57 38.0 58 25.5 59 14.5 60 10.5 61 9.0 62 7.0 63 2.0 64 2.5 65 2.0 66 0.0 67 0.0 68 0.0 69 0.0 70 0.5 71 1.0 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 0.5 84 1.0 85 0.5 86 0.0 87 0.5 88 0.5 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.5 95 0.5 96 0.0 97 0.0 98 0.0 99 0.0 100 0.5 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.2 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 0.01 25-29 0.05 30-34 0.02 35-39 0.01 40-44 0.025 45-49 0.02 50-54 0.005 55-59 0.05 60-64 0.01 65-69 0.0 70-74 0.05 75-79 0.03 80-84 0.0 85-89 0.04 90-94 0.01 95-99 0.0 100-104 0.05 105-109 0.04 110-114 0.01 115-119 0.03 120-124 0.05 125-129 0.034999999999999996 130-134 0.05 135-139 0.05 140-144 0.01 145-149 0.05 150-151 0.05 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 72.075 #Duplication Level Percentage of deduplicated Percentage of total 1 73.22233784252515 52.775000000000006 2 18.765175164758933 27.05 3 5.341657995143947 11.55 4 1.8383628165105792 5.3 5 0.5896635449184877 2.125 6 0.1387443635102324 0.6 7 0.0346860908775581 0.17500000000000002 8 0.0346860908775581 0.2 9 0.0346860908775581 0.22499999999999998 >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 TCTAGTTTACATGATGCGACAAACAAGTTTGAATTCCCTCCACTACTTGA 9 0.22499999999999998 No Hit TGGGTAGCAAGGGTGCATGGAGAGAGTTTTCATGGAATTGGTTTTATTAC 8 0.2 No Hit AGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAA 7 0.17500000000000002 No Hit CGATTGTCAACTTGATCAGCAATCCAGTTAATTCTACAGTTCCAATTGCA 6 0.15 No Hit CATTGCCCTCCATTTTCTGATGCTGTTGTTCATGCGCATGTCTCCTATGC 6 0.15 No Hit CTTCTTGTCAAAGAGGGTCATCAGGTGACCTTGTTTACCAGAGGTAAAGC 6 0.15 No Hit TCGGATTCGACAACACGCGTCAAGTGCAGTGCATCAGCTTTATTGCCGCC 6 0.15 No Hit GCAACTGTGTGGTTGAGAATGCAAAGGAGAGACCAACAATGTTTGAGGTT 5 0.125 No Hit GTTTCTGGTAACGACACTGATTTTCGTAGTGGTCGGAATAATCGCTTCGC 5 0.125 No Hit AAAATACATGATGATACCCGTTGCCTGAAATTTGTGGCCTGATTGGTAAG 5 0.125 No Hit CAGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTA 5 0.125 No Hit ATTAACTCTGTGCAATTGCAAGGAAGATGTTAAGAAGAAGGTTCATTCTG 5 0.125 No Hit GGCTAACATATTGGAGACCTCAACTCCGGTGATCGATGGGAAACAATATT 5 0.125 No Hit TTTAGGGTTAAGAAAAGAAATTGTGTGTGAGAGAGAATGGCAATGAACAA 5 0.125 No Hit GGTTTTTTTTGTTGCAAGTAGAGGACATCACGCAGAGATTGGGGGTATTA 5 0.125 No Hit CGGAGAGGCGAAGAAATGGGAAAGGACTACAACGAGGCCATTGAATCTCT 5 0.125 No Hit CCTAGGTTGAAGACTCTCAGGATCTCTACATGTTCAAATTTGGAATCTCA 5 0.125 No Hit AAAGACATCAATATTGGATGACTTCGATTTTTATGAGAGTCGCCAGAAGG 5 0.125 No Hit CCTTTCTTCGCCAGCAACCGCACCGTTACGTCTCTCTCTCTTCCTCTCTA 5 0.125 No Hit TTAATGGTATTTTTTAGGGTTTAAATGACTCCAAAACCCAAACCCAACCC 5 0.125 No Hit CCTCACAGCTATGCTCTAGCAAGAGTGGCATGTTCTCTCCTACACATGCG 5 0.125 No Hit AAGCTCAGCTGGTTGCTGGGAAGTCTCATGAGTTCGGGCCCATCAACACT 5 0.125 No Hit GCTAAACTTGATTCCCTTCAACAGGAGTTTACTTCAGTTCGTCTGAATGA 5 0.125 No Hit CAAAGAAGATGACGATGGAAATAATGAGGTTAGACATGGTAAATTCGCTA 5 0.125 No Hit >>END_MODULE >>Adapter Content warn #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 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.025 0.0 0.0 0.0 0.0 72-73 0.05 0.0 0.0 0.0 0.0 74-75 0.075 0.0 0.0 0.0 0.0 76-77 0.1 0.0 0.0 0.0 0.0 78-79 0.15 0.0 0.0 0.0 0.0 80-81 0.1875 0.0 0.0 0.0 0.0 82-83 0.25 0.0 0.0 0.0 0.0 84-85 0.275 0.0 0.0 0.0 0.0 86-87 0.275 0.0 0.0 0.0 0.0 88-89 0.32499999999999996 0.0 0.0 0.0 0.0 90-91 0.35 0.0 0.0 0.0 0.0 92-93 0.375 0.0 0.0 0.0 0.0 94-95 0.4 0.0 0.0 0.0 0.0 96-97 0.475 0.0 0.0 0.0 0.0 98-99 0.6 0.0 0.0 0.0 0.0 100-101 0.875 0.0 0.0 0.0 0.0 102-103 1.0125 0.0 0.0 0.0 0.0 104-105 1.1124999999999998 0.0 0.0 0.0 0.0 106-107 1.25 0.0 0.0 0.0 0.0 108-109 1.425 0.0 0.0 0.0 0.0 110-111 1.525 0.0 0.0 0.0 0.0 112-113 1.7 0.0 0.0 0.0 0.0 114-115 1.875 0.0 0.0 0.0 0.0 116-117 2.0625 0.0 0.0 0.0 0.0 118-119 2.425 0.0 0.0 0.0 0.0 120-121 2.7625 0.0 0.0 0.0 0.0 122-123 3.0375 0.0 0.0 0.0 0.0 124-125 3.3625 0.0 0.0 0.0 0.0 126-127 3.7625 0.0 0.0 0.0 0.0 128-129 4.5 0.0 0.0 0.0 0.0 130-131 5.137499999999999 0.0 0.0 0.0 0.0 132-133 5.362500000000001 0.0 0.0 0.0 0.0 134-135 5.7875 0.0 0.0 0.0 0.0 136-137 6.3125 0.0 0.0 0.0 0.0 138-139 6.887499999999999 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TAAATAT 10 0.006830828 145.0 1 GATTGTC 10 0.006830828 145.0 2 TATTCTA 10 0.006830828 145.0 5 TTCTATC 10 0.006830828 145.0 7 AATATTC 10 0.006830828 145.0 3 ACGACTA 10 0.006830828 145.0 145 ATTCTAT 10 0.006830828 145.0 6 ATATTCT 10 0.006830828 145.0 4 CGATTGT 10 0.006830828 145.0 1 TTTTTTT 50 0.0013298223 17.4 60-64 >>END_MODULE Read 814462 spots for SRR13695429.sra Written 814462 spots for SRR13695429.sra Read 814462 spots for SRR13695429.sra Written 814462 spots for SRR13695429.sra Read 814462 spots for SRR13695429.sra Written 814462 spots for SRR13695429.sra Read 814462 spots for SRR13695429.sra Written 814462 spots for SRR13695429.sra Read 814462 spots for SRR13695429.sra Written 814462 spots for SRR13695429.sra Read 814462 spots for SRR13695429.sra Written 814462 spots for SRR13695429.sra Read 814462 spots for SRR13695429.sra Written 814462 spots for SRR13695429.sra Read 814462 spots for SRR13695429.sra Written 814462 spots for SRR13695429.sra Read 814462 spots for SRR13695429.sra Written 814462 spots for SRR13695429.sra Read 814462 spots for SRR13695429.sra Written 814462 spots for SRR13695429.sra Read 814462 spots for SRR13695429.sra Written 814462 spots for SRR13695429.sra Read 814462 spots for SRR13695429.sra Written 814462 spots for SRR13695429.sra Read 814462 spots for SRR13695429.sra Written 814462 spots for SRR13695429.sra Read 814462 spots for SRR13695429.sra Written 814462 spots for SRR13695429.sra Read 814462 spots for SRR13695429.sra Written 814462 spots for SRR13695429.sra Read 814464 spots for SRR13695429.sra Written 814464 spots for SRR13695429.sra Read 814462 spots for SRR13695429.sra Written 814462 spots for SRR13695429.sra Read 814462 spots for SRR13695429.sra Written 814462 spots for SRR13695429.sra Read 814462 spots for SRR13695429.sra Written 814462 spots for SRR13695429.sra Read 814462 spots for SRR13695429.sra Written 814462 spots for SRR13695429.sra SRR ids: ['SRR13695429.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_dkjiees4 SRR13695429.sra spots: 16289242 blocks: [[1, 814462], [814463, 1628924], [1628925, 2443386], [2443387, 3257848], [3257849, 4072310], [4072311, 4886772], [4886773, 5701234], [5701235, 6515696], [6515697, 7330158], [7330159, 8144620], [8144621, 8959082], [8959083, 9773544], [9773545, 10588006], [10588007, 11402468], [11402469, 12216930], [12216931, 13031392], [13031393, 13845854], [13845855, 14660316], [14660317, 15474778], [15474779, 16289242]] SRR13695429 file size 5514096 SRR13695429 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 SRR13695429 SRR13695429_1.fastq SRR13695429_2.fastq Input file: SRR13695429_1.fastq Paired file: SRR13695429_2.fastq trimmed: SRR13695429-trimmed-pair1.fastq, SRR13695429-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 Wed Feb 12 02:41:51 2025 >> started Wed Feb 12 02:42:09 2025 >> done (17.721s) 16289242 read pairs processed; of these: 132 ( 0.00%) short read pairs filtered out after trimming by size control 621 ( 0.00%) empty read pairs filtered out after trimming by size control 16288489 (100.00%) read pairs available; of these: 1608936 ( 9.88%) trimmed read pairs available after processing 14679553 (90.12%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 19 2 0.00% 20 2 0.00% 21 2 0.00% 22 1 0.00% 23 1 0.00% 24 0 0.00% 25 2 0.00% 26 5 0.00% 27 2 0.00% 28 6 0.00% 29 3 0.00% 30 1 0.00% 31 5 0.00% 32 0 0.00% 33 2 0.00% 34 6 0.00% 35 5 0.00% 36 3 0.00% 37 4 0.00% 38 17 0.00% 39 18 0.00% 40 8 0.00% 41 16 0.00% 42 9 0.00% 43 19 0.00% 44 12 0.00% 45 18 0.00% 46 21 0.00% 47 24 0.00% 48 41 0.00% 49 39 0.00% 50 41 0.00% 51 55 0.00% 52 61 0.00% 53 80 0.00% 54 63 0.00% 55 72 0.00% 56 86 0.00% 57 117 0.00% 58 129 0.00% 59 146 0.00% 60 161 0.00% 61 165 0.00% 62 215 0.00% 63 253 0.00% 64 308 0.00% 65 315 0.00% 66 403 0.00% 67 411 0.00% 68 492 0.00% 69 556 0.00% 70 685 0.00% 71 743 0.00% 72 941 0.01% 73 1068 0.01% 74 1148 0.01% 75 1315 0.01% 76 1505 0.01% 77 1635 0.01% 78 1787 0.01% 79 2035 0.01% 80 2275 0.01% 81 2460 0.02% 82 2888 0.02% 83 3107 0.02% 84 3660 0.02% 85 4075 0.03% 86 4357 0.03% 87 4660 0.03% 88 5130 0.03% 89 5327 0.03% 90 5770 0.04% 91 6134 0.04% 92 6888 0.04% 93 7365 0.05% 94 7830 0.05% 95 8440 0.05% 96 8904 0.05% 97 9289 0.06% 98 10153 0.06% 99 10640 0.07% 100 11353 0.07% 101 11771 0.07% 102 12351 0.08% 103 13057 0.08% 104 13503 0.08% 105 14268 0.09% 106 15073 0.09% 107 15809 0.10% 108 16583 0.10% 109 17053 0.10% 110 17341 0.11% 111 18348 0.11% 112 18786 0.12% 113 19398 0.12% 114 20043 0.12% 115 21094 0.13% 116 22039 0.14% 117 22679 0.14% 118 23544 0.14% 119 23866 0.15% 120 25319 0.16% 121 25325 0.16% 122 26105 0.16% 123 27355 0.17% 124 27945 0.17% 125 28221 0.17% 126 29931 0.18% 127 30085 0.18% 128 31000 0.19% 129 31358 0.19% 130 33326 0.20% 131 33150 0.20% 132 33656 0.21% 133 34793 0.21% 134 35155 0.22% 135 36120 0.22% 136 36686 0.23% 137 37325 0.23% 138 38420 0.24% 139 39511 0.24% 140 40366 0.25% 141 41153 0.25% 142 41960 0.26% 143 41892 0.26% 144 43475 0.27% 145 43768 0.27% 146 44111 0.27% 147 46163 0.28% 148 46174 0.28% 149 46995 0.29% 150 47497 0.29% 151 14679553 90.12% 16288489 reads passed initial QC criterion=sequence-density sequence-density=0.32 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=24 prefix-density=0.31 prefix-fanout=2.0 sequence=GTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAGGTGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGGAGTATGAATGTGTTCTCTG criterion=fanout-score sequence-density=0.01 sequence-density-rank=28 fanout-score=807.35 fanout-score-rank=1 prefix-density=0.29 prefix-fanout=20.3 sequence=TGAAGAAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTC criterion=sequence-density sequence-density=0.39 sequence-density-rank=1 fanout-score=2.11 fanout-score-rank=25 prefix-density=0.40 prefix-fanout=2.1 sequence=TGTAAGAGATGGCTTCCTC criterion=fanout-score sequence-density=0.13 sequence-density-rank=22 fanout-score=42.59 fanout-score-rank=1 prefix-density=0.42 prefix-fanout=13.3 sequence=AAAGAAAAGAAAA SRR13695429 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 12 02:42:51 Started mapping on | Feb 12 02:42:51 Finished on | Feb 12 02:44:47 Mapping speed, Million of reads per hour | 505.50 Number of input reads | 16288489 Average input read length | 297 UNIQUE READS: Uniquely mapped reads number | 15223766 Uniquely mapped reads % | 93.46% Average mapped length | 295.87 Number of splices: Total | 14869393 Number of splices: Annotated (sjdb) | 14520218 Number of splices: GT/AG | 14566154 Number of splices: GC/AG | 237417 Number of splices: AT/AC | 8821 Number of splices: Non-canonical | 57001 Mismatch rate per base, % | 0.39% Deletion rate per base | 0.03% Deletion average length | 2.93 Insertion rate per base | 0.02% Insertion average length | 2.46 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 400339 % of reads mapped to multiple loci | 2.46% Number of reads mapped to too many loci | 136506 % of reads mapped to too many loci | 0.84% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.08% % of reads unmapped: other | 0.16% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 664573 664573 664573 N_multimapping 400339 400339 400339 N_noFeature 675064 14883649 880775 N_ambiguous 240943 1602 105399 UnstrandedReadsAssigned:14307759 PositiveStrandReadsAssigned:338515 NegativeStrandReadsAssigned:14237592 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR13695429 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: SRR13695429-trimmed-pair1.fastq SRR13695429-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 16,288,489 reads, 14,274,295 reads pseudoaligned [quant] estimated average fragment length: 262.435 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,216 rounds 52401 SRR13695429.ke.tsv 34699 SRR13695429.se.tsv 87100 total ==> SRR13695429.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1756.57 647 24.399 Potri.005G024800.1.v4.1 1035 773.565 232 19.8666 Potri.004G059700.1.v4.1 961 699.713 1 0.0946699 Potri.007G009000.2.v4.1 1416 1154.57 0 0 Potri.003G141000.2.v4.1 2943 2681.57 678 16.7484 Potri.016G087400.1.v4.1 270 81.5353 630 511.831 Potri.015G069301.1.v4.1 564 314.933 0 0 Potri.010G195200.1.v4.1 1773 1511.57 140.913 6.17529 Potri.012G127500.1.v4.1 977 715.663 58 5.36848 ==> SRR13695429.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 109 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 238 Potri.001G212900.v4.1 2 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 19 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 9 SRR13695429 completed mapping pipeline successfully