Starting /dee2/code/volunteer_pipeline.sh SRR12670133 current disk space = 3057195307008 free memory = 1182598104 SRR12670133 SRAfilesize c90fa355309008d931e4c8cdda98550b SRR12670133.sra SRR12670133.sra file validated SRR12670133 is paired end SRR12670133 is conventional basespace SRR12670133 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670133_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 36.698 37.0 37.0 37.0 37.0 37.0 2 36.51875 37.0 37.0 37.0 37.0 37.0 3 36.537 37.0 37.0 37.0 37.0 37.0 4 36.662 37.0 37.0 37.0 37.0 37.0 5 36.7035 37.0 37.0 37.0 37.0 37.0 6 36.6805 37.0 37.0 37.0 37.0 37.0 7 36.596 37.0 37.0 37.0 37.0 37.0 8 36.6635 37.0 37.0 37.0 37.0 37.0 9 36.575 37.0 37.0 37.0 37.0 37.0 10-14 36.6106 37.0 37.0 37.0 37.0 37.0 15-19 36.589200000000005 37.0 37.0 37.0 37.0 37.0 20-24 36.5369 37.0 37.0 37.0 37.0 37.0 25-29 36.53150000000001 37.0 37.0 37.0 37.0 37.0 30-34 36.4957 37.0 37.0 37.0 37.0 37.0 35-39 36.4888 37.0 37.0 37.0 37.0 37.0 40-44 36.4967 37.0 37.0 37.0 37.0 37.0 45-49 36.411199999999994 37.0 37.0 37.0 37.0 37.0 50-54 36.4365 37.0 37.0 37.0 37.0 37.0 55-59 36.382400000000004 37.0 37.0 37.0 37.0 37.0 60-64 36.327099999999994 37.0 37.0 37.0 37.0 37.0 65-69 36.3108 37.0 37.0 37.0 37.0 37.0 70-74 36.289 37.0 37.0 37.0 37.0 37.0 75-79 36.308299999999996 37.0 37.0 37.0 37.0 37.0 80-84 36.3501 37.0 37.0 37.0 37.0 37.0 85-89 36.2803 37.0 37.0 37.0 37.0 37.0 90-94 36.294799999999995 37.0 37.0 37.0 37.0 37.0 95-99 36.227700000000006 37.0 37.0 37.0 37.0 37.0 100-104 36.2161 37.0 37.0 37.0 37.0 37.0 105-109 36.2461 37.0 37.0 37.0 37.0 37.0 110-114 36.1865 37.0 37.0 37.0 37.0 37.0 115-119 36.2321 37.0 37.0 37.0 37.0 37.0 120-124 36.052 37.0 37.0 37.0 37.0 37.0 125-129 36.0056 37.0 37.0 37.0 37.0 37.0 130-134 35.933400000000006 37.0 37.0 37.0 37.0 37.0 135-139 35.833600000000004 37.0 37.0 37.0 37.0 37.0 140-144 35.5532 37.0 37.0 37.0 37.0 37.0 145-149 35.5569 37.0 37.0 37.0 37.0 37.0 150-151 35.2765 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 1.0 22 0.0 23 0.0 24 2.0 25 0.0 26 1.0 27 6.0 28 14.0 29 21.0 30 25.0 31 31.0 32 43.0 33 72.0 34 143.0 35 319.0 36 2916.0 37 406.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 41.4 9.5 7.025 42.075 2 18.864148111083313 12.284213159869903 37.87840880660495 30.97322992244183 3 18.0 16.45 27.725 37.824999999999996 4 23.400000000000002 24.55 23.599999999999998 28.449999999999996 5 24.825 29.925 23.5 21.75 6 20.175 33.75 25.15 20.925 7 15.675 26.05 41.275 17.0 8 18.224999999999998 24.6 33.15 24.025 9 18.025 23.825 34.55 23.599999999999998 10-14 20.974999999999998 28.355000000000004 28.285 22.384999999999998 15-19 20.369999999999997 28.134999999999998 27.505000000000003 23.990000000000002 20-24 20.48 27.925 27.495000000000005 24.099999999999998 25-29 21.14 28.21 26.77 23.880000000000003 30-34 20.485 28.16 28.13 23.225 35-39 20.695 28.13 27.725 23.45 40-44 21.07 27.615000000000002 28.07 23.244999999999997 45-49 21.115000000000002 28.105000000000004 26.939999999999998 23.84 50-54 20.080000000000002 28.62 27.534999999999997 23.765 55-59 20.64 28.065 27.544999999999998 23.75 60-64 21.435000000000002 28.475 27.084999999999997 23.005 65-69 20.810000000000002 27.975 27.525 23.69 70-74 21.15 27.675 28.04 23.135 75-79 20.875 27.405 27.93 23.79 80-84 21.465 28.46 26.729999999999997 23.345 85-89 21.195 28.360000000000003 27.125 23.32 90-94 20.335 28.395 27.465 23.805 95-99 21.685 28.499999999999996 26.529999999999998 23.285 100-104 21.884999999999998 28.794999999999998 26.415 22.905 105-109 21.895 28.955 26.490000000000002 22.66 110-114 21.36 28.449999999999996 26.419999999999998 23.77 115-119 21.490000000000002 28.475 25.81 24.224999999999998 120-124 22.07 28.24 25.765 23.925 125-129 21.51 28.12 26.13 24.240000000000002 130-134 21.52 28.555000000000003 25.435000000000002 24.490000000000002 135-139 21.68 27.500000000000004 26.35 24.47 140-144 21.89 27.965 25.88 24.265 145-149 22.085 28.22 24.525 25.169999999999998 150-151 21.3 27.275 25.362499999999997 26.0625 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.5 4 0.5 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 1.0 23 1.0 24 0.0 25 0.5 26 1.0 27 2.5 28 5.0 29 10.5 30 14.5 31 13.5 32 23.5 33 30.5 34 46.0 35 67.5 36 85.5 37 99.0 38 111.5 39 154.5 40 179.5 41 187.5 42 226.0 43 252.5 44 267.5 45 283.0 46 280.0 47 249.5 48 220.0 49 221.0 50 200.5 51 158.0 52 123.0 53 104.0 54 91.0 55 68.5 56 54.0 57 44.0 58 36.0 59 31.0 60 19.0 61 11.0 62 7.0 63 3.0 64 3.0 65 3.5 66 4.0 67 3.0 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 0.075 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 81.975 #Duplication Level Percentage of deduplicated Percentage of total 1 83.01311375419334 68.05 2 13.266239707227815 21.75 3 2.7142421469960354 6.675000000000001 4 0.7929246721561453 2.6 5 0.18298261665141813 0.75 6 0.0 0.0 7 0.030497102775236352 0.17500000000000002 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 GTCTTTGTGATTGTGATGCCATTCCTTTTTTTTTTCAATTATTTTCCTTG 7 0.17500000000000002 No Hit CGAGCACCTTTTCAACTCTGGAGCCATCAATACCCTTGTTCTTCAGGTTC 5 0.125 No Hit GTCAACCTCAACCTCAATTGTCTTTGCAGCCCCAGTTGTTCTGGCAGTGA 5 0.125 No Hit GGTAGAAGAAATGAAAATCAACCTGGATCTCTATTCTGAATCACCTGGCT 5 0.125 No Hit GGCTTGTTGAGGTTCTCATGGCTTCCACAGGATGGTGGTTTCTGCAATCA 5 0.125 No Hit AGCATCCATAAACAGAAAAAATAACAGCTTCTGCTCAATAAATTAACAGC 5 0.125 No Hit GACCACCAATGCATGCAATTCCAAACCCAGAAATCCACTCCTTTGTTGAA 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 0.0 0.0 0.0 0.0 0.0 56-57 0.025 0.0 0.0 0.0 0.0 58-59 0.0625 0.0 0.0 0.0 0.0 60-61 0.0875 0.0 0.0 0.0 0.0 62-63 0.15 0.0 0.0 0.0 0.0 64-65 0.1875 0.0 0.0 0.0 0.0 66-67 0.25 0.0 0.0 0.0 0.0 68-69 0.325 0.0 0.0 0.0 0.0 70-71 0.3375 0.0 0.0 0.0 0.0 72-73 0.5125 0.0 0.0 0.0 0.0 74-75 0.6375 0.0 0.0 0.0 0.0 76-77 0.7375 0.0 0.0 0.0 0.0 78-79 0.9875 0.0 0.0 0.0 0.0 80-81 1.25 0.0 0.0 0.0 0.0 82-83 1.4 0.0 0.0 0.0 0.0 84-85 1.7125 0.0 0.0 0.0 0.0 86-87 1.95 0.0 0.0 0.0 0.0 88-89 2.225 0.0 0.0 0.0 0.0 90-91 2.7875 0.0 0.0 0.0 0.0 92-93 3.35 0.0 0.0 0.0 0.0 94-95 4.0125 0.0 0.0 0.0 0.0 96-97 4.75 0.0 0.0 0.0 0.0 98-99 5.2875 0.0 0.0 0.0 0.0 100-101 6.0 0.0 0.0 0.0 0.0 102-103 6.8875 0.0 0.0 0.0 0.0 104-105 7.525 0.0 0.0 0.0 0.0 106-107 8.412500000000001 0.0 0.0 0.0 0.0 108-109 9.2125 0.0 0.0 0.0 0.0 110-111 10.25 0.0 0.0 0.0 0.0 112-113 11.2125 0.0 0.0 0.0 0.0 114-115 11.975 0.0 0.0 0.0 0.0 116-117 12.8125 0.0 0.0 0.0 0.0 118-119 13.9125 0.0 0.0 0.0 0.0 120-121 14.837499999999999 0.0 0.0 0.0 0.0 122-123 15.5875 0.0 0.0 0.0 0.0 124-125 16.674999999999997 0.0 0.0 0.0 0.0 126-127 17.7625 0.0 0.0 0.0 0.0 128-129 18.6625 0.0 0.0 0.0 0.0 130-131 19.3875 0.0 0.0 0.0 0.0 132-133 20.1875 0.0 0.0 0.0 0.0 134-135 21.25 0.0 0.0 0.0 0.0 136-137 22.174999999999997 0.0 0.0 0.0 0.0 138-139 23.075000000000003 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGTGCTA 10 0.006830828 145.0 4 GTGCTAC 10 0.006830828 145.0 5 >>END_MODULE SRR12670133 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670133_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 36.431 37.0 37.0 37.0 37.0 37.0 2 36.2615 37.0 37.0 37.0 37.0 37.0 3 36.2555 37.0 37.0 37.0 37.0 37.0 4 36.3615 37.0 37.0 37.0 37.0 37.0 5 36.3415 37.0 37.0 37.0 37.0 37.0 6 36.3555 37.0 37.0 37.0 37.0 37.0 7 36.474 37.0 37.0 37.0 37.0 37.0 8 36.5145 37.0 37.0 37.0 37.0 37.0 9 36.3355 37.0 37.0 37.0 37.0 37.0 10-14 36.4335 37.0 37.0 37.0 37.0 37.0 15-19 36.4062 37.0 37.0 37.0 37.0 37.0 20-24 36.3373 37.0 37.0 37.0 37.0 37.0 25-29 36.3076 37.0 37.0 37.0 37.0 37.0 30-34 36.2972 37.0 37.0 37.0 37.0 37.0 35-39 36.28829999999999 37.0 37.0 37.0 37.0 37.0 40-44 36.2731 37.0 37.0 37.0 37.0 37.0 45-49 36.2845 37.0 37.0 37.0 37.0 37.0 50-54 36.1773 37.0 37.0 37.0 37.0 37.0 55-59 36.2136 37.0 37.0 37.0 37.0 37.0 60-64 36.1979 37.0 37.0 37.0 37.0 37.0 65-69 36.1058 37.0 37.0 37.0 37.0 37.0 70-74 36.1139 37.0 37.0 37.0 37.0 37.0 75-79 36.090199999999996 37.0 37.0 37.0 37.0 37.0 80-84 36.0992 37.0 37.0 37.0 37.0 37.0 85-89 36.0499 37.0 37.0 37.0 37.0 37.0 90-94 36.1139 37.0 37.0 37.0 37.0 37.0 95-99 35.9931 37.0 37.0 37.0 37.0 37.0 100-104 35.929899999999996 37.0 37.0 37.0 37.0 37.0 105-109 35.8686 37.0 37.0 37.0 37.0 37.0 110-114 35.7886 37.0 37.0 37.0 37.0 37.0 115-119 35.826100000000004 37.0 37.0 37.0 37.0 37.0 120-124 35.666900000000005 37.0 37.0 37.0 37.0 37.0 125-129 35.5303 37.0 37.0 37.0 37.0 37.0 130-134 35.3985 37.0 37.0 37.0 34.6 37.0 135-139 35.2471 37.0 37.0 37.0 37.0 37.0 140-144 35.0448 37.0 37.0 37.0 25.0 37.0 145-149 34.8198 37.0 37.0 37.0 25.0 37.0 150-151 34.53475 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 2.0 14 1.0 15 1.0 16 2.0 17 0.0 18 0.0 19 0.0 20 1.0 21 1.0 22 2.0 23 3.0 24 8.0 25 8.0 26 10.0 27 15.0 28 16.0 29 16.0 30 26.0 31 25.0 32 63.0 33 74.0 34 195.0 35 606.0 36 2608.0 37 317.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 38.324999999999996 21.925 11.325000000000001 28.425 2 25.374999999999996 25.674999999999997 32.15 16.8 3 18.95 29.875 30.95 20.225 4 23.0 34.25 23.575 19.175 5 24.9 35.05 23.799999999999997 16.25 6 21.75 38.025 22.1 18.125 7 19.875 20.9 38.025 21.2 8 20.3 26.0 28.749999999999996 24.95 9 22.325 25.1 29.95 22.625 10-14 23.21 29.87 25.775 21.145 15-19 23.375 28.749999999999996 27.224999999999998 20.65 20-24 23.41 28.565 27.474999999999998 20.549999999999997 25-29 23.52 27.675 28.29 20.515 30-34 22.86 28.249999999999996 27.334999999999997 21.555 35-39 23.355 27.834999999999997 27.76 21.05 40-44 23.044999999999998 27.91 27.755000000000003 21.29 45-49 23.395 28.634999999999998 27.055 20.915 50-54 23.175 27.889999999999997 27.575 21.36 55-59 22.99 28.449999999999996 27.229999999999997 21.33 60-64 23.1 27.644999999999996 28.03 21.224999999999998 65-69 23.755000000000003 26.805 28.035 21.404999999999998 70-74 22.900000000000002 26.915 28.720000000000002 21.465 75-79 23.165 28.17 27.435 21.23 80-84 22.665 28.735 27.13 21.47 85-89 23.07 27.82 27.474999999999998 21.634999999999998 90-94 24.34 27.544999999999998 27.445000000000004 20.669999999999998 95-99 24.375 27.915 26.845000000000002 20.865000000000002 100-104 24.93 28.139999999999997 26.565 20.365 105-109 24.84 28.110000000000003 26.450000000000003 20.599999999999998 110-114 25.515 27.785 26.655 20.044999999999998 115-119 26.355 27.845 26.08 19.72 120-124 26.795 27.894999999999996 25.900000000000002 19.41 125-129 27.544999999999998 28.415000000000003 24.75 19.29 130-134 28.645 27.72 24.985 18.65 135-139 28.675 27.765 24.595 18.965 140-144 30.535 26.76 24.240000000000002 18.465 145-149 31.365 27.005000000000003 23.505000000000003 18.125 150-151 32.8375 25.7375 23.5625 17.8625 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.5 4 0.5 5 0.0 6 0.5 7 0.5 8 0.5 9 0.5 10 0.5 11 0.5 12 0.5 13 0.5 14 0.0 15 0.5 16 0.5 17 0.0 18 0.0 19 0.0 20 1.0 21 1.5 22 1.5 23 1.0 24 0.0 25 2.5 26 3.5 27 4.0 28 7.0 29 12.0 30 14.0 31 16.0 32 26.0 33 31.0 34 36.5 35 58.0 36 76.5 37 97.0 38 132.5 39 164.0 40 192.5 41 219.5 42 245.5 43 265.0 44 282.5 45 284.5 46 267.5 47 258.0 48 232.0 49 195.5 50 163.5 51 149.0 52 122.5 53 93.0 54 86.5 55 68.0 56 45.0 57 35.5 58 30.5 59 22.0 60 14.5 61 8.5 62 6.0 63 4.5 64 3.5 65 1.0 66 3.5 67 3.0 68 0.5 69 0.5 70 0.0 71 0.0 72 0.5 73 0.5 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 0.5 88 1.0 89 0.5 90 0.0 91 0.5 92 0.5 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.5 99 0.5 100 0.0 >>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 82.69999999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 83.88754534461911 69.375 2 12.787182587666262 21.15 3 2.2067714631197095 5.475 4 0.8464328899637243 2.8000000000000003 5 0.21160822249093109 0.8750000000000001 6 0.03022974607013301 0.15 7 0.03022974607013301 0.17500000000000002 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 AATGGTCTCCGTATCTCGAGACCGGACGTCGGGACTAAATTCCTGCTATT 7 0.17500000000000002 No Hit ACCACATATAGAGGGTGTAATAGCTAAGTAGCCTGTAAGAGATGGCTTCC 6 0.15 No Hit GTAATGATGCGTAAGATCTGCATAGAAGATTCTTCGGTGACAGTGTTACA 5 0.125 No Hit CCCCTCCCCCCTCTAATTCCCCGCTTCTCTGAATCCCTTTCTGTCAATCG 5 0.125 No Hit GCCTATCACTTCAAGATGGCAAAAGGGGTTGCTCGGATATCTTCATGCCT 5 0.125 No Hit GGCATAAAGAACACATTGCAGCTTATGGAGAAGGGAATGAGCGGAGACTC 5 0.125 No Hit GTGCATTCTTCTAAGTAAAAGAAATCCCTTAATTTCATCACACTTTCCTT 5 0.125 No Hit CCACAGCTCACCAGGGTACTATGATGGACGCTACTGGACTATGTGGAAGC 5 0.125 No Hit AGCGTATCAAGAGCAGGTTCTTAGTAATTGCTCAAAATTTGCTCAGAGTC 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 0.0 0.0 0.0 0.0 0.0 56-57 0.025 0.0 0.0 0.0 0.0 58-59 0.0625 0.0 0.0 0.0 0.0 60-61 0.0875 0.0 0.0 0.0 0.0 62-63 0.15 0.0 0.0 0.0 0.0 64-65 0.1875 0.0 0.0 0.0 0.0 66-67 0.25 0.0 0.0 0.0 0.0 68-69 0.325 0.0 0.0 0.0 0.0 70-71 0.3375 0.0 0.0 0.0 0.0 72-73 0.5125 0.0 0.0 0.0 0.0 74-75 0.6125 0.0 0.0 0.0 0.0 76-77 0.7 0.0 0.0 0.0 0.0 78-79 0.9375 0.0 0.0 0.0 0.0 80-81 1.2000000000000002 0.0 0.0 0.0 0.0 82-83 1.35 0.0 0.0 0.0 0.0 84-85 1.6625 0.0 0.0 0.0 0.0 86-87 1.9 0.0 0.0 0.0 0.0 88-89 2.1875 0.0 0.0 0.0 0.0 90-91 2.7625 0.0 0.0 0.0 0.0 92-93 3.3125 0.0 0.0 0.0 0.0 94-95 3.9625 0.0 0.0 0.0 0.0 96-97 4.6875 0.0 0.0 0.0 0.0 98-99 5.2125 0.0 0.0 0.0 0.0 100-101 5.9375 0.0 0.0 0.0 0.0 102-103 6.85 0.0 0.0 0.0 0.0 104-105 7.5125 0.0 0.0 0.0 0.0 106-107 8.4 0.0 0.0 0.0 0.0 108-109 9.2125 0.0 0.0 0.0 0.0 110-111 10.25 0.0 0.0 0.0 0.0 112-113 11.2125 0.0 0.0 0.0 0.0 114-115 11.9625 0.0 0.0 0.0 0.0 116-117 12.787500000000001 0.0 0.0 0.0 0.0 118-119 13.9125 0.0 0.0 0.0 0.0 120-121 14.837499999999999 0.0 0.0 0.0 0.0 122-123 15.600000000000001 0.0 0.0 0.0 0.0 124-125 16.700000000000003 0.0 0.0 0.0 0.0 126-127 17.7875 0.0 0.0 0.0 0.0 128-129 18.674999999999997 0.0 0.0 0.0 0.0 130-131 19.4125 0.0 0.0 0.0 0.0 132-133 20.2125 0.0 0.0 0.0 0.0 134-135 21.275 0.0 0.0 0.0 0.0 136-137 22.200000000000003 0.0 0.0 0.0 0.0 138-139 23.1 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CAACACT 10 0.006830828 145.0 8 GGGGGGG 245 3.274181E-11 11.836735 145 >>END_MODULE Read 550691 spots for SRR12670133.sra Written 550691 spots for SRR12670133.sra Read 550691 spots for SRR12670133.sra Written 550691 spots for SRR12670133.sra Read 550691 spots for SRR12670133.sra Written 550691 spots for SRR12670133.sra Read 550691 spots for SRR12670133.sra Written 550691 spots for SRR12670133.sra Read 550691 spots for SRR12670133.sra Written 550691 spots for SRR12670133.sra Read 550691 spots for SRR12670133.sra Written 550691 spots for SRR12670133.sra Read 550691 spots for SRR12670133.sra Written 550691 spots for SRR12670133.sra Read 550691 spots for SRR12670133.sra Written 550691 spots for SRR12670133.sra Read 550691 spots for SRR12670133.sra Written 550691 spots for SRR12670133.sra Read 550691 spots for SRR12670133.sra Written 550691 spots for SRR12670133.sra Read 550691 spots for SRR12670133.sra Written 550691 spots for SRR12670133.sra Read 550691 spots for SRR12670133.sra Written 550691 spots for SRR12670133.sra Read 550691 spots for SRR12670133.sra Written 550691 spots for SRR12670133.sra Read 550691 spots for SRR12670133.sra Written 550691 spots for SRR12670133.sra Read 550691 spots for SRR12670133.sra Written 550691 spots for SRR12670133.sra Read 550691 spots for SRR12670133.sra Written 550691 spots for SRR12670133.sra Read 550691 spots for SRR12670133.sra Written 550691 spots for SRR12670133.sra Read 550691 spots for SRR12670133.sra Written 550691 spots for SRR12670133.sra Read 550703 spots for SRR12670133.sra Written 550703 spots for SRR12670133.sra Read 550691 spots for SRR12670133.sra Written 550691 spots for SRR12670133.sra SRR ids: ['SRR12670133.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_evwhiw3y SRR12670133.sra spots: 11013832 blocks: [[1, 550691], [550692, 1101382], [1101383, 1652073], [1652074, 2202764], [2202765, 2753455], [2753456, 3304146], [3304147, 3854837], [3854838, 4405528], [4405529, 4956219], [4956220, 5506910], [5506911, 6057601], [6057602, 6608292], [6608293, 7158983], [7158984, 7709674], [7709675, 8260365], [8260366, 8811056], [8811057, 9361747], [9361748, 9912438], [9912439, 10463129], [10463130, 11013832]] SRR12670133 file size 3721281 SRR12670133 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 SRR12670133 SRR12670133_1.fastq SRR12670133_2.fastq Input file: SRR12670133_1.fastq Paired file: SRR12670133_2.fastq trimmed: SRR12670133-trimmed-pair1.fastq, SRR12670133-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 00:39:02 2025 >> started Tue Feb 11 00:39:20 2025 >> done (17.949s) 11013832 read pairs processed; of these: 54 ( 0.00%) short read pairs filtered out after trimming by size control 4459 ( 0.04%) empty read pairs filtered out after trimming by size control 11009319 (99.96%) read pairs available; of these: 2977335 (27.04%) trimmed read pairs available after processing 8031984 (72.96%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 1 0.00% 19 6 0.00% 20 8 0.00% 21 2 0.00% 22 5 0.00% 23 14 0.00% 24 20 0.00% 25 39 0.00% 26 26 0.00% 27 26 0.00% 28 26 0.00% 29 39 0.00% 30 41 0.00% 31 68 0.00% 32 50 0.00% 33 69 0.00% 34 46 0.00% 35 85 0.00% 36 87 0.00% 37 105 0.00% 38 104 0.00% 39 141 0.00% 40 134 0.00% 41 137 0.00% 42 174 0.00% 43 160 0.00% 44 187 0.00% 45 194 0.00% 46 266 0.00% 47 294 0.00% 48 303 0.00% 49 404 0.00% 50 494 0.00% 51 560 0.01% 52 598 0.01% 53 612 0.01% 54 642 0.01% 55 683 0.01% 56 771 0.01% 57 839 0.01% 58 1091 0.01% 59 1183 0.01% 60 1425 0.01% 61 1748 0.02% 62 1880 0.02% 63 2072 0.02% 64 2179 0.02% 65 2306 0.02% 66 2523 0.02% 67 2833 0.03% 68 3235 0.03% 69 3633 0.03% 70 4173 0.04% 71 4627 0.04% 72 5464 0.05% 73 6169 0.06% 74 6853 0.06% 75 7332 0.07% 76 7704 0.07% 77 8444 0.08% 78 8726 0.08% 79 9851 0.09% 80 10717 0.10% 81 12101 0.11% 82 13880 0.13% 83 15091 0.14% 84 16538 0.15% 85 17597 0.16% 86 17809 0.16% 87 19167 0.17% 88 20266 0.18% 89 21183 0.19% 90 22679 0.21% 91 24424 0.22% 92 26456 0.24% 93 28450 0.26% 94 30336 0.28% 95 31979 0.29% 96 32225 0.29% 97 32817 0.30% 98 33323 0.30% 99 34066 0.31% 100 35541 0.32% 101 36873 0.33% 102 38308 0.35% 103 40127 0.36% 104 41209 0.37% 105 42593 0.39% 106 42945 0.39% 107 43060 0.39% 108 43094 0.39% 109 43414 0.39% 110 43712 0.40% 111 44056 0.40% 112 45586 0.41% 113 46056 0.42% 114 47365 0.43% 115 48499 0.44% 116 48923 0.44% 117 48391 0.44% 118 48598 0.44% 119 47823 0.43% 120 47981 0.44% 121 48325 0.44% 122 49022 0.45% 123 49554 0.45% 124 50392 0.46% 125 50259 0.46% 126 51261 0.47% 127 51501 0.47% 128 49707 0.45% 129 49043 0.45% 130 49555 0.45% 131 48811 0.44% 132 48529 0.44% 133 49901 0.45% 134 49910 0.45% 135 50420 0.46% 136 50671 0.46% 137 51209 0.47% 138 50167 0.46% 139 50178 0.46% 140 48950 0.44% 141 48144 0.44% 142 48665 0.44% 143 48908 0.44% 144 49556 0.45% 145 49825 0.45% 146 49719 0.45% 147 49346 0.45% 148 49710 0.45% 149 48647 0.44% 150 48281 0.44% 151 8031984 72.96% 11009319 reads passed initial QC criterion=sequence-density sequence-density=0.60 sequence-density-rank=1 fanout-score=2.22 fanout-score-rank=22 prefix-density=0.63 prefix-fanout=2.1 sequence=TGAGATGCCTCAGTGCATCCAAACATGGGTAG criterion=fanout-score sequence-density=0.02 sequence-density-rank=29 fanout-score=200.81 fanout-score-rank=1 prefix-density=0.26 prefix-fanout=13.4 sequence=TGAAGAAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAG criterion=sequence-density sequence-density=0.53 sequence-density-rank=1 fanout-score=2.14 fanout-score-rank=22 prefix-density=0.54 prefix-fanout=2.1 sequence=CTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGGAGTGAACAAACAAAAGTGTCCGTGAGTGTCTTTATCTTTGTGTCTTCTTCA criterion=fanout-score sequence-density=0.01 sequence-density-rank=31 fanout-score=47.56 fanout-score-rank=1 prefix-density=0.05 prefix-fanout=5.7 sequence=AGCAAAACCACATATAGAGGGTGTAATAGCTAAGTAGCCTGTAAGAGATGGCTTCCTCTGTGATTTCATCGGCGGCCGTTGCCACAGTTAACCGCACCCC SRR12670133 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 00:40:03 Started mapping on | Feb 11 00:40:04 Finished on | Feb 11 00:41:16 Mapping speed, Million of reads per hour | 550.47 Number of input reads | 11009319 Average input read length | 284 UNIQUE READS: Uniquely mapped reads number | 10377125 Uniquely mapped reads % | 94.26% Average mapped length | 283.20 Number of splices: Total | 9928670 Number of splices: Annotated (sjdb) | 9733911 Number of splices: GT/AG | 9723048 Number of splices: GC/AG | 172092 Number of splices: AT/AC | 5937 Number of splices: Non-canonical | 27593 Mismatch rate per base, % | 0.33% Deletion rate per base | 0.03% Deletion average length | 2.71 Insertion rate per base | 0.02% Insertion average length | 2.47 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 245984 % of reads mapped to multiple loci | 2.23% Number of reads mapped to too many loci | 21539 % of reads mapped to too many loci | 0.20% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.18% % of reads unmapped: other | 0.14% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 386210 386210 386210 N_multimapping 245984 245984 245984 N_noFeature 314707 10253445 359609 N_ambiguous 138391 380 59423 UnstrandedReadsAssigned:9924027 PositiveStrandReadsAssigned:123300 NegativeStrandReadsAssigned:9958093 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=135 echo kmer=131 SRR12670133 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: SRR12670133-trimmed-pair1.fastq SRR12670133-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 11,009,319 reads, 9,994,398 reads pseudoaligned [quant] estimated average fragment length: 207.312 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,081 rounds 52401 SRR12670133.ke.tsv 34699 SRR12670133.se.tsv 87100 total ==> SRR12670133.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1811.69 302 17.4833 Potri.005G024800.1.v4.1 1035 828.688 70 8.85946 Potri.004G059700.1.v4.1 961 754.739 14 1.9455 Potri.007G009000.2.v4.1 1416 1209.69 0 0 Potri.003G141000.2.v4.1 2943 2736.69 473.418 18.1434 Potri.016G087400.1.v4.1 270 109.79 427 407.911 Potri.015G069301.1.v4.1 564 364.758 0 0 Potri.010G195200.1.v4.1 1773 1566.69 26 1.74057 Potri.012G127500.1.v4.1 977 770.716 33 4.49076 ==> SRR12670133.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 218 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 119 Potri.001G212900.v4.1 1 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 10 Potri.001G416900.v4.1 4 Potri.001G452600.v4.1 4 SRR12670133 completed mapping pipeline successfully