Starting /dee2/code/volunteer_pipeline.sh SRR12670121 current disk space = 3057321271296 free memory = 1512509240 SRR12670121 SRAfilesize aacb86e8a7deedda4305d82704b9b947 SRR12670121.sra SRR12670121.sra file validated SRR12670121 is paired end SRR12670121 is conventional basespace SRR12670121 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670121_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 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.631 37.0 37.0 37.0 37.0 37.0 2 36.48975 37.0 37.0 37.0 37.0 37.0 3 36.671 37.0 37.0 37.0 37.0 37.0 4 36.718 37.0 37.0 37.0 37.0 37.0 5 36.637 37.0 37.0 37.0 37.0 37.0 6 36.703 37.0 37.0 37.0 37.0 37.0 7 36.5305 37.0 37.0 37.0 37.0 37.0 8 36.645 37.0 37.0 37.0 37.0 37.0 9 36.6125 37.0 37.0 37.0 37.0 37.0 10-14 36.6325 37.0 37.0 37.0 37.0 37.0 15-19 36.639500000000005 37.0 37.0 37.0 37.0 37.0 20-24 36.55460000000001 37.0 37.0 37.0 37.0 37.0 25-29 36.562200000000004 37.0 37.0 37.0 37.0 37.0 30-34 36.5376 37.0 37.0 37.0 37.0 37.0 35-39 36.51279999999999 37.0 37.0 37.0 37.0 37.0 40-44 36.4597 37.0 37.0 37.0 37.0 37.0 45-49 36.4935 37.0 37.0 37.0 37.0 37.0 50-54 36.459500000000006 37.0 37.0 37.0 37.0 37.0 55-59 36.417899999999996 37.0 37.0 37.0 37.0 37.0 60-64 36.4147 37.0 37.0 37.0 37.0 37.0 65-69 36.3885 37.0 37.0 37.0 37.0 37.0 70-74 36.380100000000006 37.0 37.0 37.0 37.0 37.0 75-79 36.3505 37.0 37.0 37.0 37.0 37.0 80-84 36.3246 37.0 37.0 37.0 37.0 37.0 85-89 36.291399999999996 37.0 37.0 37.0 37.0 37.0 90-94 36.295399999999994 37.0 37.0 37.0 37.0 37.0 95-99 36.2923 37.0 37.0 37.0 37.0 37.0 100-104 36.279399999999995 37.0 37.0 37.0 37.0 37.0 105-109 36.30159999999999 37.0 37.0 37.0 37.0 37.0 110-114 36.2192 37.0 37.0 37.0 37.0 37.0 115-119 36.2281 37.0 37.0 37.0 37.0 37.0 120-124 36.10889999999999 37.0 37.0 37.0 37.0 37.0 125-129 36.03189999999999 37.0 37.0 37.0 37.0 37.0 130-134 36.0034 37.0 37.0 37.0 37.0 37.0 135-139 35.9994 37.0 37.0 37.0 37.0 37.0 140-144 35.8437 37.0 37.0 37.0 37.0 37.0 145-149 35.8505 37.0 37.0 37.0 37.0 37.0 150-151 35.748000000000005 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 22 1.0 23 1.0 24 1.0 25 2.0 26 3.0 27 9.0 28 11.0 29 15.0 30 17.0 31 38.0 32 39.0 33 57.0 34 106.0 35 282.0 36 2975.0 37 443.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 37.225 12.4 4.65 45.725 2 18.432256448785374 11.870773854244929 40.84648134234911 28.850488354620584 3 17.175 14.674999999999999 27.950000000000003 40.2 4 20.674999999999997 23.225 25.55 30.55 5 23.65 30.8 24.025 21.525 6 20.175 32.800000000000004 25.55 21.475 7 16.05 26.900000000000002 39.825 17.224999999999998 8 16.6 26.325 33.6 23.474999999999998 9 18.4 23.674999999999997 34.175 23.75 10-14 19.744999999999997 29.360000000000003 28.365000000000002 22.53 15-19 20.45 27.57 28.21 23.77 20-24 20.06 27.665 28.025 24.25 25-29 20.23 27.815 27.735 24.22 30-34 19.73 28.265 28.03 23.974999999999998 35-39 19.89 28.044999999999998 27.575 24.490000000000002 40-44 20.91 28.07 27.47 23.549999999999997 45-49 20.885 27.33 27.565 24.22 50-54 20.905 27.905 27.544999999999998 23.645 55-59 20.605 28.77 27.255000000000003 23.369999999999997 60-64 20.305 27.915 27.689999999999998 24.09 65-69 20.645 27.725 28.1 23.53 70-74 20.825 28.07 27.705000000000002 23.400000000000002 75-79 20.95 27.034999999999997 28.265 23.75 80-84 20.935000000000002 28.235 27.375 23.455000000000002 85-89 20.315 28.775000000000002 26.695 24.215 90-94 20.9 28.155 27.400000000000002 23.544999999999998 95-99 21.23 28.585 27.29 22.895 100-104 21.14 28.09 27.025 23.745 105-109 20.055 27.894999999999996 27.325 24.725 110-114 21.475 28.74 26.76 23.025000000000002 115-119 21.255 28.444999999999997 26.52 23.78 120-124 21.455 28.48 25.91 24.154999999999998 125-129 22.235 27.455000000000002 26.625 23.685000000000002 130-134 22.025 28.42 26.090000000000003 23.465 135-139 21.67 28.694999999999997 25.645 23.990000000000002 140-144 22.205 28.310000000000002 25.72 23.765 145-149 22.1 27.505000000000003 25.605 24.79 150-151 21.987499999999997 27.55 26.674999999999997 23.7875 >>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 0.5 18 0.5 19 0.0 20 0.0 21 1.0 22 2.0 23 1.0 24 1.0 25 1.5 26 1.5 27 5.0 28 6.5 29 8.5 30 14.0 31 20.0 32 30.5 33 38.5 34 47.0 35 64.5 36 80.0 37 91.5 38 122.5 39 151.0 40 177.5 41 190.5 42 205.5 43 266.5 44 288.5 45 279.5 46 294.0 47 264.0 48 204.5 49 197.0 50 198.5 51 163.5 52 132.5 53 101.5 54 73.5 55 59.5 56 54.5 57 50.0 58 32.5 59 24.0 60 19.0 61 12.0 62 7.5 63 4.5 64 3.0 65 2.0 66 1.5 67 2.5 68 2.0 69 0.0 70 0.0 71 0.0 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 0.17500000000000002 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 79.57499999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 80.58435438265788 64.125 2 14.923028589381088 23.75 3 3.2359409362236886 7.725 4 0.8482563619227144 2.7 5 0.3141690229343387 1.25 6 0.0942507068803016 0.44999999999999996 7 0.0 0.0 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 GCGCCTTCGATTTATTCAAGTTAAAATACTACCTCTTCTATGCTGTTCTG 6 0.15 No Hit CTGGGGCAACATAAGCAGGAGTTCCACACTGAGTATGCAAAAGCCCATCT 6 0.15 No Hit TGAGAAGATTTGAGCTCCAGCCTTGAACCAAACTGACTCACCGAACTTGA 6 0.15 No Hit AGGAAATACTGCTTGCCCATGGAACCTGGTTTTGCCCAGTCCTGTAACCT 5 0.125 No Hit GACAATTTTCAGCAATTGCTACCAAGCTAGCATCAGTGATCTTTCTGCAA 5 0.125 No Hit GACTAGTAGTGAACTGAAGGGATTCCGATTTCTGGGTGGTGATTGGATTT 5 0.125 No Hit GTCCTTGCTTGGCCCTCCCTTGAGCTCTTTCTTCCAGCTTTCTAATTCTT 5 0.125 No Hit GTCTCGTTTGGTTAGTAGCGCAAGAAACTCTCATCTTAGCACGACATTTA 5 0.125 No Hit CCCAGTTCTATTGAAGCCCTCAACCGTGATAAACATTCCACAAAAGAATA 5 0.125 No Hit GTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACC 5 0.125 No Hit CTCACAAATTGCATTATTTATTAAGAAAAATGTCGCAGGTAACGCCAACA 5 0.125 No Hit ATCACACAATAACTTAATATCCCCACCAGGAAGTGATTGTAATTGTGAAA 5 0.125 No Hit GTGGACAAATGGAATGAATATGAGTATTTCAGAAACAAGGGTGTTTTGCT 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 0.0125 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.037500000000000006 0.0 0.0 0.0 0.0 50-51 0.1 0.0 0.0 0.0 0.0 52-53 0.1 0.0 0.0 0.0 0.0 54-55 0.1 0.0 0.0 0.0 0.0 56-57 0.1 0.0 0.0 0.0 0.0 58-59 0.1 0.0 0.0 0.0 0.0 60-61 0.1 0.0 0.0 0.0 0.0 62-63 0.125 0.0 0.0 0.0 0.0 64-65 0.15 0.0 0.0 0.0 0.0 66-67 0.175 0.0 0.0 0.0 0.0 68-69 0.2125 0.0 0.0 0.0 0.0 70-71 0.325 0.0 0.0 0.0 0.0 72-73 0.4125 0.0 0.0 0.0 0.0 74-75 0.45 0.0 0.0 0.0 0.0 76-77 0.4875 0.0 0.0 0.0 0.0 78-79 0.6125 0.0 0.0 0.0 0.0 80-81 0.75 0.0 0.0 0.0 0.0 82-83 0.8500000000000001 0.0 0.0 0.0 0.0 84-85 0.975 0.0 0.0 0.0 0.0 86-87 1.225 0.0 0.0 0.0 0.0 88-89 1.5125000000000002 0.0 0.0 0.0 0.0 90-91 1.775 0.0 0.0 0.0 0.0 92-93 2.1125 0.0 0.0 0.0 0.0 94-95 2.4625 0.0 0.0 0.0 0.0 96-97 2.825 0.0 0.0 0.0 0.0 98-99 3.1625 0.0 0.0 0.0 0.0 100-101 3.4875 0.0 0.0 0.0 0.0 102-103 3.9250000000000003 0.0 0.0 0.0 0.0 104-105 4.325 0.0 0.0 0.0 0.0 106-107 4.85 0.0 0.0 0.0 0.0 108-109 5.2375 0.0 0.0 0.0 0.0 110-111 5.7125 0.0 0.0 0.0 0.0 112-113 6.225 0.0 0.0 0.0 0.0 114-115 6.8375 0.0 0.0 0.0 0.0 116-117 7.425 0.0 0.0 0.0 0.0 118-119 8.0125 0.0 0.0 0.0 0.0 120-121 8.524999999999999 0.0 0.0 0.0 0.0 122-123 9.1125 0.0 0.0 0.0 0.0 124-125 10.0375 0.0125 0.0 0.0 0.0 126-127 10.6375 0.025 0.0 0.0 0.0 128-129 11.524999999999999 0.025 0.0 0.0 0.0 130-131 12.3375 0.025 0.0 0.0 0.0 132-133 13.15 0.025 0.0 0.0 0.0 134-135 14.0875 0.025 0.0 0.0 0.0 136-137 15.05 0.025 0.0 0.0 0.0 138-139 15.775 0.025 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TCGGTTC 10 0.006830828 145.0 2 CCTCTTT 10 0.006830828 145.0 2 CGGTTCC 10 0.006830828 145.0 3 >>END_MODULE SRR12670121 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670121_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 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.2725 37.0 37.0 37.0 37.0 37.0 2 36.1535 37.0 37.0 37.0 37.0 37.0 3 36.139 37.0 37.0 37.0 37.0 37.0 4 36.2555 37.0 37.0 37.0 37.0 37.0 5 36.403 37.0 37.0 37.0 37.0 37.0 6 36.2405 37.0 37.0 37.0 37.0 37.0 7 36.2215 37.0 37.0 37.0 37.0 37.0 8 36.347 37.0 37.0 37.0 37.0 37.0 9 36.251 37.0 37.0 37.0 37.0 37.0 10-14 36.3119 37.0 37.0 37.0 37.0 37.0 15-19 36.324799999999996 37.0 37.0 37.0 37.0 37.0 20-24 36.2511 37.0 37.0 37.0 37.0 37.0 25-29 36.2543 37.0 37.0 37.0 37.0 37.0 30-34 36.2256 37.0 37.0 37.0 37.0 37.0 35-39 36.1392 37.0 37.0 37.0 37.0 37.0 40-44 36.137 37.0 37.0 37.0 37.0 37.0 45-49 36.138 37.0 37.0 37.0 37.0 37.0 50-54 36.1252 37.0 37.0 37.0 37.0 37.0 55-59 36.132099999999994 37.0 37.0 37.0 37.0 37.0 60-64 36.087 37.0 37.0 37.0 37.0 37.0 65-69 36.002100000000006 37.0 37.0 37.0 37.0 37.0 70-74 36.0364 37.0 37.0 37.0 37.0 37.0 75-79 36.03699999999999 37.0 37.0 37.0 37.0 37.0 80-84 35.994299999999996 37.0 37.0 37.0 37.0 37.0 85-89 35.9097 37.0 37.0 37.0 37.0 37.0 90-94 35.9529 37.0 37.0 37.0 37.0 37.0 95-99 35.84439999999999 37.0 37.0 37.0 37.0 37.0 100-104 35.8584 37.0 37.0 37.0 37.0 37.0 105-109 35.810900000000004 37.0 37.0 37.0 37.0 37.0 110-114 35.72089999999999 37.0 37.0 37.0 37.0 37.0 115-119 35.778800000000004 37.0 37.0 37.0 37.0 37.0 120-124 35.6548 37.0 37.0 37.0 37.0 37.0 125-129 35.5572 37.0 37.0 37.0 37.0 37.0 130-134 35.4744 37.0 37.0 37.0 34.6 37.0 135-139 35.3999 37.0 37.0 37.0 37.0 37.0 140-144 35.211800000000004 37.0 37.0 37.0 32.2 37.0 145-149 35.0308 37.0 37.0 37.0 25.0 37.0 150-151 34.7745 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 2.0 14 0.0 15 1.0 16 0.0 17 0.0 18 1.0 19 0.0 20 1.0 21 2.0 22 2.0 23 2.0 24 8.0 25 9.0 26 10.0 27 8.0 28 16.0 29 17.0 30 35.0 31 28.0 32 65.0 33 117.0 34 221.0 35 571.0 36 2604.0 37 280.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 33.550000000000004 25.025 9.3 32.125 2 25.825 28.075 32.275 13.825000000000001 3 19.825 26.724999999999998 33.25 20.200000000000003 4 23.150000000000002 33.25 23.925 19.675 5 23.7 37.55 21.55 17.2 6 19.0 39.800000000000004 22.925 18.275 7 19.775000000000002 22.75 39.324999999999996 18.15 8 19.5 25.575 29.849999999999998 25.074999999999996 9 21.375 25.3 29.475 23.849999999999998 10-14 23.185 28.415000000000003 27.12 21.279999999999998 15-19 22.795 28.294999999999998 27.825 21.085 20-24 22.770000000000003 28.375 28.02 20.835 25-29 23.474999999999998 27.61 28.1 20.815 30-34 22.825 27.825 28.225 21.125 35-39 22.63 27.755000000000003 27.755000000000003 21.86 40-44 22.825 27.884999999999998 28.03 21.26 45-49 22.945 27.384999999999998 28.265 21.404999999999998 50-54 23.169999999999998 27.785 27.525 21.52 55-59 23.5 28.285 27.834999999999997 20.380000000000003 60-64 23.775 27.310000000000002 26.884999999999998 22.03 65-69 22.945 26.884999999999998 28.494999999999997 21.675 70-74 23.169999999999998 27.750000000000004 27.665 21.415 75-79 23.05 28.155 27.68 21.115000000000002 80-84 23.47 27.57 27.05 21.91 85-89 23.47 27.91 26.784999999999997 21.834999999999997 90-94 22.99 28.645 26.99 21.375 95-99 23.745 27.675 27.77 20.810000000000002 100-104 24.075 28.16 27.235 20.53 105-109 24.94 27.3 27.805000000000003 19.955000000000002 110-114 24.085 28.475 26.779999999999998 20.66 115-119 24.855 27.985 26.755000000000003 20.405 120-124 25.040000000000003 27.71 26.38 20.87 125-129 25.39 27.839999999999996 26.655 20.115 130-134 25.97 27.925 26.215 19.89 135-139 26.515 27.625 26.325 19.535 140-144 26.889999999999997 27.18 26.02 19.91 145-149 27.675 27.029999999999998 26.095000000000002 19.2 150-151 27.5875 27.925 26.387500000000003 18.099999999999998 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.5 2 0.5 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 0.5 12 0.5 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 1.0 20 1.0 21 0.5 22 1.0 23 2.0 24 4.5 25 4.0 26 2.0 27 3.5 28 6.5 29 10.5 30 12.0 31 17.0 32 27.0 33 33.5 34 50.0 35 74.0 36 93.0 37 114.0 38 130.0 39 146.5 40 176.0 41 204.5 42 234.5 43 267.0 44 293.0 45 308.5 46 275.0 47 244.0 48 228.5 49 190.0 50 158.5 51 125.0 52 111.5 53 105.5 54 90.0 55 68.0 56 44.0 57 30.0 58 27.0 59 27.0 60 16.0 61 11.0 62 8.0 63 5.0 64 5.0 65 2.5 66 1.5 67 1.5 68 1.0 69 0.5 70 0.0 71 0.0 72 0.0 73 0.5 74 0.5 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 0.5 85 0.0 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 0.0 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 80.175 #Duplication Level Percentage of deduplicated Percentage of total 1 81.25974430932335 65.14999999999999 2 14.468350483317744 23.200000000000003 3 3.086997193638915 7.425 4 0.7483629560336763 2.4 5 0.3429996881821017 1.375 6 0.09354536950420954 0.44999999999999996 7 0.0 0.0 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 CTTCGATTAACAGCTGGTGTCTCACCTCTGTCTCTGCCTCTAAGAGATCA 6 0.15 No Hit TTTTGATGGATTCCATCAGAATTAGCATCTCTTCAATCCTTTCTTGGATT 6 0.15 No Hit GAAGGATTTTACATTAGATCAGGGATCACAGCCGTCCTGAAGAATGCAAC 6 0.15 No Hit GACAAGTCACTGCTACAGGATTGCTTACCGATCCATGGAACGTTCACTTA 5 0.125 No Hit GTCTTGGACTGCACTCACAGCAGCCCTCAGTTTTGCGATTCTTGATTTCG 5 0.125 No Hit GGCAGGTCTTGTTAAGGTGAATCTTAGTGGTTGCATGAGTTTGACCGATG 5 0.125 No Hit GTCATCGCCTCTTTGATTGTGATGCCAAGGAACTAAGTTGATCACGTTGG 5 0.125 No Hit CAGCCTTCCAGGTGACTTCGGATTCGACCCACTCGGACTTTCAGACCCTG 5 0.125 No Hit TTTTTCTCCTGATCGTGTTATGGAGAGAATCAGACTTTGACTGTGAACTT 5 0.125 No Hit AGTCAGCCTTGATAGAGTAAGAGAAAAGCAGAGCAAGCGACTTAGAGGCA 5 0.125 No Hit GGGAAATAACTTTGTTGAATCCAATTTGGATCCATTCCAAGAATTCCGGG 5 0.125 No Hit CTTTTCTTTCCGATTTAACACTAGATTGTAAGAAAGGAAGGAAAAAAACC 5 0.125 No Hit GTGGAAAAGCTCTTCGAGATTGATCCTGATGCAACTGTTATGGCTTTTGC 5 0.125 No Hit CGCAAGCTGAGATCTTTCTTTTAACCTGAATGTTCTTGCCTTCTCGTCCA 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 0.0125 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.037500000000000006 0.0 0.0 0.0 0.0 50-51 0.1 0.0 0.0 0.0 0.0 52-53 0.1 0.0 0.0 0.0 0.0 54-55 0.1 0.0 0.0 0.0 0.0 56-57 0.1 0.0 0.0 0.0 0.0 58-59 0.1 0.0 0.0 0.0 0.0 60-61 0.1 0.0 0.0 0.0 0.0 62-63 0.125 0.0 0.0 0.0 0.0 64-65 0.15 0.0 0.0 0.0 0.0 66-67 0.175 0.0 0.0 0.0 0.0 68-69 0.2125 0.0 0.0 0.0 0.0 70-71 0.325 0.0 0.0 0.0 0.0 72-73 0.4125 0.0 0.0 0.0 0.0 74-75 0.45 0.0 0.0 0.0 0.0 76-77 0.4875 0.0 0.0 0.0 0.0 78-79 0.6125 0.0 0.0 0.0 0.0 80-81 0.75 0.0 0.0 0.0 0.0 82-83 0.8500000000000001 0.0 0.0 0.0 0.0 84-85 1.0 0.0 0.0 0.0 0.0 86-87 1.25 0.0 0.0 0.0 0.0 88-89 1.5375 0.0 0.0 0.0 0.0 90-91 1.8 0.0 0.0 0.0 0.0 92-93 2.1125 0.0 0.0 0.0 0.0 94-95 2.4625 0.0 0.0 0.0 0.0 96-97 2.825 0.0 0.0 0.0 0.0 98-99 3.1625 0.0 0.0 0.0 0.0 100-101 3.4625 0.0 0.0 0.0 0.0 102-103 3.875 0.0 0.0 0.0 0.0 104-105 4.262499999999999 0.0 0.0 0.0 0.0 106-107 4.775 0.0 0.0 0.0 0.0 108-109 5.1625 0.0 0.0 0.0 0.0 110-111 5.6625 0.0 0.0 0.0 0.0 112-113 6.175 0.0 0.0 0.0 0.0 114-115 6.7875 0.0 0.0 0.0 0.0 116-117 7.375 0.0 0.0 0.0 0.0 118-119 7.9625 0.0 0.0 0.0 0.0 120-121 8.475000000000001 0.0 0.0 0.0 0.0 122-123 9.0875 0.0 0.0 0.0 0.0 124-125 10.024999999999999 0.0 0.0 0.0 0.0 126-127 10.6625 0.0 0.0 0.0 0.0 128-129 11.55 0.0 0.0 0.0 0.0 130-131 12.4125 0.0 0.0 0.0 0.0 132-133 13.275 0.0 0.0 0.0 0.0 134-135 14.2125 0.0 0.0 0.0 0.0 136-137 15.15 0.0 0.0 0.0 0.0 138-139 15.8625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTGCAAT 10 0.006830828 145.0 3 CATATGC 10 0.006830828 145.0 5 TCATATG 10 0.006830828 145.0 4 >>END_MODULE Read 644944 spots for SRR12670121.sra Written 644944 spots for SRR12670121.sra Read 644944 spots for SRR12670121.sra Written 644944 spots for SRR12670121.sra Read 644944 spots for SRR12670121.sra Written 644944 spots for SRR12670121.sra Read 644944 spots for SRR12670121.sra Written 644944 spots for SRR12670121.sra Read 644944 spots for SRR12670121.sra Written 644944 spots for SRR12670121.sra Read 644944 spots for SRR12670121.sra Written 644944 spots for SRR12670121.sra Read 644944 spots for SRR12670121.sra Written 644944 spots for SRR12670121.sra Read 644944 spots for SRR12670121.sra Written 644944 spots for SRR12670121.sra Read 644944 spots for SRR12670121.sra Written 644944 spots for SRR12670121.sra Read 644944 spots for SRR12670121.sra Written 644944 spots for SRR12670121.sra Read 644944 spots for SRR12670121.sra Written 644944 spots for SRR12670121.sra Read 644944 spots for SRR12670121.sra Written 644944 spots for SRR12670121.sra Read 644955 spots for SRR12670121.sra Written 644955 spots for SRR12670121.sra Read 644944 spots for SRR12670121.sra Written 644944 spots for SRR12670121.sra Read 644944 spots for SRR12670121.sra Written 644944 spots for SRR12670121.sra Read 644944 spots for SRR12670121.sra Written 644944 spots for SRR12670121.sra Read 644944 spots for SRR12670121.sra Written 644944 spots for SRR12670121.sra Read 644944 spots for SRR12670121.sra Written 644944 spots for SRR12670121.sra Read 644944 spots for SRR12670121.sra Written 644944 spots for SRR12670121.sra Read 644944 spots for SRR12670121.sra Written 644944 spots for SRR12670121.sra SRR ids: ['SRR12670121.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_rn3j4b5_ SRR12670121.sra spots: 12898891 blocks: [[1, 644944], [644945, 1289888], [1289889, 1934832], [1934833, 2579776], [2579777, 3224720], [3224721, 3869664], [3869665, 4514608], [4514609, 5159552], [5159553, 5804496], [5804497, 6449440], [6449441, 7094384], [7094385, 7739328], [7739329, 8384272], [8384273, 9029216], [9029217, 9674160], [9674161, 10319104], [10319105, 10964048], [10964049, 11608992], [11608993, 12253936], [12253937, 12898891]] SRR12670121 file size 4361907 SRR12670121 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 SRR12670121 SRR12670121_1.fastq SRR12670121_2.fastq Input file: SRR12670121_1.fastq Paired file: SRR12670121_2.fastq trimmed: SRR12670121-trimmed-pair1.fastq, SRR12670121-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 00:26:06 2025 >> started Tue Feb 11 00:26:26 2025 >> done (20.425s) 12898891 read pairs processed; of these: 84 ( 0.00%) short read pairs filtered out after trimming by size control 2542 ( 0.02%) empty read pairs filtered out after trimming by size control 12896265 (99.98%) read pairs available; of these: 2597908 (20.14%) trimmed read pairs available after processing 10298357 (79.86%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 8 0.00% 19 4 0.00% 20 9 0.00% 21 12 0.00% 22 11 0.00% 23 14 0.00% 24 23 0.00% 25 19 0.00% 26 46 0.00% 27 49 0.00% 28 47 0.00% 29 43 0.00% 30 41 0.00% 31 58 0.00% 32 60 0.00% 33 56 0.00% 34 73 0.00% 35 94 0.00% 36 70 0.00% 37 91 0.00% 38 102 0.00% 39 99 0.00% 40 99 0.00% 41 107 0.00% 42 127 0.00% 43 153 0.00% 44 158 0.00% 45 168 0.00% 46 179 0.00% 47 201 0.00% 48 218 0.00% 49 263 0.00% 50 353 0.00% 51 362 0.00% 52 383 0.00% 53 400 0.00% 54 423 0.00% 55 466 0.00% 56 549 0.00% 57 603 0.00% 58 689 0.01% 59 803 0.01% 60 987 0.01% 61 1100 0.01% 62 1249 0.01% 63 1375 0.01% 64 1574 0.01% 65 1696 0.01% 66 1840 0.01% 67 2124 0.02% 68 2321 0.02% 69 2586 0.02% 70 3111 0.02% 71 3325 0.03% 72 3903 0.03% 73 4363 0.03% 74 4730 0.04% 75 5179 0.04% 76 5722 0.04% 77 5950 0.05% 78 6676 0.05% 79 7324 0.06% 80 7983 0.06% 81 8936 0.07% 82 9911 0.08% 83 10778 0.08% 84 11785 0.09% 85 12551 0.10% 86 13603 0.11% 87 14377 0.11% 88 14891 0.12% 89 15626 0.12% 90 16655 0.13% 91 17712 0.14% 92 18636 0.14% 93 20108 0.16% 94 21205 0.16% 95 22755 0.18% 96 23357 0.18% 97 24190 0.19% 98 24814 0.19% 99 25504 0.20% 100 26282 0.20% 101 27166 0.21% 102 28437 0.22% 103 28985 0.22% 104 30113 0.23% 105 31138 0.24% 106 32343 0.25% 107 32735 0.25% 108 33611 0.26% 109 33935 0.26% 110 34104 0.26% 111 34831 0.27% 112 35809 0.28% 113 36275 0.28% 114 37637 0.29% 115 38358 0.30% 116 39415 0.31% 117 40025 0.31% 118 41058 0.32% 119 41062 0.32% 120 41942 0.33% 121 42006 0.33% 122 42336 0.33% 123 43170 0.33% 124 43584 0.34% 125 43839 0.34% 126 45600 0.35% 127 46400 0.36% 128 46030 0.36% 129 46826 0.36% 130 47479 0.37% 131 47060 0.36% 132 47288 0.37% 133 47786 0.37% 134 48080 0.37% 135 48467 0.38% 136 49475 0.38% 137 50143 0.39% 138 50113 0.39% 139 51639 0.40% 140 51607 0.40% 141 51305 0.40% 142 51611 0.40% 143 51165 0.40% 144 52325 0.41% 145 51998 0.40% 146 51746 0.40% 147 52071 0.40% 148 54056 0.42% 149 53569 0.42% 150 53628 0.42% 151 10298357 79.86% 12896265 reads passed initial QC criterion=sequence-density sequence-density=0.34 sequence-density-rank=1 fanout-score=2.24 fanout-score-rank=21 prefix-density=0.36 prefix-fanout=2.1 sequence=TGAGATGCCTCAGTGCATCCAAACATGGGTAG criterion=fanout-score sequence-density=0.01 sequence-density-rank=32 fanout-score=311.57 fanout-score-rank=1 prefix-density=0.26 prefix-fanout=17.3 sequence=TGAAGAAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAGGTGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGGGGTATGAATGTGTTCTCTGTG criterion=sequence-density sequence-density=0.53 sequence-density-rank=1 fanout-score=2.12 fanout-score-rank=31 prefix-density=0.54 prefix-fanout=2.1 sequence=TGTAAGAGATGGCTTCCTC criterion=fanout-score sequence-density=0.01 sequence-density-rank=36 fanout-score=29.46 fanout-score-rank=1 prefix-density=0.11 prefix-fanout=2.7 sequence=CCACCACTAAACCCAAAGCTCAAAAAAAATCTTAACTGCACCCGCTCATCCAGCAATGGCAGCAGCAACAATGGCCCTCTCCTCCCCTTCGCTAGCCGGAAAGGCGGTGAAGCTCAACCCCTCCTCCTCTGAGATCATGGGCAATGGCCGTGTCTCCATGAGGAAAACCACCAAGCCTGTTCCCTCCGGGAGCCCATGGTACGGACCAGACCGTGTTAAATACTTGGGCCCGTTCTCTGGTGAGCCCCCATCCTACTTGACTGGTGAGTTCCCTGGTGACTACGGCTGGGACACTGCTGG SRR12670121 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 00:27:07 Started mapping on | Feb 11 00:27:07 Finished on | Feb 11 00:28:40 Mapping speed, Million of reads per hour | 499.21 Number of input reads | 12896265 Average input read length | 290 UNIQUE READS: Uniquely mapped reads number | 12125155 Uniquely mapped reads % | 94.02% Average mapped length | 288.85 Number of splices: Total | 11803766 Number of splices: Annotated (sjdb) | 11548032 Number of splices: GT/AG | 11566204 Number of splices: GC/AG | 193833 Number of splices: AT/AC | 6960 Number of splices: Non-canonical | 36769 Mismatch rate per base, % | 0.36% Deletion rate per base | 0.03% Deletion average length | 2.87 Insertion rate per base | 0.02% Insertion average length | 2.39 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 309402 % of reads mapped to multiple loci | 2.40% Number of reads mapped to too many loci | 150255 % of reads mapped to too many loci | 1.17% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.21% % of reads unmapped: other | 0.21% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 461708 461708 461708 N_multimapping 309402 309402 309402 N_noFeature 508773 11943858 585491 N_ambiguous 175359 719 70343 UnstrandedReadsAssigned:11441023 PositiveStrandReadsAssigned:180578 NegativeStrandReadsAssigned:11469321 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=150 echo kmer=145 SRR12670121 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: SRR12670121-trimmed-pair1.fastq SRR12670121-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 12,896,265 reads, 11,540,424 reads pseudoaligned [quant] estimated average fragment length: 225.49 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,114 rounds 52401 SRR12670121.ke.tsv 34699 SRR12670121.se.tsv 87100 total ==> SRR12670121.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1793.51 517 24.6159 Potri.005G024800.1.v4.1 1035 810.51 170 17.911 Potri.004G059700.1.v4.1 961 736.596 0 0 Potri.007G009000.2.v4.1 1416 1191.51 0 0 Potri.003G141000.2.v4.1 2943 2718.51 624.139 19.6056 Potri.016G087400.1.v4.1 270 100.284 511 435.131 Potri.015G069301.1.v4.1 564 348.512 0 0 Potri.010G195200.1.v4.1 1773 1548.51 92 5.07344 Potri.012G127500.1.v4.1 977 752.572 60 6.8082 ==> SRR12670121.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 282 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 209 Potri.001G212900.v4.1 7 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 9 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 0 SRR12670121 completed mapping pipeline successfully