Starting /dee2/code/volunteer_pipeline.sh SRR12455400 current disk space = 1524497281024 free memory = 1552956076 SRR12455400 SRAfilesize b5c70751b6bd7ffc0501bc47ad54f644 SRR12455400.sra SRR12455400.sra file validated SRR12455400 is paired end SRR12455400 is conventional basespace SRR12455400 read1 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12455400_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 150 %GC 53 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.483 37.0 37.0 37.0 37.0 37.0 2 35.90775 37.0 37.0 37.0 37.0 37.0 3 36.0745 37.0 37.0 37.0 37.0 37.0 4 36.1235 37.0 37.0 37.0 37.0 37.0 5 36.038 37.0 37.0 37.0 37.0 37.0 6 36.0615 37.0 37.0 37.0 37.0 37.0 7 35.8825 37.0 37.0 37.0 37.0 37.0 8 36.087 37.0 37.0 37.0 37.0 37.0 9 36.083 37.0 37.0 37.0 37.0 37.0 10-14 36.2174 37.0 37.0 37.0 37.0 37.0 15-19 36.1923 37.0 37.0 37.0 37.0 37.0 20-24 36.1165 37.0 37.0 37.0 37.0 37.0 25-29 36.0713 37.0 37.0 37.0 37.0 37.0 30-34 36.06510000000001 37.0 37.0 37.0 37.0 37.0 35-39 35.974000000000004 37.0 37.0 37.0 37.0 37.0 40-44 35.984700000000004 37.0 37.0 37.0 37.0 37.0 45-49 35.9199 37.0 37.0 37.0 37.0 37.0 50-54 35.9507 37.0 37.0 37.0 37.0 37.0 55-59 35.9488 37.0 37.0 37.0 37.0 37.0 60-64 35.926100000000005 37.0 37.0 37.0 37.0 37.0 65-69 35.874100000000006 37.0 37.0 37.0 37.0 37.0 70-74 35.8591 37.0 37.0 37.0 37.0 37.0 75-79 35.8437 37.0 37.0 37.0 37.0 37.0 80-84 35.802800000000005 37.0 37.0 37.0 37.0 37.0 85-89 35.785000000000004 37.0 37.0 37.0 37.0 37.0 90-94 35.7451 37.0 37.0 37.0 37.0 37.0 95-99 35.7307 37.0 37.0 37.0 37.0 37.0 100-104 35.6877 37.0 37.0 37.0 37.0 37.0 105-109 35.6738 37.0 37.0 37.0 37.0 37.0 110-114 35.64640000000001 37.0 37.0 37.0 37.0 37.0 115-119 35.6211 37.0 37.0 37.0 37.0 37.0 120-124 35.6114 37.0 37.0 37.0 37.0 37.0 125-129 35.6019 37.0 37.0 37.0 37.0 37.0 130-134 35.3865 37.0 37.0 37.0 37.0 37.0 135-139 35.3984 37.0 37.0 37.0 37.0 37.0 140-144 35.413799999999995 37.0 37.0 37.0 37.0 37.0 145-149 35.301700000000004 37.0 37.0 37.0 34.6 37.0 150 35.5005 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 1.0 22 1.0 23 2.0 24 4.0 25 6.0 26 14.0 27 19.0 28 24.0 29 46.0 30 50.0 31 78.0 32 129.0 33 137.0 34 188.0 35 409.0 36 2480.0 37 412.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 29.625 14.025000000000002 10.975 45.375 2 26.481620405101275 21.75543885971493 31.957989497374346 19.80495123780945 3 24.325 25.474999999999998 20.474999999999998 29.725 4 28.325 29.275000000000002 17.474999999999998 24.925 5 27.125 31.525 19.15 22.2 6 21.9 33.175 22.05 22.875 7 20.175 15.975 38.4 25.45 8 21.45 19.975 26.224999999999998 32.35 9 23.575 19.175 28.349999999999998 28.9 10-14 24.85 25.75 22.725 26.674999999999997 15-19 25.91 24.075 23.365 26.650000000000002 20-24 25.55 24.04 23.29 27.12 25-29 26.265 23.82 23.235 26.68 30-34 25.590000000000003 24.404999999999998 23.535 26.47 35-39 25.779999999999998 23.630000000000003 23.369999999999997 27.22 40-44 25.64 23.07 23.655 27.634999999999998 45-49 26.8 22.905 23.35 26.945000000000004 50-54 26.290000000000003 23.885 22.814999999999998 27.01 55-59 25.895000000000003 23.805 22.869999999999997 27.43 60-64 26.724999999999998 23.119999999999997 23.39 26.765 65-69 26.595000000000002 23.87 22.775000000000002 26.76 70-74 26.68 23.525 22.345000000000002 27.450000000000003 75-79 26.705000000000002 23.375 22.6 27.32 80-84 26.985 23.34 22.384999999999998 27.29 85-89 26.825 23.215 22.264999999999997 27.694999999999997 90-94 27.005000000000003 23.385 22.23 27.38 95-99 27.034999999999997 23.395 22.485 27.084999999999997 100-104 26.72 22.98 22.814999999999998 27.485 105-109 27.26 23.485 21.7 27.555000000000003 110-114 27.38 23.535 21.765 27.32 115-119 26.87 23.23 22.105 27.794999999999998 120-124 26.979999999999997 23.935000000000002 21.634999999999998 27.450000000000003 125-129 27.05 23.330000000000002 22.425 27.195000000000004 130-134 26.995 23.150000000000002 22.86 26.995 135-139 26.855 23.46 22.25 27.435 140-144 27.38 22.595000000000002 22.405 27.62 145-149 26.575 22.905 23.05 27.47 150 27.775 21.65 23.025000000000002 27.55 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 1.0 1 1.0 2 0.5 3 0.0 4 0.0 5 0.0 6 0.5 7 0.5 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 0.5 21 1.5 22 1.0 23 0.0 24 0.5 25 1.0 26 1.0 27 1.5 28 4.0 29 4.0 30 6.0 31 10.0 32 10.5 33 11.5 34 19.5 35 30.0 36 37.0 37 52.0 38 61.0 39 66.5 40 88.5 41 115.0 42 138.0 43 150.5 44 135.0 45 125.5 46 142.5 47 145.5 48 138.0 49 135.0 50 135.0 51 125.0 52 116.0 53 124.5 54 122.0 55 104.5 56 99.0 57 98.5 58 89.5 59 83.0 60 80.5 61 83.5 62 83.0 63 83.5 64 86.5 65 86.0 66 87.0 67 78.0 68 79.0 69 79.0 70 66.0 71 69.0 72 64.5 73 53.0 74 47.5 75 40.0 76 31.0 77 22.5 78 16.0 79 10.0 80 8.0 81 6.0 82 4.0 83 2.0 84 0.5 85 1.0 86 0.5 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 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 0.025 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 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 87.075 #Duplication Level Percentage of deduplicated Percentage of total 1 87.19494688486937 75.925 2 11.13982199253517 19.400000000000002 3 1.3781223083548666 3.5999999999999996 4 0.22968705139247778 0.8 5 0.028710881424059722 0.125 6 0.028710881424059722 0.15 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 CAAGGATTGACAGACTGAGAGCTCTTTCTTGATTCTATGGGTGGTGGTGC 6 0.15 No Hit ATCCAGAGCGATGGCTTGCTTTGAGCACTCTAATTTCTTCAAAGTAACGA 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #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 0.025 0.0 0.0 0.0 0.0 9 0.025 0.0 0.0 0.0 0.0 10-11 0.025 0.0 0.0 0.0 0.0 12-13 0.05 0.0 0.0 0.0 0.0 14-15 0.075 0.0 0.0 0.0 0.0 16-17 0.075 0.0 0.0 0.0 0.0 18-19 0.075 0.0 0.0 0.0 0.0 20-21 0.075 0.0 0.0 0.0 0.0 22-23 0.075 0.0 0.0 0.0 0.0 24-25 0.075 0.0 0.0 0.0 0.0 26-27 0.075 0.0 0.0 0.0 0.0 28-29 0.075 0.0 0.0 0.0 0.0 30-31 0.075 0.0 0.0 0.0 0.0 32-33 0.075 0.0 0.0 0.0 0.0 34-35 0.075 0.0 0.0 0.0 0.0 36-37 0.075 0.0 0.0 0.0 0.0 38-39 0.075 0.0 0.0 0.0 0.0 40-41 0.075 0.0 0.0 0.0 0.0 42-43 0.075 0.0 0.0 0.0 0.0 44-45 0.075 0.0 0.0 0.0 0.0 46-47 0.075 0.0 0.0 0.0 0.0 48-49 0.075 0.0 0.0 0.0 0.0 50-51 0.075 0.0 0.0 0.0 0.0 52-53 0.075 0.0 0.0 0.0 0.0 54-55 0.075 0.0 0.0 0.0 0.0 56-57 0.075 0.0 0.0 0.0 0.0 58-59 0.075 0.0 0.0 0.0 0.0 60-61 0.075 0.0 0.0 0.0 0.0 62-63 0.075 0.0 0.0 0.0 0.0 64-65 0.075 0.0 0.0 0.0 0.0 66-67 0.075 0.0 0.0 0.0 0.0 68-69 0.075 0.0 0.0 0.0 0.0 70-71 0.075 0.0 0.0 0.0 0.0 72-73 0.1 0.0 0.0 0.0 0.0 74-75 0.1 0.0 0.0 0.0 0.0 76-77 0.1 0.0 0.0 0.0 0.0 78-79 0.1 0.0 0.0 0.0 0.0 80-81 0.125 0.0 0.0 0.0 0.0 82-83 0.125 0.0 0.0 0.0 0.0 84-85 0.125 0.0 0.0 0.0 0.0 86-87 0.15 0.0 0.0 0.0 0.0 88-89 0.16249999999999998 0.0 0.0 0.0 0.0 90-91 0.175 0.0 0.0 0.0 0.0 92-93 0.225 0.0 0.0 0.0 0.0 94-95 0.2625 0.0 0.0 0.0 0.0 96-97 0.3125 0.0 0.0 0.0 0.0 98-99 0.325 0.0 0.0 0.0 0.0 100-101 0.35 0.0 0.0 0.0 0.0 102-103 0.4 0.0 0.0 0.0 0.0 104-105 0.5125 0.0 0.0 0.0 0.0 106-107 0.6125 0.0 0.0 0.0 0.0 108-109 0.65 0.0 0.0 0.0 0.0 110-111 0.7 0.0 0.0 0.0 0.0 112-113 0.7625 0.0 0.0 0.0 0.0 114-115 0.7875000000000001 0.0 0.0 0.0 0.0 116-117 0.825 0.0 0.0 0.0 0.0 118-119 0.8374999999999999 0.0 0.0 0.0 0.0 120-121 0.95 0.0 0.0 0.0 0.0 122-123 1.0625 0.0 0.0 0.0 0.0 124-125 1.125 0.0 0.0 0.0 0.0 126-127 1.1625 0.0 0.0 0.0 0.0 128-129 1.2125 0.0 0.0 0.0 0.0 130-131 1.3 0.0 0.0 0.0 0.0 132-133 1.4 0.0 0.0 0.0 0.0 134-135 1.5125 0.0 0.0 0.0 0.0 136-137 1.525 0.0 0.0 0.0 0.0 138 1.55 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CACACTC 10 0.006973645 144.0 7 AAACACA 10 0.006973645 144.0 4 ACACTCA 10 0.006973645 144.0 8 ACACACT 10 0.006973645 144.0 6 TCAAACA 10 0.006973645 144.0 2 CGAATTG 10 0.006973645 144.0 3 CACTCAT 10 0.006973645 144.0 9 CAAACAC 10 0.006973645 144.0 3 >>END_MODULE SRR12455400 read2 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12455400_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 150 %GC 53 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.7705 37.0 37.0 37.0 37.0 37.0 2 35.6395 37.0 37.0 37.0 37.0 37.0 3 35.8035 37.0 37.0 37.0 37.0 37.0 4 35.733 37.0 37.0 37.0 37.0 37.0 5 35.7945 37.0 37.0 37.0 37.0 37.0 6 35.8415 37.0 37.0 37.0 37.0 37.0 7 35.811 37.0 37.0 37.0 37.0 37.0 8 35.8135 37.0 37.0 37.0 37.0 37.0 9 35.8155 37.0 37.0 37.0 37.0 37.0 10-14 35.8132 37.0 37.0 37.0 37.0 37.0 15-19 35.8462 37.0 37.0 37.0 37.0 37.0 20-24 35.8678 37.0 37.0 37.0 37.0 37.0 25-29 35.808299999999996 37.0 37.0 37.0 37.0 37.0 30-34 35.7954 37.0 37.0 37.0 37.0 37.0 35-39 35.7921 37.0 37.0 37.0 37.0 37.0 40-44 35.7702 37.0 37.0 37.0 37.0 37.0 45-49 35.7053 37.0 37.0 37.0 37.0 37.0 50-54 35.6856 37.0 37.0 37.0 37.0 37.0 55-59 35.694100000000006 37.0 37.0 37.0 37.0 37.0 60-64 35.6962 37.0 37.0 37.0 37.0 37.0 65-69 35.659000000000006 37.0 37.0 37.0 37.0 37.0 70-74 35.575900000000004 37.0 37.0 37.0 37.0 37.0 75-79 35.5722 37.0 37.0 37.0 37.0 37.0 80-84 35.585899999999995 37.0 37.0 37.0 37.0 37.0 85-89 35.548199999999994 37.0 37.0 37.0 37.0 37.0 90-94 35.4696 37.0 37.0 37.0 37.0 37.0 95-99 35.5932 37.0 37.0 37.0 37.0 37.0 100-104 35.475199999999994 37.0 37.0 37.0 37.0 37.0 105-109 35.5282 37.0 37.0 37.0 37.0 37.0 110-114 35.4478 37.0 37.0 37.0 37.0 37.0 115-119 35.43919999999999 37.0 37.0 37.0 37.0 37.0 120-124 35.3481 37.0 37.0 37.0 34.6 37.0 125-129 35.2556 37.0 37.0 37.0 32.2 37.0 130-134 35.261799999999994 37.0 37.0 37.0 29.8 37.0 135-139 35.0597 37.0 37.0 37.0 27.4 37.0 140-144 35.2534 37.0 37.0 37.0 32.2 37.0 145-149 35.2091 37.0 37.0 37.0 27.4 37.0 150 35.097 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 18 1.0 19 1.0 20 2.0 21 2.0 22 6.0 23 5.0 24 10.0 25 13.0 26 26.0 27 34.0 28 30.0 29 37.0 30 61.0 31 72.0 32 90.0 33 129.0 34 234.0 35 566.0 36 2468.0 37 213.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 30.475 14.374999999999998 12.725 42.425000000000004 2 26.6 21.625 30.75 21.025 3 25.3 24.525 21.775 28.4 4 27.35 28.475 17.549999999999997 26.625 5 26.625 30.75 20.549999999999997 22.075 6 21.45 33.45 21.575 23.525 7 20.974999999999998 16.8 35.775 26.450000000000003 8 19.725 20.125 27.075 33.074999999999996 9 22.6 20.3 27.55 29.549999999999997 10-14 24.205 25.290000000000003 23.26 27.245 15-19 25.430000000000003 23.98 23.24 27.35 20-24 26.090000000000003 24.035 22.925 26.950000000000003 25-29 25.055 24.55 22.814999999999998 27.58 30-34 25.505 24.45 23.150000000000002 26.895000000000003 35-39 26.005 23.71 23.355 26.93 40-44 26.365 23.925 22.86 26.85 45-49 25.945 23.555 23.155 27.345000000000002 50-54 26.474999999999998 23.145 22.615 27.765 55-59 26.395000000000003 23.075000000000003 23.23 27.3 60-64 26.69 22.650000000000002 23.435 27.224999999999998 65-69 26.575 23.630000000000003 22.625 27.169999999999998 70-74 27.36 23.03 22.495 27.115000000000002 75-79 26.75 23.46 22.395 27.395000000000003 80-84 26.495 23.580000000000002 22.755 27.169999999999998 85-89 26.855 23.5 22.720000000000002 26.924999999999997 90-94 26.545 23.515 22.685 27.255000000000003 95-99 27.49 23.435 22.655 26.419999999999998 100-104 26.77 23.57 22.685 26.974999999999998 105-109 27.08 23.285 22.71 26.924999999999997 110-114 27.134999999999998 23.015 22.575 27.275 115-119 26.790000000000003 22.79 22.814999999999998 27.605 120-124 27.73 22.759999999999998 22.38 27.13 125-129 27.72 22.825 22.7 26.755000000000003 130-134 27.905 22.825 22.845 26.424999999999997 135-139 27.310000000000002 23.085 22.82 26.784999999999997 140-144 27.3 23.255 22.505 26.939999999999998 145-149 27.400000000000002 22.895 23.455000000000002 26.25 150 27.375 23.474999999999998 22.625 26.525 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 1.0 1 0.5 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 0.5 20 1.5 21 1.0 22 0.5 23 0.5 24 1.5 25 1.5 26 0.0 27 1.5 28 3.0 29 4.5 30 7.0 31 12.5 32 14.5 33 14.5 34 19.5 35 30.5 36 44.0 37 53.5 38 56.0 39 66.0 40 85.0 41 109.0 42 119.0 43 136.0 44 152.0 45 139.0 46 136.0 47 133.0 48 136.0 49 140.5 50 143.0 51 136.5 52 119.5 53 115.5 54 110.5 55 108.5 56 99.5 57 84.5 58 98.0 59 97.0 60 84.5 61 86.5 62 79.0 63 74.0 64 84.5 65 94.0 66 90.0 67 84.0 68 78.0 69 75.5 70 68.0 71 68.5 72 68.5 73 48.0 74 36.0 75 31.0 76 26.0 77 24.5 78 17.0 79 12.0 80 12.5 81 9.0 82 4.0 83 5.0 84 4.5 85 0.5 86 0.0 87 0.0 88 0.5 89 0.5 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 0.0 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 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 88.14999999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 88.11684628474191 77.67500000000001 2 10.465116279069768 18.45 3 1.3045944412932502 3.45 4 0.08508224617129892 0.3 5 0.02836074872376631 0.125 6 0.0 0.0 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 AAAGGATTCAGCCCGCCGCCCGTGGGGAAGGGAGCTTCGAGGCGGCCGGA 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #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 0.025 0.0 0.0 0.0 0.0 9 0.025 0.0 0.0 0.0 0.0 10-11 0.025 0.0 0.0 0.0 0.0 12-13 0.05 0.0 0.0 0.0 0.0 14-15 0.075 0.0 0.0 0.0 0.0 16-17 0.075 0.0 0.0 0.0 0.0 18-19 0.075 0.0 0.0 0.0 0.0 20-21 0.075 0.0 0.0 0.0 0.0 22-23 0.075 0.0 0.0 0.0 0.0 24-25 0.075 0.0 0.0 0.0 0.0 26-27 0.1 0.0 0.0 0.0 0.0 28-29 0.1 0.0 0.0 0.0 0.0 30-31 0.1 0.0 0.0 0.0 0.0 32-33 0.125 0.0 0.0 0.0 0.0 34-35 0.125 0.0 0.0 0.0 0.0 36-37 0.125 0.0 0.0 0.0 0.0 38-39 0.125 0.0 0.0 0.0 0.0 40-41 0.125 0.0 0.0 0.0 0.0 42-43 0.125 0.0 0.0 0.0 0.0 44-45 0.125 0.0 0.0 0.0 0.0 46-47 0.125 0.0 0.0 0.0 0.0 48-49 0.125 0.0 0.0 0.0 0.0 50-51 0.125 0.0 0.0 0.0 0.0 52-53 0.125 0.0 0.0 0.0 0.0 54-55 0.125 0.0 0.0 0.0 0.0 56-57 0.125 0.0 0.0 0.0 0.0 58-59 0.125 0.0 0.0 0.0 0.0 60-61 0.125 0.0 0.0 0.0 0.0 62-63 0.125 0.0 0.0 0.0 0.0 64-65 0.125 0.0 0.0 0.0 0.0 66-67 0.125 0.0 0.0 0.0 0.0 68-69 0.125 0.0 0.0 0.0 0.0 70-71 0.125 0.0 0.0 0.0 0.0 72-73 0.125 0.0 0.0 0.0 0.0 74-75 0.125 0.0 0.0 0.0 0.0 76-77 0.125 0.0 0.0 0.0 0.0 78-79 0.125 0.0 0.0 0.0 0.0 80-81 0.15 0.0 0.0 0.0 0.0 82-83 0.15 0.0 0.0 0.0 0.0 84-85 0.15 0.0 0.0 0.0 0.0 86-87 0.175 0.0 0.0 0.0 0.0 88-89 0.1875 0.0 0.0 0.0 0.0 90-91 0.2 0.0 0.0 0.0 0.0 92-93 0.25 0.0 0.0 0.0 0.0 94-95 0.2875 0.0 0.0 0.0 0.0 96-97 0.3375 0.0 0.0 0.0 0.0 98-99 0.35 0.0 0.0 0.0 0.0 100-101 0.375 0.0 0.0 0.0 0.0 102-103 0.4125 0.0 0.0 0.0 0.0 104-105 0.5125 0.0 0.0 0.0 0.0 106-107 0.6125 0.0 0.0 0.0 0.0 108-109 0.65 0.0 0.0 0.0 0.0 110-111 0.6875 0.0 0.0 0.0 0.0 112-113 0.7375 0.0 0.0 0.0 0.0 114-115 0.7625 0.0 0.0 0.0 0.0 116-117 0.8 0.0 0.0 0.0 0.0 118-119 0.8125 0.0 0.0 0.0 0.0 120-121 0.925 0.0 0.0 0.0 0.0 122-123 1.0375 0.0 0.0 0.0 0.0 124-125 1.125 0.0 0.0 0.0 0.0 126-127 1.1375 0.0 0.0 0.0 0.0 128-129 1.1875 0.0 0.0 0.0 0.0 130-131 1.275 0.0 0.0 0.0 0.0 132-133 1.35 0.0 0.0 0.0 0.0 134-135 1.4625 0.0 0.0 0.0 0.0 136-137 1.475 0.0 0.0 0.0 0.0 138 1.5 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GTTGATC 10 0.006973645 144.0 8 CATCCTC 10 0.006973645 144.0 5 TCACGCG 10 0.006973645 144.0 2 TTGATCG 10 0.006973645 144.0 9 CTCACGC 10 0.006973645 144.0 1 >>END_MODULE Read 1643145 spots for SRR12455400.sra Written 1643145 spots for SRR12455400.sra Read 1643145 spots for SRR12455400.sra Written 1643145 spots for SRR12455400.sra Read 1643145 spots for SRR12455400.sra Written 1643145 spots for SRR12455400.sra Read 1643145 spots for SRR12455400.sra Written 1643145 spots for SRR12455400.sra Read 1643145 spots for SRR12455400.sra Written 1643145 spots for SRR12455400.sra Read 1643145 spots for SRR12455400.sra Written 1643145 spots for SRR12455400.sra Read 1643145 spots for SRR12455400.sra Written 1643145 spots for SRR12455400.sra Read 1643145 spots for SRR12455400.sra Written 1643145 spots for SRR12455400.sra Read 1643145 spots for SRR12455400.sra Written 1643145 spots for SRR12455400.sra Read 1643145 spots for SRR12455400.sra Written 1643145 spots for SRR12455400.sra Read 1643145 spots for SRR12455400.sra Written 1643145 spots for SRR12455400.sra Read 1643145 spots for SRR12455400.sra Written 1643145 spots for SRR12455400.sra Read 1643145 spots for SRR12455400.sra Written 1643145 spots for SRR12455400.sra Read 1643145 spots for SRR12455400.sra Written 1643145 spots for SRR12455400.sra Read 1643145 spots for SRR12455400.sra Written 1643145 spots for SRR12455400.sra Read 1643148 spots for SRR12455400.sra Written 1643148 spots for SRR12455400.sra Read 1643145 spots for SRR12455400.sra Written 1643145 spots for SRR12455400.sra Read 1643145 spots for SRR12455400.sra Written 1643145 spots for SRR12455400.sra Read 1643145 spots for SRR12455400.sra Written 1643145 spots for SRR12455400.sra Read 1643145 spots for SRR12455400.sra Written 1643145 spots for SRR12455400.sra SRR ids: ['SRR12455400.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_c_ct508s SRR12455400.sra spots: 32862903 blocks: [[1, 1643145], [1643146, 3286290], [3286291, 4929435], [4929436, 6572580], [6572581, 8215725], [8215726, 9858870], [9858871, 11502015], [11502016, 13145160], [13145161, 14788305], [14788306, 16431450], [16431451, 18074595], [18074596, 19717740], [19717741, 21360885], [21360886, 23004030], [23004031, 24647175], [24647176, 26290320], [26290321, 27933465], [27933466, 29576610], [29576611, 31219755], [31219756, 32862903]] SRR12455400 file size 11082366 SRR12455400 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 SRR12455400 SRR12455400_1.fastq SRR12455400_2.fastq Input file: SRR12455400_1.fastq Paired file: SRR12455400_2.fastq trimmed: SRR12455400-trimmed-pair1.fastq, SRR12455400-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 Dec 10 10:31:02 2024 >> started Tue Dec 10 10:33:19 2024 >> done (137.505s) 32862903 read pairs processed; of these: 7409 ( 0.02%) short read pairs filtered out after trimming by size control 1920 ( 0.01%) empty read pairs filtered out after trimming by size control 32853574 (99.97%) read pairs available; of these: 600585 ( 1.83%) trimmed read pairs available after processing 32252989 (98.17%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 92 0.00% 19 196 0.00% 20 162 0.00% 21 155 0.00% 22 530 0.00% 23 89 0.00% 24 276 0.00% 25 692 0.00% 26 211 0.00% 27 278 0.00% 28 517 0.00% 29 322 0.00% 30 362 0.00% 31 2895 0.01% 32 120 0.00% 33 122 0.00% 34 141 0.00% 35 219 0.00% 36 144 0.00% 37 178 0.00% 38 342 0.00% 39 202 0.00% 40 233 0.00% 41 321 0.00% 42 235 0.00% 43 245 0.00% 44 389 0.00% 45 181 0.00% 46 156 0.00% 47 186 0.00% 48 176 0.00% 49 155 0.00% 50 164 0.00% 51 229 0.00% 52 214 0.00% 53 195 0.00% 54 274 0.00% 55 249 0.00% 56 244 0.00% 57 260 0.00% 58 237 0.00% 59 239 0.00% 60 252 0.00% 61 275 0.00% 62 290 0.00% 63 298 0.00% 64 345 0.00% 65 400 0.00% 66 381 0.00% 67 396 0.00% 68 468 0.00% 69 519 0.00% 70 557 0.00% 71 581 0.00% 72 694 0.00% 73 787 0.00% 74 726 0.00% 75 872 0.00% 76 930 0.00% 77 1012 0.00% 78 1079 0.00% 79 1249 0.00% 80 1308 0.00% 81 1515 0.00% 82 1505 0.00% 83 1770 0.01% 84 1869 0.01% 85 1922 0.01% 86 2121 0.01% 87 2367 0.01% 88 2513 0.01% 89 2619 0.01% 90 2726 0.01% 91 2865 0.01% 92 3085 0.01% 93 3396 0.01% 94 3591 0.01% 95 3798 0.01% 96 3922 0.01% 97 4032 0.01% 98 4424 0.01% 99 4467 0.01% 100 4692 0.01% 101 4859 0.01% 102 4972 0.02% 103 5174 0.02% 104 5487 0.02% 105 5447 0.02% 106 5753 0.02% 107 6143 0.02% 108 6294 0.02% 109 6469 0.02% 110 6758 0.02% 111 7255 0.02% 112 7084 0.02% 113 7297 0.02% 114 7685 0.02% 115 7580 0.02% 116 7821 0.02% 117 8031 0.02% 118 8406 0.03% 119 8576 0.03% 120 9103 0.03% 121 9092 0.03% 122 9343 0.03% 123 9630 0.03% 124 9733 0.03% 125 10308 0.03% 126 10500 0.03% 127 10695 0.03% 128 10713 0.03% 129 11033 0.03% 130 11236 0.03% 131 11578 0.04% 132 12090 0.04% 133 12238 0.04% 134 12620 0.04% 135 12827 0.04% 136 13021 0.04% 137 13427 0.04% 138 13609 0.04% 139 14103 0.04% 140 14530 0.04% 141 15004 0.05% 142 15129 0.05% 143 15506 0.05% 144 15615 0.05% 145 16005 0.05% 146 16740 0.05% 147 17108 0.05% 148 17556 0.05% 149 17957 0.05% 150 32252989 98.17% 32853574 reads passed initial QC criterion=sequence-density sequence-density=0.25 sequence-density-rank=1 fanout-score=3.58 fanout-score-rank=15 prefix-density=0.30 prefix-fanout=3.0 sequence=CTGCAAGTGCGGCA criterion=fanout-score sequence-density=0.14 sequence-density-rank=13 fanout-score=131.96 fanout-score-rank=1 prefix-density=0.88 prefix-fanout=20.2 sequence=CGGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAA criterion=sequence-density sequence-density=0.25 sequence-density-rank=1 fanout-score=3.55 fanout-score-rank=16 prefix-density=0.30 prefix-fanout=3.0 sequence=CTGCAAGTGCGGCA criterion=fanout-score sequence-density=0.13 sequence-density-rank=17 fanout-score=128.25 fanout-score-rank=1 prefix-density=0.85 prefix-fanout=20.0 sequence=CGGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAA SRR12455400 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 10 10:34:19 Started mapping on | Dec 10 10:34:20 Finished on | Dec 10 10:39:01 Mapping speed, Million of reads per hour | 420.90 Number of input reads | 32853574 Average input read length | 299 UNIQUE READS: Uniquely mapped reads number | 28989617 Uniquely mapped reads % | 88.24% Average mapped length | 297.46 Number of splices: Total | 26842652 Number of splices: Annotated (sjdb) | 25336773 Number of splices: GT/AG | 26468088 Number of splices: GC/AG | 308699 Number of splices: AT/AC | 15014 Number of splices: Non-canonical | 50851 Mismatch rate per base, % | 0.32% Deletion rate per base | 0.01% Deletion average length | 2.45 Insertion rate per base | 0.01% Insertion average length | 2.36 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 457536 % of reads mapped to multiple loci | 1.39% Number of reads mapped to too many loci | 291810 % of reads mapped to too many loci | 0.89% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.13% % of reads unmapped: other | 7.35% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 3406421 3406421 3406421 N_multimapping 457536 457536 457536 N_noFeature 856900 14586670 14725346 N_ambiguous 692102 83822 82630 UnstrandedReadsAssigned:27440615 PositiveStrandReadsAssigned:14319125 NegativeStrandReadsAssigned:14181641 Dataset is classified unstranded MeadianReadLen=150 20thPercentileLength=150 echo kmer=145 SRR12455400 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: 52,972 [index] number of k-mers: 66,720,672 [index] number of equivalence classes: 111,837 [quant] running in paired-end mode [quant] will process pair 1: SRR12455400-trimmed-pair1.fastq SRR12455400-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 32,853,574 reads, 28,900,130 reads pseudoaligned [quant] estimated average fragment length: 285.632 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,148 rounds 52973 SRR12455400.ke.tsv 35125 SRR12455400.se.tsv 88098 total ==> SRR12455400.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 651.765 0 0 PNS24247 1044 759.368 36.5978 1.88707 PNS24249 1928 1643.37 338.317 8.06073 PNS24246 1044 759.368 36.5978 1.88707 PNS24248 1044 759.368 36.5978 1.88707 PNS24244 1471 1186.37 53.8893 1.77856 PNS24243 293 54.0515 11 7.96839 KQK14069 1603 1318.37 17787.4 528.275 KQK14071 474 194.035 283.872 57.2834 ==> SRR12455400.se.tsv <== BRADI_1g14170v3 19252 BRADI_1g53295v3 57 BRADI_1g59795v3 343 BRADI_1g07683v3 0 BRADI_1g00485v3 51 BRADI_1g20270v3 2745 BRADI_1g74790v3 998 BRADI_1g09890v3 9 BRADI_1g77505v3 451 BRADI_1g48960v3 0 SRR12455400 completed mapping pipeline successfully