Starting /dee2/code/volunteer_pipeline.sh SRR12671328 current disk space = 3049599991808 free memory = 1462561732 SRR12671328 SRAfilesize bdfedda89010ecaf53ee88be54853bf6 SRR12671328.sra SRR12671328.sra file validated SRR12671328 is paired end SRR12671328 is conventional basespace SRR12671328 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12671328_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 36.6945 37.0 37.0 37.0 37.0 37.0 2 36.46525 37.0 37.0 37.0 37.0 37.0 3 36.6465 37.0 37.0 37.0 37.0 37.0 4 36.598 37.0 37.0 37.0 37.0 37.0 5 36.6395 37.0 37.0 37.0 37.0 37.0 6 36.6475 37.0 37.0 37.0 37.0 37.0 7 36.53 37.0 37.0 37.0 37.0 37.0 8 36.586 37.0 37.0 37.0 37.0 37.0 9 36.641 37.0 37.0 37.0 37.0 37.0 10-14 36.64149999999999 37.0 37.0 37.0 37.0 37.0 15-19 36.6283 37.0 37.0 37.0 37.0 37.0 20-24 36.545100000000005 37.0 37.0 37.0 37.0 37.0 25-29 36.5449 37.0 37.0 37.0 37.0 37.0 30-34 36.53099999999999 37.0 37.0 37.0 37.0 37.0 35-39 36.477700000000006 37.0 37.0 37.0 37.0 37.0 40-44 36.4996 37.0 37.0 37.0 37.0 37.0 45-49 36.4739 37.0 37.0 37.0 37.0 37.0 50-54 36.4555 37.0 37.0 37.0 37.0 37.0 55-59 36.3987 37.0 37.0 37.0 37.0 37.0 60-64 36.3981 37.0 37.0 37.0 37.0 37.0 65-69 36.3608 37.0 37.0 37.0 37.0 37.0 70-74 36.3347 37.0 37.0 37.0 37.0 37.0 75-79 36.3472 37.0 37.0 37.0 37.0 37.0 80-84 36.3058 37.0 37.0 37.0 37.0 37.0 85-89 36.2645 37.0 37.0 37.0 37.0 37.0 90-94 36.3067 37.0 37.0 37.0 37.0 37.0 95-99 36.232600000000005 37.0 37.0 37.0 37.0 37.0 100-104 36.191700000000004 37.0 37.0 37.0 37.0 37.0 105-109 36.21 37.0 37.0 37.0 37.0 37.0 110-114 36.1697 37.0 37.0 37.0 37.0 37.0 115-119 36.1425 37.0 37.0 37.0 37.0 37.0 120-124 36.0997 37.0 37.0 37.0 37.0 37.0 125-129 36.0608 37.0 37.0 37.0 37.0 37.0 130-134 36.0257 37.0 37.0 37.0 37.0 37.0 135-139 35.9992 37.0 37.0 37.0 37.0 37.0 140-144 35.962900000000005 37.0 37.0 37.0 37.0 37.0 145-149 35.9354 37.0 37.0 37.0 37.0 37.0 150-151 35.792500000000004 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 1.0 21 3.0 22 2.0 23 3.0 24 5.0 25 2.0 26 5.0 27 1.0 28 4.0 29 12.0 30 19.0 31 39.0 32 49.0 33 66.0 34 122.0 35 253.0 36 2936.0 37 478.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 41.9 12.475 5.075 40.550000000000004 2 19.82434127979925 9.786700125470514 37.66624843161857 32.72271016311167 3 18.5 13.825000000000001 28.7 38.975 4 23.200000000000003 19.15 26.224999999999998 31.424999999999997 5 25.624999999999996 28.225 23.75 22.400000000000002 6 19.675 31.275 24.925 24.125 7 13.850000000000001 28.499999999999996 41.075 16.575 8 15.174999999999999 27.125 33.875 23.825 9 16.75 22.875 37.3 23.075000000000003 10-14 19.355 31.045 28.21 21.39 15-19 20.105 28.660000000000004 27.185 24.05 20-24 19.2 29.4 28.29 23.11 25-29 19.8 28.065 28.535 23.599999999999998 30-34 19.705000000000002 28.505000000000003 28.444999999999997 23.345 35-39 19.275000000000002 28.915000000000003 27.634999999999998 24.175 40-44 19.785 29.37 27.224999999999998 23.62 45-49 19.830000000000002 29.095 27.315 23.76 50-54 19.655 28.59 27.91 23.845 55-59 19.794999999999998 28.34 27.944999999999997 23.919999999999998 60-64 20.06 28.28 27.815 23.845 65-69 20.330000000000002 28.65 27.21 23.810000000000002 70-74 19.814999999999998 28.27 26.995 24.92 75-79 20.25 28.1 28.294999999999998 23.355 80-84 20.21 28.345 28.07 23.375 85-89 19.825 28.720000000000002 27.665 23.79 90-94 20.315 28.435 26.810000000000002 24.44 95-99 19.77 28.285 27.43 24.515 100-104 19.384999999999998 28.455000000000002 28.01 24.15 105-109 20.19 28.560000000000002 27.505000000000003 23.745 110-114 20.3 28.910000000000004 27.495000000000005 23.294999999999998 115-119 20.380000000000003 28.185 27.775 23.66 120-124 20.39 27.860000000000003 27.994999999999997 23.755000000000003 125-129 20.04 28.599999999999998 27.51 23.849999999999998 130-134 20.75 28.355000000000004 26.900000000000002 23.995 135-139 20.72 27.384999999999998 27.084999999999997 24.81 140-144 20.89 28.065 27.685 23.36 145-149 20.71 27.905 27.229999999999997 24.154999999999998 150-151 20.849999999999998 27.275 27.6625 24.212500000000002 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 2.0 1 1.5 2 1.0 3 1.5 4 1.0 5 0.0 6 0.5 7 0.5 8 0.5 9 0.5 10 0.0 11 0.0 12 0.0 13 0.0 14 0.5 15 0.5 16 0.5 17 0.5 18 0.0 19 1.0 20 1.0 21 1.0 22 3.5 23 2.5 24 4.5 25 7.0 26 5.5 27 6.0 28 8.5 29 12.5 30 23.0 31 27.0 32 33.0 33 45.5 34 54.5 35 76.5 36 93.0 37 105.5 38 137.0 39 159.0 40 171.5 41 216.5 42 243.5 43 225.0 44 246.5 45 278.0 46 252.5 47 230.5 48 227.0 49 204.0 50 180.0 51 154.0 52 115.0 53 92.0 54 82.0 55 66.0 56 57.0 57 45.0 58 26.5 59 20.0 60 15.0 61 13.0 62 8.5 63 3.0 64 2.5 65 0.5 66 0.5 67 3.5 68 3.0 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 0.375 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 82.675 #Duplication Level Percentage of deduplicated Percentage of total 1 83.15693982461445 68.75 2 13.66797701844572 22.6 3 2.6005442999697608 6.45 4 0.3326277592984578 1.0999999999999999 5 0.18143332325370426 0.75 6 0.03023888720895071 0.15 7 0.0 0.0 8 0.03023888720895071 0.2 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 CCACACCAGAGGCCACAGACATGGCCAATACATAACAATGAAGAAGACAC 8 0.2 No Hit AGCTCCACCAGGTTGGTCAACAAAAAATTTCTGGCCAGGCAATCTAGATA 6 0.15 No Hit TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 5 0.125 No Hit CTGGCCAAAAGATAAGGAAAGTTGTACTTGGTAAGATGCTCTCTGAACCT 5 0.125 No Hit GCTTCTTCGAATCCACTGGAGAACTTTATTTATTTTCCGCACATAAATAG 5 0.125 No Hit CTCCAGAGTTGTAGCCTGTTTCAAAGCAACTGCTAAACCAGCAATTGTGT 5 0.125 No Hit GGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGA 5 0.125 No Hit GCTTCAACAACCATGTTGCATAATGTCATCCGCTCTTCCATAGTTAAACT 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 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0125 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.025 0.0 0.0 0.0 0.0 68-69 0.025 0.0 0.0 0.0 0.0 70-71 0.037500000000000006 0.0 0.0 0.0 0.0 72-73 0.05 0.0 0.0 0.0 0.0 74-75 0.05 0.0 0.0 0.0 0.0 76-77 0.05 0.0 0.0 0.0 0.0 78-79 0.075 0.0 0.0 0.0 0.0 80-81 0.075 0.0 0.0 0.0 0.0 82-83 0.075 0.0 0.0 0.0 0.0 84-85 0.2 0.0 0.0 0.0 0.0 86-87 0.2375 0.0 0.0 0.0 0.0 88-89 0.2625 0.0 0.0 0.0 0.0 90-91 0.275 0.0 0.0 0.0 0.0 92-93 0.2875 0.0 0.0 0.0 0.0 94-95 0.3 0.0 0.0 0.0 0.0 96-97 0.3375 0.0 0.0 0.0 0.0 98-99 0.44999999999999996 0.0 0.0 0.0 0.0 100-101 0.475 0.0 0.0 0.0 0.0 102-103 0.5 0.0 0.0 0.0 0.0 104-105 0.6 0.0 0.0 0.0 0.0 106-107 0.7 0.0 0.0 0.0 0.0 108-109 0.775 0.0 0.0 0.0 0.0 110-111 0.85 0.0 0.0 0.0 0.0 112-113 0.9874999999999999 0.0 0.0 0.0 0.0 114-115 1.1875 0.0 0.0 0.0 0.0 116-117 1.4375 0.0 0.0 0.0 0.0 118-119 1.5125000000000002 0.0 0.0 0.0 0.0 120-121 1.625 0.0 0.0 0.0 0.0 122-123 1.8 0.0 0.0 0.0 0.0 124-125 2.075 0.0 0.0 0.0 0.0 126-127 2.5 0.0 0.0 0.0 0.0 128-129 2.725 0.0 0.0 0.0 0.0 130-131 2.9000000000000004 0.0 0.0 0.0 0.0 132-133 3.125 0.0 0.0 0.0 0.0 134-135 3.1875 0.0 0.0 0.0 0.0 136-137 3.3125 0.0 0.0 0.0 0.0 138-139 3.6500000000000004 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CCCATAA 10 0.006830828 145.0 4 AAGCAAC 10 0.006830828 145.0 9 >>END_MODULE SRR12671328 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12671328_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 36.313 37.0 37.0 37.0 37.0 37.0 2 36.197 37.0 37.0 37.0 37.0 37.0 3 36.252 37.0 37.0 37.0 37.0 37.0 4 36.305 37.0 37.0 37.0 37.0 37.0 5 36.312 37.0 37.0 37.0 37.0 37.0 6 36.3805 37.0 37.0 37.0 37.0 37.0 7 36.314 37.0 37.0 37.0 37.0 37.0 8 36.375 37.0 37.0 37.0 37.0 37.0 9 36.3595 37.0 37.0 37.0 37.0 37.0 10-14 36.3288 37.0 37.0 37.0 37.0 37.0 15-19 36.372400000000006 37.0 37.0 37.0 37.0 37.0 20-24 36.3114 37.0 37.0 37.0 37.0 37.0 25-29 36.298 37.0 37.0 37.0 37.0 37.0 30-34 36.2281 37.0 37.0 37.0 37.0 37.0 35-39 36.2282 37.0 37.0 37.0 37.0 37.0 40-44 36.2282 37.0 37.0 37.0 37.0 37.0 45-49 36.2213 37.0 37.0 37.0 37.0 37.0 50-54 36.1631 37.0 37.0 37.0 37.0 37.0 55-59 36.186 37.0 37.0 37.0 37.0 37.0 60-64 36.10459999999999 37.0 37.0 37.0 37.0 37.0 65-69 36.145799999999994 37.0 37.0 37.0 37.0 37.0 70-74 36.0034 37.0 37.0 37.0 37.0 37.0 75-79 36.086 37.0 37.0 37.0 37.0 37.0 80-84 36.0321 37.0 37.0 37.0 37.0 37.0 85-89 36.023 37.0 37.0 37.0 37.0 37.0 90-94 36.051 37.0 37.0 37.0 37.0 37.0 95-99 36.008300000000006 37.0 37.0 37.0 37.0 37.0 100-104 35.921800000000005 37.0 37.0 37.0 37.0 37.0 105-109 35.9153 37.0 37.0 37.0 37.0 37.0 110-114 35.9189 37.0 37.0 37.0 37.0 37.0 115-119 35.90560000000001 37.0 37.0 37.0 37.0 37.0 120-124 35.9005 37.0 37.0 37.0 37.0 37.0 125-129 35.8925 37.0 37.0 37.0 37.0 37.0 130-134 35.7652 37.0 37.0 37.0 37.0 37.0 135-139 35.7109 37.0 37.0 37.0 37.0 37.0 140-144 35.7939 37.0 37.0 37.0 37.0 37.0 145-149 35.709999999999994 37.0 37.0 37.0 37.0 37.0 150-151 35.48125 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 3.0 14 3.0 15 1.0 16 0.0 17 1.0 18 0.0 19 0.0 20 2.0 21 2.0 22 3.0 23 3.0 24 4.0 25 3.0 26 5.0 27 7.0 28 11.0 29 16.0 30 21.0 31 34.0 32 39.0 33 78.0 34 168.0 35 504.0 36 2826.0 37 266.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 37.075 28.375 7.9 26.650000000000002 2 27.224999999999998 26.775 31.025000000000002 14.975 3 19.3 27.05 34.975 18.675 4 22.725 34.675 23.75 18.85 5 26.224999999999998 36.9 21.375 15.5 6 20.125 41.05 21.9 16.925 7 20.8 23.225 37.574999999999996 18.4 8 19.675 26.900000000000002 28.1 25.324999999999996 9 20.025000000000002 24.275 32.525 23.175 10-14 22.215 29.5 27.02 21.265 15-19 23.49 27.775 27.465 21.27 20-24 22.75 28.884999999999998 26.96 21.404999999999998 25-29 22.509999999999998 27.589999999999996 28.455000000000002 21.445 30-34 22.52 27.735 28.845 20.9 35-39 22.32 28.24 27.05 22.39 40-44 22.384999999999998 28.955 27.915 20.745 45-49 23.04 28.050000000000004 28.055000000000003 20.855 50-54 23.44 28.03 27.43 21.099999999999998 55-59 22.705000000000002 28.23 27.889999999999997 21.175 60-64 22.965 28.325 27.51 21.2 65-69 22.42 27.794999999999998 28.835 20.95 70-74 24.104999999999997 27.445000000000004 27.400000000000002 21.05 75-79 23.345 27.200000000000003 27.985 21.47 80-84 22.78 27.905 27.794999999999998 21.52 85-89 23.935000000000002 27.800000000000004 27.810000000000002 20.455000000000002 90-94 23.89 28.675 26.479999999999997 20.955 95-99 23.549999999999997 28.24 27.095000000000002 21.115000000000002 100-104 23.87 27.875 27.98 20.275000000000002 105-109 23.330000000000002 27.32 28.405 20.945 110-114 24.14 27.71 28.084999999999997 20.064999999999998 115-119 24.240000000000002 28.294999999999998 27.060000000000002 20.405 120-124 24.38 28.26 27.43 19.93 125-129 24.095 27.935 27.415 20.555 130-134 24.025 28.1 27.389999999999997 20.485 135-139 25.155 27.750000000000004 27.500000000000004 19.595000000000002 140-144 24.82 28.13 27.16 19.89 145-149 24.14 27.68 28.005000000000003 20.175 150-151 25.424999999999997 27.55 27.3375 19.6875 >>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 0.5 8 0.5 9 0.0 10 0.0 11 0.0 12 0.5 13 0.5 14 0.5 15 0.5 16 0.0 17 0.0 18 0.0 19 0.5 20 1.0 21 1.5 22 1.5 23 2.0 24 2.5 25 6.0 26 10.5 27 6.5 28 5.5 29 11.5 30 19.0 31 21.0 32 25.0 33 37.0 34 49.0 35 66.0 36 80.5 37 105.5 38 138.0 39 157.5 40 203.5 41 239.5 42 247.0 43 265.5 44 279.0 45 277.5 46 266.0 47 242.0 48 223.5 49 197.0 50 153.0 51 130.0 52 106.0 53 88.5 54 80.0 55 60.5 56 44.5 57 36.0 58 29.0 59 24.5 60 19.0 61 16.0 62 11.5 63 2.5 64 0.0 65 1.5 66 2.0 67 0.5 68 0.0 69 0.0 70 0.0 71 0.0 72 0.0 73 0.0 74 0.0 75 0.5 76 0.5 77 0.0 78 0.5 79 0.5 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 0.5 91 0.5 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 0.0 >>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 82.75 #Duplication Level Percentage of deduplicated Percentage of total 1 83.95770392749245 69.475 2 12.83987915407855 21.25 3 2.5377643504531724 6.3 4 0.3323262839879154 1.0999999999999999 5 0.1510574018126888 0.625 6 0.060422960725075525 0.3 7 0.0 0.0 8 0.030211480362537763 0.2 9 0.030211480362537763 0.22499999999999998 >10 0.060422960725075525 0.525 >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 AGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAA 11 0.27499999999999997 No Hit AGAGAACACATTCATACCCCAAGTCTTTTAGTTCATCCATTTAAGCTTAA 10 0.25 No Hit CAGAGAACACATTCATACCCCAAGTCTTTTAGTTCATCCATTTAAGCTTA 9 0.22499999999999998 No Hit CAGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTA 8 0.2 No Hit GGTACACAGGTTGAAAACCTTCAACCCAGTCCGGTGACTTCCTTTGCACA 6 0.15 No Hit AGAACACATTCATACCCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATC 6 0.15 No Hit GTCACATAGATTTCCAAGATGAAGGCCTTTCTTATCGCATGCATTCTCTT 5 0.125 No Hit CACACATTAGTGGATTGGTTGCAGCTGGTGTCATCCCATCGCCTTTTGAG 5 0.125 No Hit GCCAGCATATACCAGAGATGTTTCCATTGGAGAAACTTGTTCATTCATGA 5 0.125 No Hit GTTAGGAACAGACTCACACACATGTACTGCTGGAGCATTTGGCCAATTTG 5 0.125 No Hit ATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATCAATCAAT 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 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0125 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.025 0.0 0.0 0.0 0.0 68-69 0.025 0.0 0.0 0.0 0.0 70-71 0.037500000000000006 0.0 0.0 0.0 0.0 72-73 0.05 0.0 0.0 0.0 0.0 74-75 0.05 0.0 0.0 0.0 0.0 76-77 0.05 0.0 0.0 0.0 0.0 78-79 0.075 0.0 0.0 0.0 0.0 80-81 0.075 0.0 0.0 0.0 0.0 82-83 0.075 0.0 0.0 0.0 0.0 84-85 0.2 0.0 0.0 0.0 0.0 86-87 0.2375 0.0 0.0 0.0 0.0 88-89 0.2625 0.0 0.0 0.0 0.0 90-91 0.275 0.0 0.0 0.0 0.0 92-93 0.2875 0.0 0.0 0.0 0.0 94-95 0.3 0.0 0.0 0.0 0.0 96-97 0.3375 0.0 0.0 0.0 0.0 98-99 0.44999999999999996 0.0 0.0 0.0 0.0 100-101 0.475 0.0 0.0 0.0 0.0 102-103 0.5 0.0 0.0 0.0 0.0 104-105 0.6 0.0 0.0 0.0 0.0 106-107 0.7 0.0 0.0 0.0 0.0 108-109 0.775 0.0 0.0 0.0 0.0 110-111 0.85 0.0 0.0 0.0 0.0 112-113 0.9625 0.0 0.0 0.0 0.0 114-115 1.1625 0.0 0.0 0.0 0.0 116-117 1.425 0.0 0.0 0.0 0.0 118-119 1.5125000000000002 0.0 0.0 0.0 0.0 120-121 1.625 0.0 0.0 0.0 0.0 122-123 1.7625 0.0 0.0 0.0 0.0 124-125 2.0 0.0 0.0 0.0 0.0 126-127 2.425 0.0 0.0 0.0 0.0 128-129 2.65 0.0 0.0 0.0 0.0 130-131 2.825 0.0 0.0 0.0 0.0 132-133 3.05 0.0 0.0 0.0 0.0 134-135 3.1125 0.0 0.0 0.0 0.0 136-137 3.2249999999999996 0.0 0.0 0.0 0.0 138-139 3.55 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CACATTC 10 0.006830828 145.0 8 ACACATT 10 0.006830828 145.0 7 ACATTCA 10 0.006830828 145.0 9 GAACACA 10 0.006830828 145.0 5 CGTCGAG 10 0.006830828 145.0 145 >>END_MODULE Read 812008 spots for SRR12671328.sra Written 812008 spots for SRR12671328.sra Read 812008 spots for SRR12671328.sra Written 812008 spots for SRR12671328.sra Read 812008 spots for SRR12671328.sra Written 812008 spots for SRR12671328.sra Read 812008 spots for SRR12671328.sra Written 812008 spots for SRR12671328.sra Read 812008 spots for SRR12671328.sra Written 812008 spots for SRR12671328.sra Read 812008 spots for SRR12671328.sra Written 812008 spots for SRR12671328.sra Read 812008 spots for SRR12671328.sra Written 812008 spots for SRR12671328.sra Read 812008 spots for SRR12671328.sra Written 812008 spots for SRR12671328.sra Read 812008 spots for SRR12671328.sra Written 812008 spots for SRR12671328.sra Read 812008 spots for SRR12671328.sra Written 812008 spots for SRR12671328.sra Read 812008 spots for SRR12671328.sra Written 812008 spots for SRR12671328.sra Read 812008 spots for SRR12671328.sra Written 812008 spots for SRR12671328.sra Read 812008 spots for SRR12671328.sra Written 812008 spots for SRR12671328.sra Read 812008 spots for SRR12671328.sra Written 812008 spots for SRR12671328.sra Read 812008 spots for SRR12671328.sra Written 812008 spots for SRR12671328.sra Read 812008 spots for SRR12671328.sra Written 812008 spots for SRR12671328.sra Read 812008 spots for SRR12671328.sra Written 812008 spots for SRR12671328.sra Read 812008 spots for SRR12671328.sra Written 812008 spots for SRR12671328.sra Read 812008 spots for SRR12671328.sra Written 812008 spots for SRR12671328.sra Read 812023 spots for SRR12671328.sra Written 812023 spots for SRR12671328.sra SRR ids: ['SRR12671328.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_yc5qsj9e SRR12671328.sra spots: 16240175 blocks: [[1, 812008], [812009, 1624016], [1624017, 2436024], [2436025, 3248032], [3248033, 4060040], [4060041, 4872048], [4872049, 5684056], [5684057, 6496064], [6496065, 7308072], [7308073, 8120080], [8120081, 8932088], [8932089, 9744096], [9744097, 10556104], [10556105, 11368112], [11368113, 12180120], [12180121, 12992128], [12992129, 13804136], [13804137, 14616144], [14616145, 15428152], [15428153, 16240175]] SRR12671328 file size 5497421 SRR12671328 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 SRR12671328 SRR12671328_1.fastq SRR12671328_2.fastq Input file: SRR12671328_1.fastq Paired file: SRR12671328_2.fastq trimmed: SRR12671328-trimmed-pair1.fastq, SRR12671328-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 15:27:47 2025 >> started Tue Feb 11 15:28:06 2025 >> done (18.326s) 16240175 read pairs processed; of these: 75 ( 0.00%) short read pairs filtered out after trimming by size control 13670 ( 0.08%) empty read pairs filtered out after trimming by size control 16226430 (99.92%) read pairs available; of these: 881947 ( 5.44%) trimmed read pairs available after processing 15344483 (94.56%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 15 0.00% 19 6 0.00% 20 11 0.00% 21 6 0.00% 22 12 0.00% 23 20 0.00% 24 11 0.00% 25 19 0.00% 26 24 0.00% 27 27 0.00% 28 23 0.00% 29 21 0.00% 30 21 0.00% 31 25 0.00% 32 22 0.00% 33 27 0.00% 34 33 0.00% 35 23 0.00% 36 29 0.00% 37 31 0.00% 38 33 0.00% 39 25 0.00% 40 44 0.00% 41 54 0.00% 42 46 0.00% 43 33 0.00% 44 34 0.00% 45 40 0.00% 46 33 0.00% 47 39 0.00% 48 51 0.00% 49 74 0.00% 50 76 0.00% 51 75 0.00% 52 82 0.00% 53 86 0.00% 54 93 0.00% 55 109 0.00% 56 108 0.00% 57 135 0.00% 58 148 0.00% 59 199 0.00% 60 190 0.00% 61 237 0.00% 62 264 0.00% 63 320 0.00% 64 341 0.00% 65 339 0.00% 66 376 0.00% 67 404 0.00% 68 505 0.00% 69 518 0.00% 70 661 0.00% 71 713 0.00% 72 770 0.00% 73 911 0.01% 74 1094 0.01% 75 1084 0.01% 76 1225 0.01% 77 1292 0.01% 78 1500 0.01% 79 1663 0.01% 80 1654 0.01% 81 2042 0.01% 82 2210 0.01% 83 2323 0.01% 84 2601 0.02% 85 2824 0.02% 86 3134 0.02% 87 3298 0.02% 88 3574 0.02% 89 3692 0.02% 90 3849 0.02% 91 4217 0.03% 92 4298 0.03% 93 4505 0.03% 94 5091 0.03% 95 5378 0.03% 96 5782 0.04% 97 6028 0.04% 98 6091 0.04% 99 6422 0.04% 100 6602 0.04% 101 6826 0.04% 102 7057 0.04% 103 7352 0.05% 104 7728 0.05% 105 8271 0.05% 106 8474 0.05% 107 8662 0.05% 108 8883 0.05% 109 9316 0.06% 110 9636 0.06% 111 9777 0.06% 112 10131 0.06% 113 10487 0.06% 114 10533 0.06% 115 10984 0.07% 116 11675 0.07% 117 12359 0.08% 118 12769 0.08% 119 12499 0.08% 120 12951 0.08% 121 13378 0.08% 122 13811 0.09% 123 14117 0.09% 124 14747 0.09% 125 14963 0.09% 126 15316 0.09% 127 16281 0.10% 128 16282 0.10% 129 16656 0.10% 130 16915 0.10% 131 17200 0.11% 132 17441 0.11% 133 18003 0.11% 134 18281 0.11% 135 18364 0.11% 136 19134 0.12% 137 19600 0.12% 138 20110 0.12% 139 21043 0.13% 140 21225 0.13% 141 22203 0.14% 142 22087 0.14% 143 22423 0.14% 144 23113 0.14% 145 23365 0.14% 146 23837 0.15% 147 24350 0.15% 148 26152 0.16% 149 25751 0.16% 150 27384 0.17% 151 15344483 94.56% 16226430 reads passed initial QC criterion=sequence-density sequence-density=0.60 sequence-density-rank=1 fanout-score=1.72 fanout-score-rank=35 prefix-density=1.00 prefix-fanout=1.0 sequence=TGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAGGTGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGGA criterion=fanout-score sequence-density=0.01 sequence-density-rank=35 fanout-score=39.92 fanout-score-rank=1 prefix-density=0.07 prefix-fanout=6.8 sequence=AAACAGAATATTTACTTTTAGCGCAAGTTTCAATTCATGAGCTCGTTACATCACAAGTTAACATTACAAGCCAATAGTCCCAGCACAGAAAAAACTCTTTTGTTGCTCACTTTCCGGGAACGAAGTTTGTGGCATATGCCCAGGCGTTGTTGTTTACTGGGTCAGAAAGGTGGTCAGCCAGGTTCTCCAGTGGTCCCTTTCCGGTCACAATGGCCTGGACAAAGAATCCGAACATTGAGAACATAGCCAACCT criterion=sequence-density sequence-density=0.75 sequence-density-rank=1 fanout-score=1.53 fanout-score-rank=35 prefix-density=1.15 prefix-fanout=1.0 sequence=CACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATCAATCAATCATCATGTCTAGCACCTGCGACACCTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAA criterion=fanout-score sequence-density=0.02 sequence-density-rank=32 fanout-score=31.03 fanout-score-rank=1 prefix-density=0.09 prefix-fanout=7.6 sequence=AAACCCAAAGCTCAAAAAAAATCTTAACTGCACCCGCTCATCCAGCAATGGCAGCAGCAACAATGGCCCTCTCCTCCCCTTCGCTAGCCGGAAAGGCGGTGAAGCTCAACCCCTCCTCCTCTGAGATCATGGGCAATGGCCGTGTCTCCATGAGGAAAACCACCAAGCCTGTTCCCTCCGGGAGCCCATGGTACGGACCAGACCGTGTTAAATACTTGGGCCCGTTCTCTGGTGAGCCCCCATCCTACTTGACTGGTGAGTTCCCTGGTGACTACGGCTGGGACACTGCTGG SRR12671328 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 15:28:51 Started mapping on | Feb 11 15:28:52 Finished on | Feb 11 15:31:21 Mapping speed, Million of reads per hour | 392.05 Number of input reads | 16226430 Average input read length | 299 UNIQUE READS: Uniquely mapped reads number | 14962218 Uniquely mapped reads % | 92.21% Average mapped length | 297.83 Number of splices: Total | 14680772 Number of splices: Annotated (sjdb) | 14384200 Number of splices: GT/AG | 14403517 Number of splices: GC/AG | 224092 Number of splices: AT/AC | 9342 Number of splices: Non-canonical | 43821 Mismatch rate per base, % | 0.39% Deletion rate per base | 0.03% Deletion average length | 2.83 Insertion rate per base | 0.02% Insertion average length | 2.18 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 475726 % of reads mapped to multiple loci | 2.93% Number of reads mapped to too many loci | 29997 % of reads mapped to too many loci | 0.18% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.58% % of reads unmapped: other | 0.10% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 788486 788486 788486 N_multimapping 475726 475726 475726 N_noFeature 466192 14636053 537019 N_ambiguous 363441 1089 107680 UnstrandedReadsAssigned:14132585 PositiveStrandReadsAssigned:325076 NegativeStrandReadsAssigned:14317519 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12671328 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: SRR12671328-trimmed-pair1.fastq SRR12671328-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 16,226,430 reads, 14,241,741 reads pseudoaligned [quant] estimated average fragment length: 292.008 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,039 rounds 52401 SRR12671328.ke.tsv 34699 SRR12671328.se.tsv 87100 total ==> SRR12671328.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1726.99 653 18.2173 Potri.005G024800.1.v4.1 1035 743.992 250 16.1895 Potri.004G059700.1.v4.1 961 670.194 0 0 Potri.007G009000.2.v4.1 1416 1124.99 0 0 Potri.003G141000.2.v4.1 2943 2651.99 560 10.1736 Potri.016G087400.1.v4.1 270 72.586 803.323 533.209 Potri.015G069301.1.v4.1 564 290.676 0 0 Potri.010G195200.1.v4.1 1773 1481.99 144 4.68142 Potri.012G127500.1.v4.1 977 686.104 101 7.09238 ==> SRR12671328.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 225 Potri.001G233950.v4.1 6 Potri.001G122700.v4.1 230 Potri.001G212900.v4.1 238 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 9 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 9 SRR12671328 completed mapping pipeline successfully