Starting /dee2/code/volunteer_pipeline.sh SRR12671399 current disk space = 3052284608512 free memory = 1471770028 SRR12671399 SRAfilesize a8f567456c0fce8cd380a97d99c4d4c7 SRR12671399.sra SRR12671399.sra file validated SRR12671399 is paired end SRR12671399 is conventional basespace SRR12671399 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12671399_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 36.703 37.0 37.0 37.0 37.0 37.0 2 36.48 37.0 37.0 37.0 37.0 37.0 3 36.679 37.0 37.0 37.0 37.0 37.0 4 36.6745 37.0 37.0 37.0 37.0 37.0 5 36.6525 37.0 37.0 37.0 37.0 37.0 6 36.6325 37.0 37.0 37.0 37.0 37.0 7 36.5765 37.0 37.0 37.0 37.0 37.0 8 36.587 37.0 37.0 37.0 37.0 37.0 9 36.6225 37.0 37.0 37.0 37.0 37.0 10-14 36.6188 37.0 37.0 37.0 37.0 37.0 15-19 36.5648 37.0 37.0 37.0 37.0 37.0 20-24 36.553900000000006 37.0 37.0 37.0 37.0 37.0 25-29 36.508900000000004 37.0 37.0 37.0 37.0 37.0 30-34 36.5118 37.0 37.0 37.0 37.0 37.0 35-39 36.4264 37.0 37.0 37.0 37.0 37.0 40-44 36.373999999999995 37.0 37.0 37.0 37.0 37.0 45-49 36.3491 37.0 37.0 37.0 37.0 37.0 50-54 36.349000000000004 37.0 37.0 37.0 37.0 37.0 55-59 36.3005 37.0 37.0 37.0 37.0 37.0 60-64 36.271100000000004 37.0 37.0 37.0 37.0 37.0 65-69 36.1634 37.0 37.0 37.0 37.0 37.0 70-74 36.218900000000005 37.0 37.0 37.0 37.0 37.0 75-79 36.1879 37.0 37.0 37.0 37.0 37.0 80-84 36.232299999999995 37.0 37.0 37.0 37.0 37.0 85-89 36.1726 37.0 37.0 37.0 37.0 37.0 90-94 36.1362 37.0 37.0 37.0 37.0 37.0 95-99 36.1594 37.0 37.0 37.0 37.0 37.0 100-104 36.1616 37.0 37.0 37.0 37.0 37.0 105-109 36.084500000000006 37.0 37.0 37.0 37.0 37.0 110-114 36.062400000000004 37.0 37.0 37.0 37.0 37.0 115-119 36.0464 37.0 37.0 37.0 37.0 37.0 120-124 36.0376 37.0 37.0 37.0 37.0 37.0 125-129 35.9847 37.0 37.0 37.0 37.0 37.0 130-134 35.94349999999999 37.0 37.0 37.0 37.0 37.0 135-139 35.9277 37.0 37.0 37.0 37.0 37.0 140-144 35.854699999999994 37.0 37.0 37.0 37.0 37.0 145-149 35.8298 37.0 37.0 37.0 37.0 37.0 150-151 35.64575000000001 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 17 1.0 18 0.0 19 2.0 20 1.0 21 6.0 22 2.0 23 7.0 24 5.0 25 7.0 26 8.0 27 8.0 28 9.0 29 14.0 30 25.0 31 33.0 32 44.0 33 69.0 34 122.0 35 241.0 36 2929.0 37 467.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 50.0 12.15 9.0 28.849999999999998 2 21.957936905358036 12.318477716574861 38.23234852278418 27.491236855282924 3 18.125 18.875 31.525 31.474999999999998 4 21.4 25.4 26.424999999999997 26.775 5 22.5 31.674999999999997 26.950000000000003 18.875 6 20.3 34.725 25.900000000000002 19.075 7 13.525 29.825000000000003 43.05 13.600000000000001 8 15.15 28.1 34.35 22.400000000000002 9 16.475 25.0 36.95 21.575 10-14 19.42 32.57 27.63 20.380000000000003 15-19 19.064999999999998 31.165 27.48 22.29 20-24 19.975 30.72 27.134999999999998 22.17 25-29 19.575 30.514999999999997 27.825 22.085 30-34 18.715 30.95 27.639999999999997 22.695 35-39 19.89 30.425 27.250000000000004 22.435 40-44 19.78 30.659999999999997 27.325 22.235 45-49 19.744999999999997 30.435000000000002 26.96 22.86 50-54 20.62 30.11 26.77 22.5 55-59 19.68 30.044999999999998 27.305 22.97 60-64 19.685 29.875 27.6 22.84 65-69 20.025000000000002 31.005 26.88 22.09 70-74 20.7 30.759999999999998 26.075 22.465 75-79 20.45 29.104999999999997 27.694999999999997 22.75 80-84 19.615 29.385 27.415 23.585 85-89 20.3 29.659999999999997 27.310000000000002 22.73 90-94 20.23 29.215000000000003 27.439999999999998 23.115 95-99 20.62 29.494999999999997 27.255000000000003 22.63 100-104 20.560000000000002 30.325000000000003 26.43 22.685 105-109 20.465 29.330000000000002 27.105 23.1 110-114 19.900000000000002 29.330000000000002 27.595 23.175 115-119 21.17 28.83 26.705000000000002 23.294999999999998 120-124 20.195 29.57 26.495 23.74 125-129 20.77 29.37 26.650000000000002 23.21 130-134 20.919999999999998 28.225 26.729999999999997 24.125 135-139 21.04 28.98 26.695 23.285 140-144 21.725 29.005 25.319999999999997 23.95 145-149 21.09 28.735 26.075 24.099999999999998 150-151 21.525 28.5625 25.624999999999996 24.2875 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 1.0 1 1.0 2 1.0 3 1.0 4 0.5 5 0.0 6 1.0 7 2.0 8 2.0 9 1.5 10 1.5 11 2.0 12 1.5 13 2.0 14 2.0 15 1.0 16 1.5 17 1.5 18 2.0 19 3.5 20 5.5 21 4.5 22 2.0 23 5.5 24 7.0 25 8.5 26 13.5 27 15.0 28 21.5 29 30.5 30 39.0 31 50.0 32 65.0 33 84.0 34 98.5 35 120.5 36 135.5 37 147.5 38 171.5 39 187.0 40 187.5 41 201.0 42 209.0 43 186.0 44 173.5 45 199.5 46 217.0 47 201.0 48 183.0 49 170.5 50 157.0 51 137.0 52 114.0 53 101.0 54 93.0 55 66.5 56 45.0 57 36.5 58 25.0 59 11.0 60 7.0 61 5.0 62 1.5 63 5.0 64 5.5 65 6.5 66 7.0 67 3.5 68 1.0 69 0.5 70 0.5 71 0.0 72 0.5 73 0.5 74 0.0 75 0.5 76 0.5 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 0.15 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 82.1 #Duplication Level Percentage of deduplicated Percentage of total 1 83.37393422655298 68.45 2 12.880633373934227 21.15 3 2.8014616321559074 6.9 4 0.6699147381242387 2.1999999999999997 5 0.18270401948842874 0.75 6 0.03045066991473812 0.15 7 0.0 0.0 8 0.06090133982947624 0.4 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 GATCGGAAGAGCACACGTCTGAACTCCAGTCACCCTTGATCATCTCGTAT 8 0.2 TruSeq Adapter, Index 8 (97% over 39bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACCCTTGATCATCGCGTAT 8 0.2 TruSeq Adapter, Index 8 (97% over 39bp) GCCCGATTCAGCATCCGAATCCAGAAGCTAAAAACAAAAACAAAGTAGAA 6 0.15 No Hit CGAATCTCTCGCTAATGCCGAGGGGAAAATACATAAGCATCACAATCCAT 5 0.125 No Hit CATGTAAGTACCACCACCAGCTACAGAGAAGAAAAGGCAACCAACTTCAC 5 0.125 No Hit CTCTTTCTGAGTCTCCAATTTAGCCAGTGCTTCTTGCAAGTCAGCCTCAA 5 0.125 No Hit ATGCTGCCTTCAATTCATCTCTGCGAACAAAATGCTGCTGATCGCCCCTA 5 0.125 No Hit CCTTGAGTGCCTTGTATGCTGTAGGAGGCAGCCTAGTGATGACCGTACCG 5 0.125 No Hit AGCATATTTTCTCTTAGATGTGATCATGCAAGTAGTATGGAGATGTAGAT 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 0.05 0.0 0.0 0.0 0.0 44-45 0.05 0.0 0.0 0.0 0.0 46-47 0.05 0.0 0.0 0.0 0.0 48-49 0.05 0.0 0.0 0.0 0.0 50-51 0.05 0.0 0.0 0.0 0.0 52-53 0.05 0.0 0.0 0.0 0.0 54-55 0.05 0.0 0.0 0.0 0.0 56-57 0.05 0.0 0.0 0.0 0.0 58-59 0.05 0.0 0.0 0.0 0.0 60-61 0.05 0.0 0.0 0.0 0.0 62-63 0.05 0.0 0.0 0.0 0.0 64-65 0.05 0.0 0.0 0.0 0.0 66-67 0.05 0.0 0.0 0.0 0.0 68-69 0.05 0.0 0.0 0.0 0.0 70-71 0.075 0.0 0.0 0.0 0.0 72-73 0.075 0.0 0.0 0.0 0.0 74-75 0.075 0.0 0.0 0.0 0.0 76-77 0.0875 0.0 0.0 0.0 0.0 78-79 0.125 0.0 0.0 0.0 0.0 80-81 0.2375 0.0 0.0 0.0 0.0 82-83 0.275 0.0 0.0 0.0 0.0 84-85 0.30000000000000004 0.0 0.0 0.0 0.0 86-87 0.3875 0.0 0.0 0.0 0.0 88-89 0.44999999999999996 0.0 0.0 0.0 0.0 90-91 0.5 0.0 0.0 0.0 0.0 92-93 0.575 0.0 0.0 0.0 0.0 94-95 0.7749999999999999 0.0 0.0 0.0 0.0 96-97 0.9624999999999999 0.0 0.0 0.0 0.0 98-99 1.1875 0.0 0.0 0.0 0.0 100-101 1.275 0.0 0.0 0.0 0.0 102-103 1.3875 0.0 0.0 0.0 0.0 104-105 1.55 0.0 0.0 0.0 0.0 106-107 1.7625000000000002 0.0 0.0 0.0 0.0 108-109 1.9749999999999999 0.0 0.0 0.0 0.0 110-111 2.4000000000000004 0.0 0.0 0.0 0.0 112-113 2.775 0.0 0.0 0.0 0.0 114-115 2.975 0.0 0.0 0.0 0.0 116-117 3.275 0.0 0.0 0.0 0.0 118-119 3.6 0.0 0.0 0.0 0.0 120-121 3.7875 0.0 0.0 0.0 0.0 122-123 4.1 0.0 0.0 0.0 0.0 124-125 4.5625 0.0 0.0 0.0 0.0 126-127 4.7625 0.0 0.0 0.0 0.0 128-129 5.199999999999999 0.0 0.0 0.0 0.0 130-131 5.5875 0.0 0.0 0.0 0.0 132-133 6.125 0.0 0.0 0.0 0.0 134-135 6.7375 0.0 0.0 0.0 0.0 136-137 7.4625 0.0 0.0 0.0 0.0 138-139 8.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTTTTTT 165 0.0021791477 21.969698 1 >>END_MODULE SRR12671399 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12671399_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 36.4095 37.0 37.0 37.0 37.0 37.0 2 36.2035 37.0 37.0 37.0 37.0 37.0 3 36.255 37.0 37.0 37.0 37.0 37.0 4 36.332 37.0 37.0 37.0 37.0 37.0 5 36.3455 37.0 37.0 37.0 37.0 37.0 6 36.365 37.0 37.0 37.0 37.0 37.0 7 36.2795 37.0 37.0 37.0 37.0 37.0 8 36.2875 37.0 37.0 37.0 37.0 37.0 9 36.2655 37.0 37.0 37.0 37.0 37.0 10-14 36.2866 37.0 37.0 37.0 37.0 37.0 15-19 36.2328 37.0 37.0 37.0 37.0 37.0 20-24 36.2226 37.0 37.0 37.0 37.0 37.0 25-29 36.16 37.0 37.0 37.0 37.0 37.0 30-34 36.0984 37.0 37.0 37.0 37.0 37.0 35-39 36.1734 37.0 37.0 37.0 37.0 37.0 40-44 36.081700000000005 37.0 37.0 37.0 37.0 37.0 45-49 36.1119 37.0 37.0 37.0 37.0 37.0 50-54 36.0942 37.0 37.0 37.0 37.0 37.0 55-59 36.085300000000004 37.0 37.0 37.0 37.0 37.0 60-64 36.124900000000004 37.0 37.0 37.0 37.0 37.0 65-69 36.0794 37.0 37.0 37.0 37.0 37.0 70-74 35.9944 37.0 37.0 37.0 37.0 37.0 75-79 36.0268 37.0 37.0 37.0 37.0 37.0 80-84 35.9771 37.0 37.0 37.0 37.0 37.0 85-89 36.041199999999996 37.0 37.0 37.0 37.0 37.0 90-94 36.012100000000004 37.0 37.0 37.0 37.0 37.0 95-99 36.0394 37.0 37.0 37.0 37.0 37.0 100-104 35.9339 37.0 37.0 37.0 37.0 37.0 105-109 35.88289999999999 37.0 37.0 37.0 37.0 37.0 110-114 35.8554 37.0 37.0 37.0 37.0 37.0 115-119 35.910199999999996 37.0 37.0 37.0 37.0 37.0 120-124 35.869800000000005 37.0 37.0 37.0 37.0 37.0 125-129 35.862199999999994 37.0 37.0 37.0 37.0 37.0 130-134 35.6443 37.0 37.0 37.0 37.0 37.0 135-139 35.6414 37.0 37.0 37.0 37.0 37.0 140-144 35.6297 37.0 37.0 37.0 37.0 37.0 145-149 35.523 37.0 37.0 37.0 37.0 37.0 150-151 35.29275 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 2.0 13 6.0 14 2.0 15 8.0 16 2.0 17 3.0 18 1.0 19 3.0 20 5.0 21 1.0 22 2.0 23 8.0 24 6.0 25 9.0 26 11.0 27 9.0 28 15.0 29 10.0 30 14.0 31 30.0 32 38.0 33 61.0 34 141.0 35 421.0 36 2817.0 37 375.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 46.775 26.724999999999998 7.3 19.2 2 31.2 23.849999999999998 27.650000000000002 17.299999999999997 3 22.275 26.0 35.075 16.650000000000002 4 26.674999999999997 31.374999999999996 24.075 17.875 5 26.275 37.35 20.025000000000002 16.35 6 23.875 38.324999999999996 20.575 17.224999999999998 7 21.75 23.65 36.575 18.025 8 22.15 26.900000000000002 26.875 24.075 9 23.724999999999998 24.8 27.900000000000002 23.575 10-14 24.48 28.655 26.224999999999998 20.64 15-19 24.654999999999998 27.47 27.04 20.835 20-24 23.990000000000002 28.189999999999998 27.01 20.810000000000002 25-29 24.865000000000002 27.815 27.215 20.105 30-34 24.265 27.839999999999996 26.83 21.065 35-39 24.245 27.72 27.115000000000002 20.919999999999998 40-44 23.57 28.055000000000003 27.785 20.59 45-49 23.815 27.950000000000003 27.860000000000003 20.375 50-54 23.7 27.04 28.32 20.94 55-59 24.125 28.155 27.11 20.61 60-64 23.745 28.035 27.215 21.005 65-69 24.015 27.405 28.194999999999997 20.385 70-74 23.855 27.48 27.48 21.185000000000002 75-79 23.865 27.73 27.650000000000002 20.755000000000003 80-84 23.315 27.950000000000003 27.644999999999996 21.09 85-89 23.935000000000002 28.01 27.639999999999997 20.415 90-94 24.295 28.01 27.3 20.395 95-99 23.615 27.6 27.889999999999997 20.895 100-104 24.33 27.965 27.189999999999998 20.515 105-109 22.945 27.83 27.994999999999997 21.23 110-114 24.465 27.794999999999998 27.439999999999998 20.3 115-119 24.529999999999998 27.73 27.384999999999998 20.355 120-124 24.25 28.1 27.21 20.44 125-129 24.775 27.46 27.884999999999998 19.88 130-134 24.695 28.215 27.18 19.91 135-139 24.645 27.735 27.595 20.025000000000002 140-144 25.119999999999997 28.475 26.669999999999998 19.735 145-149 25.802580258025802 27.532753275327533 27.38773877387739 19.276927692769277 150-151 25.1 26.8125 28.125 19.9625 >>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 1.0 6 1.0 7 0.0 8 1.0 9 1.5 10 1.5 11 2.0 12 1.5 13 1.0 14 0.5 15 0.0 16 1.0 17 1.5 18 2.0 19 2.0 20 0.5 21 1.0 22 2.0 23 1.5 24 3.0 25 5.0 26 3.0 27 3.0 28 4.5 29 9.5 30 15.0 31 18.0 32 27.5 33 35.0 34 47.0 35 62.5 36 70.5 37 94.0 38 124.5 39 156.5 40 193.5 41 201.0 42 226.5 43 269.0 44 265.0 45 250.0 46 245.5 47 234.5 48 219.0 49 207.5 50 182.0 51 152.0 52 140.0 53 104.0 54 82.5 55 81.0 56 57.5 57 43.5 58 37.5 59 27.5 60 17.0 61 11.5 62 7.0 63 6.5 64 7.5 65 4.0 66 0.5 67 1.0 68 1.5 69 0.5 70 0.0 71 0.5 72 0.5 73 0.0 74 0.0 75 0.0 76 0.0 77 0.5 78 1.0 79 0.5 80 0.0 81 0.5 82 0.5 83 0.0 84 0.5 85 1.5 86 2.0 87 1.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.5 94 0.5 95 0.5 96 2.0 97 2.5 98 2.0 99 2.5 100 2.5 >>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 0.01 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 82.72500000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 84.22484134179511 69.675 2 12.360229676639468 20.45 3 2.4176488365064976 6.0 4 0.543970988213962 1.7999999999999998 5 0.271985494106981 1.125 6 0.12088244182532487 0.6 7 0.060441220912662436 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 CAGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTA 7 0.17500000000000002 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 7 0.17500000000000002 No Hit GGGAAATGGAGCCCTGGGTGCTCGTATGGATTTCATTGGTTCGCCCACAA 6 0.15 No Hit GTGGAAACTACCCATGTTTGGATGCACTGAGGCATCTCAGGTGCTGATTG 6 0.15 No Hit AGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAA 6 0.15 No Hit GCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCCTCCTATG 6 0.15 No Hit AAGCAATAATGGCTTGTTCGGCCAGGCAGCCGGTTTGCTAGGACTAAGCT 5 0.125 No Hit AGAGGTAGGAATGGGAGTATTTGCACTTGTGGTAACGGTATTTGCATTAT 5 0.125 No Hit TATTCATCACCTTGATAGCACTCCCTCACATGACAATACGGGATGTTATA 5 0.125 No Hit ACAACAAACCCTTTTCTTGTTTCCTCTCCTCTCCTCTTTTTCTCTAACAA 5 0.125 No Hit GCCATGTACATGAAACTTACGGTCAAGCAGCCTGGACTCGAGATGTCTAC 5 0.125 No Hit GCCATTCAAATGTTCTAATAGGTTAGTAAATAGGATGGCTCCTAAAATCC 5 0.125 No Hit ATGGCGCTGAATTGGATGGCAGAGCAATTCGAGTCTCAGTTGCAGAAGCT 5 0.125 No Hit ACATCTGAAGAAGTTAAGCAACTTGAAGAACAGGCTGCTGCTGTTATGAG 5 0.125 No Hit CGAAAAAGAAAAAAAACTAAAATCAACTGCTTGCTGTGTTTTTGGGTTTA 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 0.05 0.0 0.0 0.0 0.0 44-45 0.05 0.0 0.0 0.0 0.0 46-47 0.05 0.0 0.0 0.0 0.0 48-49 0.05 0.0 0.0 0.0 0.0 50-51 0.05 0.0 0.0 0.0 0.0 52-53 0.05 0.0 0.0 0.0 0.0 54-55 0.05 0.0 0.0 0.0 0.0 56-57 0.05 0.0 0.0 0.0 0.0 58-59 0.05 0.0 0.0 0.0 0.0 60-61 0.05 0.0 0.0 0.0 0.0 62-63 0.05 0.0 0.0 0.0 0.0 64-65 0.05 0.0 0.0 0.0 0.0 66-67 0.05 0.0 0.0 0.0 0.0 68-69 0.05 0.0 0.0 0.0 0.0 70-71 0.075 0.0 0.0 0.0 0.0 72-73 0.075 0.0 0.0 0.0 0.0 74-75 0.075 0.0 0.0 0.0 0.0 76-77 0.0875 0.0 0.0 0.0 0.0 78-79 0.125 0.0 0.0 0.0 0.0 80-81 0.2375 0.0 0.0 0.0 0.0 82-83 0.275 0.0 0.0 0.0 0.0 84-85 0.30000000000000004 0.0 0.0 0.0 0.0 86-87 0.3875 0.0 0.0 0.0 0.0 88-89 0.44999999999999996 0.0 0.0 0.0 0.0 90-91 0.5 0.0 0.0 0.0 0.0 92-93 0.575 0.0 0.0 0.0 0.0 94-95 0.7749999999999999 0.0 0.0 0.0 0.0 96-97 0.9624999999999999 0.0 0.0 0.0 0.0 98-99 1.1875 0.0 0.0 0.0 0.0 100-101 1.275 0.0 0.0 0.0 0.0 102-103 1.4 0.0 0.0 0.0 0.0 104-105 1.575 0.0 0.0 0.0 0.0 106-107 1.7875 0.0 0.0 0.0 0.0 108-109 2.0 0.0 0.0 0.0 0.0 110-111 2.45 0.0 0.0 0.0 0.0 112-113 2.825 0.0 0.0 0.0 0.0 114-115 3.025 0.0 0.0 0.0 0.0 116-117 3.3625 0.0 0.0 0.0 0.0 118-119 3.7 0.0 0.0 0.0 0.0 120-121 3.8875 0.0 0.0 0.0 0.0 122-123 4.2 0.0 0.0 0.0 0.0 124-125 4.6625 0.0 0.0 0.0 0.0 126-127 4.8625 0.0 0.0 0.0 0.0 128-129 5.324999999999999 0.0 0.0 0.0 0.0 130-131 5.7125 0.0 0.0 0.0 0.0 132-133 6.25 0.0 0.0 0.0 0.0 134-135 6.8625 0.0 0.0 0.0 0.0 136-137 7.6125 0.0 0.0 0.0 0.0 138-139 8.1375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 767826 spots for SRR12671399.sra Written 767826 spots for SRR12671399.sra Read 767826 spots for SRR12671399.sra Written 767826 spots for SRR12671399.sra Read 767826 spots for SRR12671399.sra Written 767826 spots for SRR12671399.sra Read 767826 spots for SRR12671399.sra Written 767826 spots for SRR12671399.sra Read 767828 spots for SRR12671399.sra Written 767828 spots for SRR12671399.sra Read 767826 spots for SRR12671399.sra Written 767826 spots for SRR12671399.sra Read 767826 spots for SRR12671399.sra Written 767826 spots for SRR12671399.sra Read 767826 spots for SRR12671399.sra Written 767826 spots for SRR12671399.sra Read 767826 spots for SRR12671399.sra Written 767826 spots for SRR12671399.sra Read 767826 spots for SRR12671399.sra Written 767826 spots for SRR12671399.sra Read 767826 spots for SRR12671399.sra Written 767826 spots for SRR12671399.sra Read 767826 spots for SRR12671399.sra Written 767826 spots for SRR12671399.sra Read 767826 spots for SRR12671399.sra Written 767826 spots for SRR12671399.sra Read 767826 spots for SRR12671399.sra Written 767826 spots for SRR12671399.sra Read 767826 spots for SRR12671399.sra Written 767826 spots for SRR12671399.sra Read 767826 spots for SRR12671399.sra Written 767826 spots for SRR12671399.sra Read 767826 spots for SRR12671399.sra Written 767826 spots for SRR12671399.sra Read 767826 spots for SRR12671399.sra Written 767826 spots for SRR12671399.sra Read 767826 spots for SRR12671399.sra Written 767826 spots for SRR12671399.sra Read 767826 spots for SRR12671399.sra Written 767826 spots for SRR12671399.sra SRR ids: ['SRR12671399.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_weljr2h_ SRR12671399.sra spots: 15356522 blocks: [[1, 767826], [767827, 1535652], [1535653, 2303478], [2303479, 3071304], [3071305, 3839130], [3839131, 4606956], [4606957, 5374782], [5374783, 6142608], [6142609, 6910434], [6910435, 7678260], [7678261, 8446086], [8446087, 9213912], [9213913, 9981738], [9981739, 10749564], [10749565, 11517390], [11517391, 12285216], [12285217, 13053042], [13053043, 13820868], [13820869, 14588694], [14588695, 15356522]] SRR12671399 file size 5197117 SRR12671399 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 SRR12671399 SRR12671399_1.fastq SRR12671399_2.fastq Input file: SRR12671399_1.fastq Paired file: SRR12671399_2.fastq trimmed: SRR12671399-trimmed-pair1.fastq, SRR12671399-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 22:28:47 2025 >> started Tue Feb 11 22:29:04 2025 >> done (17.192s) 15356522 read pairs processed; of these: 97 ( 0.00%) short read pairs filtered out after trimming by size control 53107 ( 0.35%) empty read pairs filtered out after trimming by size control 15303318 (99.65%) read pairs available; of these: 1556841 (10.17%) trimmed read pairs available after processing 13746477 (89.83%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 13 0.00% 19 19 0.00% 20 16 0.00% 21 31 0.00% 22 21 0.00% 23 32 0.00% 24 45 0.00% 25 42 0.00% 26 74 0.00% 27 54 0.00% 28 73 0.00% 29 67 0.00% 30 69 0.00% 31 46 0.00% 32 56 0.00% 33 74 0.00% 34 58 0.00% 35 82 0.00% 36 60 0.00% 37 52 0.00% 38 67 0.00% 39 117 0.00% 40 86 0.00% 41 74 0.00% 42 98 0.00% 43 79 0.00% 44 85 0.00% 45 82 0.00% 46 117 0.00% 47 127 0.00% 48 119 0.00% 49 169 0.00% 50 179 0.00% 51 200 0.00% 52 192 0.00% 53 225 0.00% 54 246 0.00% 55 243 0.00% 56 272 0.00% 57 340 0.00% 58 380 0.00% 59 414 0.00% 60 524 0.00% 61 589 0.00% 62 674 0.00% 63 773 0.01% 64 827 0.01% 65 768 0.01% 66 940 0.01% 67 1067 0.01% 68 1180 0.01% 69 1370 0.01% 70 1592 0.01% 71 1698 0.01% 72 1942 0.01% 73 2254 0.01% 74 2337 0.02% 75 2581 0.02% 76 2774 0.02% 77 3103 0.02% 78 3509 0.02% 79 3649 0.02% 80 3879 0.03% 81 4539 0.03% 82 5039 0.03% 83 5793 0.04% 84 6242 0.04% 85 6493 0.04% 86 6998 0.05% 87 7287 0.05% 88 7696 0.05% 89 7943 0.05% 90 8498 0.06% 91 9191 0.06% 92 9667 0.06% 93 10479 0.07% 94 11037 0.07% 95 11650 0.08% 96 12319 0.08% 97 12702 0.08% 98 12503 0.08% 99 13306 0.09% 100 13734 0.09% 101 13869 0.09% 102 14881 0.10% 103 15238 0.10% 104 16228 0.11% 105 16748 0.11% 106 17342 0.11% 107 17846 0.12% 108 18024 0.12% 109 18091 0.12% 110 18839 0.12% 111 19445 0.13% 112 19822 0.13% 113 20068 0.13% 114 21082 0.14% 115 22143 0.14% 116 22710 0.15% 117 23120 0.15% 118 22862 0.15% 119 23321 0.15% 120 23945 0.16% 121 23977 0.16% 122 24676 0.16% 123 24800 0.16% 124 26383 0.17% 125 26748 0.17% 126 27421 0.18% 127 27923 0.18% 128 28428 0.19% 129 28514 0.19% 130 28899 0.19% 131 28480 0.19% 132 29066 0.19% 133 30121 0.20% 134 30790 0.20% 135 31456 0.21% 136 32019 0.21% 137 32439 0.21% 138 33202 0.22% 139 33759 0.22% 140 33624 0.22% 141 33461 0.22% 142 34145 0.22% 143 34521 0.23% 144 35051 0.23% 145 35850 0.23% 146 36349 0.24% 147 36935 0.24% 148 38441 0.25% 149 38352 0.25% 150 39346 0.26% 151 13746477 89.83% 15303318 reads passed initial QC criterion=sequence-density sequence-density=0.62 sequence-density-rank=1 fanout-score=2.47 fanout-score-rank=16 prefix-density=0.68 prefix-fanout=2.3 sequence=CACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAGGTGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGGAGTATGAATGTGTTCTCTG criterion=fanout-score sequence-density=0.02 sequence-density-rank=31 fanout-score=21.95 fanout-score-rank=1 prefix-density=0.07 prefix-fanout=5.9 sequence=GTTTCATCAATGGCACTCTCTCACAGCCAATAACTTCAACAACTTCCCTATCTTTAATCCTCTCACTCCACAAATTCATAAGCTTCACCATTTTACTTCACCAATTCCTTAGAGATGTAATAGCCCATAACAATAGGAAATATCAGAAATCCAATAAGAATCAGCAATTCAGGAAGAAATATGACAAGGAGTAGTAGTGTGGATGTTGTTGTTAGACACTTCTTTTTGTCTTTAAATATAAGGCGTGGTAGAATTACTGGCACTCCAATGATTCCATATAACGGCCATAATGGAGCTATAGAATACAACACCAACGTCGCAAAAAACCAGCAAAAATTCTTAACATTATTTTTAGAAATCCCATACTGCCACCGAATATTCAGTCCTTTAAGAAATCGAACAGCATACCCAACATAGTAAAAACCA criterion=sequence-density sequence-density=0.53 sequence-density-rank=1 fanout-score=2.75 fanout-score-rank=18 prefix-density=0.57 prefix-fanout=2.6 sequence=TGCAAGTGCGGCAG criterion=fanout-score sequence-density=0.01 sequence-density-rank=31 fanout-score=55.49 fanout-score-rank=1 prefix-density=0.08 prefix-fanout=7.0 sequence=CAAAACCACATATAGAGGGTGTAATAGCTAAGTAGCCTGTAAGAGATGGCTTCCTCTGTGATTTCATCGGCGGCCGTTGCCACAGTTAACCGCACCCCGGCACAGGCCAACATGGTTGCACCATTCAACGGCCTCAAGTCTACCTCAGCTTTCCCGGTCACCAGAAAGGCTAACAATGACATTACTTCCATTGCAAGCAATGGCGGAAGAGTTCAATGCATGCAGGTGTGGCCTCCAACTGGATTGAAGAAGTTCGAGACTCTTTCTTACCTTCCAGATCTCAC SRR12671399 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 22:29:52 Started mapping on | Feb 11 22:29:53 Finished on | Feb 11 22:33:10 Mapping speed, Million of reads per hour | 279.65 Number of input reads | 15303318 Average input read length | 296 UNIQUE READS: Uniquely mapped reads number | 13493020 Uniquely mapped reads % | 88.17% Average mapped length | 294.49 Number of splices: Total | 10529720 Number of splices: Annotated (sjdb) | 10307946 Number of splices: GT/AG | 10282457 Number of splices: GC/AG | 200886 Number of splices: AT/AC | 8146 Number of splices: Non-canonical | 38231 Mismatch rate per base, % | 0.37% Deletion rate per base | 0.04% Deletion average length | 2.99 Insertion rate per base | 0.03% Insertion average length | 2.16 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 361304 % of reads mapped to multiple loci | 2.36% Number of reads mapped to too many loci | 31593 % of reads mapped to too many loci | 0.21% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 9.07% % of reads unmapped: other | 0.19% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1448994 1448994 1448994 N_multimapping 361304 361304 361304 N_noFeature 367303 13129060 461509 N_ambiguous 373447 1222 103183 UnstrandedReadsAssigned:12752270 PositiveStrandReadsAssigned:362738 NegativeStrandReadsAssigned:12928328 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12671399 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: SRR12671399-trimmed-pair1.fastq SRR12671399-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 15,303,318 reads, 12,936,991 reads pseudoaligned [quant] estimated average fragment length: 249.155 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,258 rounds 52401 SRR12671399.ke.tsv 34699 SRR12671399.se.tsv 87100 total ==> SRR12671399.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1769.85 627 20.3225 Potri.005G024800.1.v4.1 1035 786.845 165 12.0293 Potri.004G059700.1.v4.1 961 712.875 0 0 Potri.007G009000.2.v4.1 1416 1167.85 0 0 Potri.003G141000.2.v4.1 2943 2694.85 790 16.8166 Potri.016G087400.1.v4.1 270 81.6485 769 540.285 Potri.015G069301.1.v4.1 564 321.608 0 0 Potri.010G195200.1.v4.1 1773 1524.85 140 5.2668 Potri.012G127500.1.v4.1 977 728.865 92 7.24077 ==> SRR12671399.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 45 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 411 Potri.001G212900.v4.1 54 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 3 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 0 SRR12671399 completed mapping pipeline successfully