Starting /dee2/code/volunteer_pipeline.sh ERR3450054 current disk space = 1543166496768 free memory = 1602399996 ERR3450054 SRAfilesize 00d628ecb2aebf04919b7939305469b0 ERR3450054.sra ERR3450054.sra file validated ERR3450054 is paired end ERR3450054 is conventional basespace ERR3450054 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3450054_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 101 %GC 51 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.07525 37.0 37.0 37.0 37.0 37.0 2 36.217 37.0 37.0 37.0 37.0 37.0 3 36.403 37.0 37.0 37.0 37.0 37.0 4 36.4505 37.0 37.0 37.0 37.0 37.0 5 36.5515 37.0 37.0 37.0 37.0 37.0 6 36.427 37.0 37.0 37.0 37.0 37.0 7 36.444 37.0 37.0 37.0 37.0 37.0 8 36.464 37.0 37.0 37.0 37.0 37.0 9 36.467 37.0 37.0 37.0 37.0 37.0 10-11 36.460499999999996 37.0 37.0 37.0 37.0 37.0 12-13 36.50975 37.0 37.0 37.0 37.0 37.0 14-15 36.50075 37.0 37.0 37.0 37.0 37.0 16-17 36.47325 37.0 37.0 37.0 37.0 37.0 18-19 36.51925 37.0 37.0 37.0 37.0 37.0 20-21 36.4815 37.0 37.0 37.0 37.0 37.0 22-23 36.5015 37.0 37.0 37.0 37.0 37.0 24-25 36.45025 37.0 37.0 37.0 37.0 37.0 26-27 36.439 37.0 37.0 37.0 37.0 37.0 28-29 36.3485 37.0 37.0 37.0 37.0 37.0 30-31 36.459500000000006 37.0 37.0 37.0 37.0 37.0 32-33 36.36175 37.0 37.0 37.0 37.0 37.0 34-35 36.39075 37.0 37.0 37.0 37.0 37.0 36-37 36.3625 37.0 37.0 37.0 37.0 37.0 38-39 36.33125 37.0 37.0 37.0 37.0 37.0 40-41 36.322 37.0 37.0 37.0 37.0 37.0 42-43 36.335750000000004 37.0 37.0 37.0 37.0 37.0 44-45 36.22825 37.0 37.0 37.0 37.0 37.0 46-47 36.228 37.0 37.0 37.0 37.0 37.0 48-49 36.291250000000005 37.0 37.0 37.0 37.0 37.0 50-51 36.22125 37.0 37.0 37.0 37.0 37.0 52-53 36.2295 37.0 37.0 37.0 37.0 37.0 54-55 36.18325 37.0 37.0 37.0 37.0 37.0 56-57 36.166250000000005 37.0 37.0 37.0 37.0 37.0 58-59 36.20225 37.0 37.0 37.0 37.0 37.0 60-61 36.125249999999994 37.0 37.0 37.0 37.0 37.0 62-63 36.132000000000005 37.0 37.0 37.0 37.0 37.0 64-65 36.06375 37.0 37.0 37.0 37.0 37.0 66-67 36.088750000000005 37.0 37.0 37.0 37.0 37.0 68-69 36.109 37.0 37.0 37.0 37.0 37.0 70-71 36.11475 37.0 37.0 37.0 37.0 37.0 72-73 36.131 37.0 37.0 37.0 37.0 37.0 74-75 36.1315 37.0 37.0 37.0 37.0 37.0 76-77 36.11475 37.0 37.0 37.0 37.0 37.0 78-79 36.2035 37.0 37.0 37.0 37.0 37.0 80-81 36.17525 37.0 37.0 37.0 37.0 37.0 82-83 36.1325 37.0 37.0 37.0 37.0 37.0 84-85 36.114000000000004 37.0 37.0 37.0 37.0 37.0 86-87 36.1195 37.0 37.0 37.0 37.0 37.0 88-89 36.05575 37.0 37.0 37.0 37.0 37.0 90-91 36.061 37.0 37.0 37.0 37.0 37.0 92-93 36.166 37.0 37.0 37.0 37.0 37.0 94-95 36.102000000000004 37.0 37.0 37.0 37.0 37.0 96-97 36.066 37.0 37.0 37.0 37.0 37.0 98-99 36.00975 37.0 37.0 37.0 37.0 37.0 100-101 35.956 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 18 1.0 19 0.0 20 1.0 21 0.0 22 3.0 23 5.0 24 6.0 25 10.0 26 12.0 27 19.0 28 25.0 29 23.0 30 32.0 31 32.0 32 63.0 33 82.0 34 104.0 35 174.0 36 1747.0 37 1661.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 39.062891505888246 9.371084941117514 12.427962916562265 39.13806063643197 2 24.0 13.950000000000001 28.375 33.675 3 22.425 17.575 25.724999999999998 34.275 4 28.549999999999997 23.325000000000003 18.6 29.525000000000002 5 28.075 28.225 20.974999999999998 22.725 6 25.0 30.349999999999998 23.45 21.2 7 20.875 22.6 37.75 18.775 8 21.475 20.525 28.999999999999996 28.999999999999996 9 22.225 22.15 30.375000000000004 25.25 10-11 24.275 28.4125 22.075 25.2375 12-13 24.8 21.837500000000002 26.137500000000003 27.224999999999998 14-15 22.912499999999998 24.837500000000002 25.887500000000003 26.3625 16-17 24.025 24.2625 25.424999999999997 26.2875 18-19 24.2 25.412499999999998 24.55 25.837500000000002 20-21 24.3125 25.474999999999998 24.625 25.587500000000002 22-23 23.7875 25.0375 24.6 26.575 24-25 25.412499999999998 24.2875 24.3625 25.937500000000004 26-27 24.349999999999998 25.650000000000002 23.4125 26.5875 28-29 24.4125 24.125 24.712500000000002 26.75 30-31 24.224999999999998 24.4375 24.6 26.737499999999997 32-33 24.8125 24.837500000000002 24.0125 26.337500000000002 34-35 24.837500000000002 24.9375 24.375 25.85 36-37 24.7375 23.962500000000002 24.775 26.525 38-39 23.65 25.124999999999996 24.425 26.8 40-41 24.637500000000003 24.1125 24.4875 26.7625 42-43 25.474999999999998 24.0125 23.7875 26.724999999999998 44-45 24.8625 25.2 23.9 26.0375 46-47 26.5625 24.3875 23.575 25.474999999999998 48-49 24.5375 24.125 23.8125 27.525 50-51 25.7125 24.325 24.3875 25.575 52-53 25.1875 24.875 23.6375 26.3 54-55 25.1875 24.4875 23.474999999999998 26.85 56-57 24.837500000000002 24.8125 24.224999999999998 26.125 58-59 25.412499999999998 24.5375 23.45 26.6 60-61 25.775 24.637500000000003 23.5875 26.0 62-63 24.5 24.0125 23.95 27.537499999999998 64-65 25.174999999999997 24.1875 23.7875 26.85 66-67 25.05 24.2375 24.0 26.7125 68-69 23.3125 24.5375 24.4375 27.712500000000002 70-71 25.8 25.2875 23.3125 25.6 72-73 25.5375 24.45 23.525 26.487500000000004 74-75 26.150000000000002 23.7125 23.200000000000003 26.937499999999996 76-77 25.937500000000004 24.7375 23.4625 25.8625 78-79 26.125 23.8125 23.175 26.887499999999996 80-81 24.85 24.0625 23.6625 27.425 82-83 26.137500000000003 24.9375 22.95 25.974999999999998 84-85 26.150000000000002 23.95 23.0375 26.8625 86-87 25.5625 25.0375 22.3625 27.037499999999998 88-89 25.650000000000002 24.7 23.4125 26.237500000000004 90-91 25.650000000000002 24.125 23.5875 26.637499999999996 92-93 25.5375 24.9 23.4375 26.125 94-95 26.174999999999997 23.549999999999997 22.6 27.675 96-97 24.637500000000003 25.137500000000003 23.5125 26.7125 98-99 25.2625 23.775 23.925 27.037499999999998 100-101 25.087500000000002 25.15 23.35 26.4125 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 8.0 1 4.0 2 0.0 3 0.0 4 0.0 5 2.0 6 3.5 7 2.5 8 2.0 9 1.5 10 1.5 11 1.5 12 0.5 13 0.5 14 0.5 15 0.5 16 0.5 17 0.5 18 1.0 19 1.0 20 0.5 21 0.0 22 1.0 23 1.0 24 0.0 25 0.0 26 1.0 27 2.5 28 2.0 29 2.0 30 3.5 31 3.5 32 7.0 33 10.0 34 15.0 35 25.5 36 26.0 37 33.0 38 58.0 39 72.0 40 87.0 41 115.5 42 138.0 43 153.0 44 166.5 45 174.0 46 175.0 47 184.5 48 181.0 49 159.0 50 156.5 51 162.5 52 141.5 53 136.0 54 132.5 55 106.5 56 91.0 57 94.5 58 93.0 59 86.5 60 81.5 61 66.5 62 64.0 63 69.0 64 78.5 65 72.5 66 61.0 67 66.0 68 64.0 69 56.0 70 50.5 71 37.5 72 32.5 73 39.5 74 33.0 75 20.0 76 14.5 77 13.0 78 11.0 79 10.5 80 11.0 81 8.0 82 5.0 83 3.0 84 3.0 85 2.0 86 0.5 87 1.0 88 0.5 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.22499999999999998 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-11 0.0 12-13 0.0 14-15 0.0 16-17 0.0 18-19 0.0 20-21 0.0 22-23 0.0 24-25 0.0 26-27 0.0 28-29 0.0 30-31 0.0 32-33 0.0 34-35 0.0 36-37 0.0 38-39 0.0 40-41 0.0 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.0 54-55 0.0 56-57 0.0 58-59 0.0 60-61 0.0 62-63 0.0 64-65 0.0 66-67 0.0 68-69 0.0 70-71 0.0 72-73 0.0 74-75 0.0 76-77 0.0 78-79 0.0 80-81 0.0 82-83 0.0 84-85 0.0 86-87 0.0 88-89 0.0 90-91 0.0 92-93 0.0 94-95 0.0 96-97 0.0 98-99 0.0 100-101 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 101 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 89.725 #Duplication Level Percentage of deduplicated Percentage of total 1 90.19225410977988 80.925 2 8.581777653942604 15.4 3 1.0866536639732516 2.9250000000000003 4 0.08358874338255781 0.3 5 0.0 0.0 6 0.0 0.0 7 0.02786291446085261 0.17500000000000002 8 0.0 0.0 9 0.0 0.0 >10 0.02786291446085261 0.27499999999999997 >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 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 11 0.27499999999999997 No Hit CCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCT 7 0.17500000000000002 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 0.0125 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.0625 0.0 0.0 0.0 0.0 44-45 0.11249999999999999 0.0 0.0 0.0 0.0 46-47 0.15 0.0 0.0 0.0 0.0 48-49 0.2 0.0 0.0 0.0 0.0 50-51 0.2625 0.0 0.0 0.0 0.0 52-53 0.36250000000000004 0.0 0.0 0.0 0.0 54-55 0.5125 0.0 0.0 0.0 0.0 56-57 0.6875 0.0 0.0 0.0 0.0 58-59 0.9375 0.0 0.0 0.0 0.0 60-61 1.0375 0.0 0.0 0.0 0.0 62-63 1.15 0.0 0.0 0.0 0.0 64-65 1.25 0.0 0.0 0.0 0.0 66-67 1.55 0.0 0.0 0.0 0.0 68-69 1.7875 0.0 0.0 0.0 0.0 70-71 1.8875 0.0 0.0 0.0 0.0 72-73 2.0375 0.0 0.0 0.0 0.0 74-75 2.3375 0.0 0.0 0.0 0.0 76-77 2.6875 0.0 0.0 0.0 0.0 78-79 3.0625 0.0 0.0 0.0 0.0 80-81 3.5125 0.0 0.0 0.0 0.0 82-83 3.9124999999999996 0.0 0.0 0.0 0.0 84-85 4.325 0.0 0.0 0.0 0.0 86-87 4.675 0.0 0.0 0.0 0.0 88-89 5.0625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE ERR3450054 read2 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3450054_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 101 %GC 52 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.1545 37.0 37.0 37.0 37.0 37.0 2 36.07175 37.0 37.0 37.0 37.0 37.0 3 36.0075 37.0 37.0 37.0 37.0 37.0 4 36.1965 37.0 37.0 37.0 37.0 37.0 5 36.3035 37.0 37.0 37.0 37.0 37.0 6 36.247 37.0 37.0 37.0 37.0 37.0 7 36.1885 37.0 37.0 37.0 37.0 37.0 8 36.252 37.0 37.0 37.0 37.0 37.0 9 36.2865 37.0 37.0 37.0 37.0 37.0 10-11 36.3105 37.0 37.0 37.0 37.0 37.0 12-13 36.3145 37.0 37.0 37.0 37.0 37.0 14-15 36.2315 37.0 37.0 37.0 37.0 37.0 16-17 36.222 37.0 37.0 37.0 37.0 37.0 18-19 36.24525 37.0 37.0 37.0 37.0 37.0 20-21 36.26375 37.0 37.0 37.0 37.0 37.0 22-23 36.27875 37.0 37.0 37.0 37.0 37.0 24-25 36.201 37.0 37.0 37.0 37.0 37.0 26-27 36.093 37.0 37.0 37.0 37.0 37.0 28-29 36.1995 37.0 37.0 37.0 37.0 37.0 30-31 36.1525 37.0 37.0 37.0 37.0 37.0 32-33 36.1635 37.0 37.0 37.0 37.0 37.0 34-35 36.141999999999996 37.0 37.0 37.0 37.0 37.0 36-37 36.14375 37.0 37.0 37.0 37.0 37.0 38-39 36.06075 37.0 37.0 37.0 37.0 37.0 40-41 35.9785 37.0 37.0 37.0 37.0 37.0 42-43 36.005875 37.0 37.0 37.0 37.0 37.0 44-45 35.88775 37.0 37.0 37.0 37.0 37.0 46-47 36.00125 37.0 37.0 37.0 37.0 37.0 48-49 35.96575 37.0 37.0 37.0 37.0 37.0 50-51 35.96 37.0 37.0 37.0 37.0 37.0 52-53 36.07275 37.0 37.0 37.0 37.0 37.0 54-55 35.864000000000004 37.0 37.0 37.0 37.0 37.0 56-57 35.9385 37.0 37.0 37.0 37.0 37.0 58-59 35.914249999999996 37.0 37.0 37.0 37.0 37.0 60-61 35.85925 37.0 37.0 37.0 37.0 37.0 62-63 35.907 37.0 37.0 37.0 37.0 37.0 64-65 35.71775 37.0 37.0 37.0 37.0 37.0 66-67 35.8885 37.0 37.0 37.0 37.0 37.0 68-69 35.792500000000004 37.0 37.0 37.0 37.0 37.0 70-71 35.761 37.0 37.0 37.0 37.0 37.0 72-73 35.724125 37.0 37.0 37.0 37.0 37.0 74-75 35.832875 37.0 37.0 37.0 37.0 37.0 76-77 35.86475 37.0 37.0 37.0 37.0 37.0 78-79 35.7745 37.0 37.0 37.0 37.0 37.0 80-81 35.79625 37.0 37.0 37.0 37.0 37.0 82-83 35.67875 37.0 37.0 37.0 37.0 37.0 84-85 35.797 37.0 37.0 37.0 37.0 37.0 86-87 35.89125 37.0 37.0 37.0 37.0 37.0 88-89 35.89775 37.0 37.0 37.0 37.0 37.0 90-91 35.8945 37.0 37.0 37.0 37.0 37.0 92-93 35.861375 37.0 37.0 37.0 37.0 37.0 94-95 35.82025 37.0 37.0 37.0 37.0 37.0 96-97 35.82925 37.0 37.0 37.0 37.0 37.0 98-99 35.804 37.0 37.0 37.0 37.0 37.0 100-101 35.83125 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 14 1.0 15 2.0 16 5.0 17 1.0 18 6.0 19 1.0 20 8.0 21 7.0 22 11.0 23 13.0 24 14.0 25 12.0 26 18.0 27 16.0 28 22.0 29 19.0 30 24.0 31 39.0 32 54.0 33 59.0 34 128.0 35 210.0 36 2151.0 37 1179.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 40.275 16.650000000000002 13.0 30.075000000000003 2 26.406601650412604 21.48037009252313 26.30657664416104 25.806451612903224 3 25.0 23.225 27.900000000000002 23.875 4 30.85 25.974999999999998 18.95 24.224999999999998 5 29.075 28.975 19.400000000000002 22.55 6 24.6 31.4 20.9 23.1 7 25.825 18.4 29.7 26.075 8 25.074999999999996 21.099999999999998 24.0 29.825000000000003 9 27.1 20.825 24.75 27.325 10-11 28.8625 27.5875 18.875 24.675 12-13 28.212500000000002 21.5375 22.975 27.275 14-15 27.187499999999996 24.65 22.95 25.2125 16-17 28.449999999999996 24.675 21.9375 24.9375 18-19 26.3625 24.0625 23.75 25.825 20-21 27.525 24.85 21.712500000000002 25.912499999999998 22-23 27.750000000000004 24.4 22.2125 25.637500000000003 24-25 27.750000000000004 24.4375 22.4875 25.324999999999996 26-27 27.35 24.762500000000003 22.9375 24.95 28-29 28.275 24.6625 21.875 25.1875 30-31 27.025 24.375 23.4375 25.162499999999998 32-33 27.9125 24.3125 22.5875 25.1875 34-35 27.187499999999996 24.8125 22.8125 25.1875 36-37 26.187500000000004 23.8875 22.75 27.175 38-39 26.987499999999997 23.9375 23.8375 25.2375 40-41 27.200000000000003 24.7875 22.7 25.3125 42-43 26.16577072134017 23.827978497312163 23.91548943617952 26.090761345168147 44-45 26.3 24.3875 24.025 25.2875 46-47 27.3125 24.2375 22.7 25.75 48-49 26.55 24.75 23.2125 25.4875 50-51 27.3125 24.65 23.25 24.7875 52-53 27.1125 24.212500000000002 22.925 25.75 54-55 26.700000000000003 24.2375 23.325000000000003 25.7375 56-57 27.737499999999997 24.0125 22.675 25.575 58-59 26.724999999999998 24.9375 23.425 24.9125 60-61 26.937499999999996 24.224999999999998 23.05 25.7875 62-63 26.6625 23.775 23.75 25.8125 64-65 27.224999999999998 24.0 23.95 24.825 66-67 27.250000000000004 23.962500000000002 23.225 25.5625 68-69 26.424999999999997 24.6625 24.25 24.6625 70-71 28.575 24.75 22.75 23.925 72-73 26.915864483060382 24.715589448681087 23.91548943617952 24.453056632079008 74-75 26.478309788723593 24.090511313914238 23.415426928366045 26.015751968996128 76-77 27.0 23.6375 23.9875 25.374999999999996 78-79 26.974999999999998 24.2 24.4 24.425 80-81 27.325 24.575 22.662499999999998 25.4375 82-83 28.15 24.6625 22.8625 24.325 84-85 26.674999999999997 24.275 24.625 24.425 86-87 27.400000000000002 24.5 23.8125 24.2875 88-89 28.3875 25.3 22.162499999999998 24.15 90-91 27.8875 25.074999999999996 22.2 24.837500000000002 92-93 27.753469183647955 25.54069258657332 22.202775346918365 24.50306288286036 94-95 29.125 24.474999999999998 22.0625 24.337500000000002 96-97 28.287499999999998 24.725 22.6125 24.375 98-99 27.537499999999998 25.4 22.85 24.212500000000002 100-101 28.025 24.9 21.8875 25.1875 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 1.0 3 1.0 4 0.0 5 1.5 6 1.5 7 0.5 8 2.0 9 3.0 10 2.5 11 1.5 12 2.5 13 4.0 14 3.0 15 1.5 16 3.5 17 3.0 18 0.0 19 0.0 20 0.0 21 1.5 22 2.0 23 0.5 24 1.0 25 1.0 26 0.0 27 0.0 28 0.5 29 3.5 30 6.5 31 7.0 32 6.5 33 6.5 34 8.5 35 19.5 36 28.0 37 42.0 38 57.0 39 70.5 40 87.0 41 98.5 42 126.0 43 142.0 44 137.0 45 144.0 46 169.5 47 177.5 48 162.5 49 160.0 50 161.0 51 148.0 52 140.0 53 127.5 54 111.0 55 112.0 56 98.0 57 95.0 58 92.5 59 85.5 60 82.5 61 77.0 62 76.0 63 77.0 64 89.5 65 75.0 66 60.0 67 70.0 68 72.0 69 69.0 70 64.0 71 54.0 72 53.5 73 47.5 74 36.0 75 29.0 76 23.5 77 22.5 78 16.0 79 6.0 80 3.5 81 5.5 82 5.0 83 3.0 84 4.0 85 3.0 86 0.5 87 0.5 88 0.5 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.5 100 3.0 >>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 10-11 0.0 12-13 0.0 14-15 0.0 16-17 0.0 18-19 0.0 20-21 0.0 22-23 0.0 24-25 0.0 26-27 0.0 28-29 0.0 30-31 0.0 32-33 0.0 34-35 0.0 36-37 0.0 38-39 0.0 40-41 0.0 42-43 0.0125 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.0 54-55 0.0 56-57 0.0 58-59 0.0 60-61 0.0 62-63 0.0 64-65 0.0 66-67 0.0 68-69 0.0 70-71 0.0 72-73 0.0125 74-75 0.0125 76-77 0.0 78-79 0.0 80-81 0.0 82-83 0.0 84-85 0.0 86-87 0.0 88-89 0.0 90-91 0.0 92-93 0.0125 94-95 0.0 96-97 0.0 98-99 0.0 100-101 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 101 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 90.3 #Duplication Level Percentage of deduplicated Percentage of total 1 90.61461794019934 81.825 2 8.333333333333332 15.049999999999999 3 0.9413067552602437 2.55 4 0.02768549280177187 0.1 5 0.0 0.0 6 0.05537098560354374 0.3 7 0.02768549280177187 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 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 7 0.17500000000000002 No Hit GTTTGAGGCAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCCGCAC 6 0.15 No Hit CTTACCAGGTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTT 6 0.15 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 0.0125 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.0625 0.0 0.0 0.0 0.0 44-45 0.11249999999999999 0.0 0.0 0.0 0.0 46-47 0.15 0.0 0.0 0.0 0.0 48-49 0.2 0.0 0.0 0.0 0.0 50-51 0.2875 0.0 0.0 0.0 0.0 52-53 0.3625 0.0 0.0 0.0 0.0 54-55 0.48750000000000004 0.0 0.0 0.0 0.0 56-57 0.6625 0.0 0.0 0.0 0.0 58-59 0.8875 0.0 0.0 0.0 0.0 60-61 0.9875 0.0 0.0 0.0 0.0 62-63 1.1 0.0 0.0 0.0 0.0 64-65 1.2 0.0 0.0 0.0 0.0 66-67 1.5 0.0 0.0 0.0 0.0 68-69 1.7375 0.0 0.0 0.0 0.0 70-71 1.8375 0.0 0.0 0.0 0.0 72-73 1.9875 0.0 0.0 0.0 0.0 74-75 2.2750000000000004 0.0 0.0 0.0 0.0 76-77 2.6125 0.0 0.0 0.0 0.0 78-79 2.9875 0.0 0.0 0.0 0.0 80-81 3.4375 0.0 0.0 0.0 0.0 82-83 3.85 0.0 0.0 0.0 0.0 84-85 4.275 0.0 0.0 0.0 0.0 86-87 4.625 0.0 0.0 0.0 0.0 88-89 5.0125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 583290 spots for ERR3450054.sra Written 583290 spots for ERR3450054.sra Read 583290 spots for ERR3450054.sra Written 583290 spots for ERR3450054.sra Read 583290 spots for ERR3450054.sra Written 583290 spots for ERR3450054.sra Read 583290 spots for ERR3450054.sra Written 583290 spots for ERR3450054.sra Read 583290 spots for ERR3450054.sra Written 583290 spots for ERR3450054.sra Read 583290 spots for ERR3450054.sra Written 583290 spots for ERR3450054.sra Read 583290 spots for ERR3450054.sra Written 583290 spots for ERR3450054.sra Read 583290 spots for ERR3450054.sra Written 583290 spots for ERR3450054.sra Read 583290 spots for ERR3450054.sra Written 583290 spots for ERR3450054.sra Read 583290 spots for ERR3450054.sra Written 583290 spots for ERR3450054.sra Read 583290 spots for ERR3450054.sra Written 583290 spots for ERR3450054.sra Read 583290 spots for ERR3450054.sra Written 583290 spots for ERR3450054.sra Read 583290 spots for ERR3450054.sra Written 583290 spots for ERR3450054.sra Read 583290 spots for ERR3450054.sra Written 583290 spots for ERR3450054.sra Read 583299 spots for ERR3450054.sra Written 583299 spots for ERR3450054.sra Read 583290 spots for ERR3450054.sra Written 583290 spots for ERR3450054.sra Read 583290 spots for ERR3450054.sra Written 583290 spots for ERR3450054.sra Read 583290 spots for ERR3450054.sra Written 583290 spots for ERR3450054.sra Read 583290 spots for ERR3450054.sra Written 583290 spots for ERR3450054.sra Read 583290 spots for ERR3450054.sra Written 583290 spots for ERR3450054.sra SRR ids: ['ERR3450054.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_bytbk0sd ERR3450054.sra spots: 11665809 blocks: [[1, 583290], [583291, 1166580], [1166581, 1749870], [1749871, 2333160], [2333161, 2916450], [2916451, 3499740], [3499741, 4083030], [4083031, 4666320], [4666321, 5249610], [5249611, 5832900], [5832901, 6416190], [6416191, 6999480], [6999481, 7582770], [7582771, 8166060], [8166061, 8749350], [8749351, 9332640], [9332641, 9915930], [9915931, 10499220], [10499221, 11082510], [11082511, 11665809]] ERR3450054 file size 2792220 ERR3450054 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 ERR3450054 ERR3450054_1.fastq ERR3450054_2.fastq Input file: ERR3450054_1.fastq Paired file: ERR3450054_2.fastq trimmed: ERR3450054-trimmed-pair1.fastq, ERR3450054-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 Sat Dec 7 14:06:09 2024 >> started Sat Dec 7 14:06:20 2024 >> done (11.566s) 11665809 read pairs processed; of these: 102 ( 0.00%) short read pairs filtered out after trimming by size control 20808 ( 0.18%) empty read pairs filtered out after trimming by size control 11644899 (99.82%) read pairs available; of these: 1106704 ( 9.50%) trimmed read pairs available after processing 10538195 (90.50%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 16 0.00% 19 45 0.00% 20 105 0.00% 21 255 0.00% 22 324 0.00% 23 189 0.00% 24 178 0.00% 25 233 0.00% 26 313 0.00% 27 448 0.00% 28 643 0.01% 29 806 0.01% 30 981 0.01% 31 1228 0.01% 32 1258 0.01% 33 1173 0.01% 34 1216 0.01% 35 1166 0.01% 36 1318 0.01% 37 1498 0.01% 38 1635 0.01% 39 1858 0.02% 40 2219 0.02% 41 2616 0.02% 42 2973 0.03% 43 3022 0.03% 44 2773 0.02% 45 2792 0.02% 46 2871 0.02% 47 3135 0.03% 48 3557 0.03% 49 3885 0.03% 50 4431 0.04% 51 4829 0.04% 52 5061 0.04% 53 5452 0.05% 54 5690 0.05% 55 5887 0.05% 56 6142 0.05% 57 6549 0.06% 58 6947 0.06% 59 7720 0.07% 60 8205 0.07% 61 8860 0.08% 62 9984 0.09% 63 10396 0.09% 64 10858 0.09% 65 11344 0.10% 66 11636 0.10% 67 12155 0.10% 68 12818 0.11% 69 13484 0.12% 70 14360 0.12% 71 15195 0.13% 72 16225 0.14% 73 17265 0.15% 74 17915 0.15% 75 18662 0.16% 76 19433 0.17% 77 20046 0.17% 78 20741 0.18% 79 21815 0.19% 80 23023 0.20% 81 23562 0.20% 82 25180 0.22% 83 26345 0.23% 84 27140 0.23% 85 28603 0.25% 86 29040 0.25% 87 29910 0.26% 88 31237 0.27% 89 31690 0.27% 90 32977 0.28% 91 34405 0.30% 92 35724 0.31% 93 37458 0.32% 94 38593 0.33% 95 39440 0.34% 96 39809 0.34% 97 41115 0.35% 98 42030 0.36% 99 43274 0.37% 100 49315 0.42% 101 10538195 90.50% 11644899 reads passed initial QC criterion=sequence-density sequence-density=0.19 sequence-density-rank=1 fanout-score=1.96 fanout-score-rank=29 prefix-density=0.19 prefix-fanout=1.9 sequence=GTATTTAGCCTTG criterion=fanout-score sequence-density=0.09 sequence-density-rank=20 fanout-score=192.06 fanout-score-rank=1 prefix-density=0.73 prefix-fanout=22.5 sequence=CGCCGCCGCCGC criterion=sequence-density sequence-density=0.19 sequence-density-rank=1 fanout-score=2.77 fanout-score-rank=23 prefix-density=0.21 prefix-fanout=2.5 sequence=CAGGTGCTCAAGGAGCTGGAGGAGGTCAAGAAGGAGTACCCGGACGCCTA criterion=fanout-score sequence-density=0.10 sequence-density-rank=20 fanout-score=215.03 fanout-score-rank=1 prefix-density=0.91 prefix-fanout=23.3 sequence=CGGCGGCGGCGA ERR3450054 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 14:06:59 Started mapping on | Dec 07 14:06:59 Finished on | Dec 07 14:07:45 Mapping speed, Million of reads per hour | 911.34 Number of input reads | 11644899 Average input read length | 198 UNIQUE READS: Uniquely mapped reads number | 9841856 Uniquely mapped reads % | 84.52% Average mapped length | 197.85 Number of splices: Total | 6094927 Number of splices: Annotated (sjdb) | 5782118 Number of splices: GT/AG | 6013006 Number of splices: GC/AG | 71000 Number of splices: AT/AC | 3388 Number of splices: Non-canonical | 7533 Mismatch rate per base, % | 0.23% Deletion rate per base | 0.01% Deletion average length | 2.15 Insertion rate per base | 0.01% Insertion average length | 1.91 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 666824 % of reads mapped to multiple loci | 5.73% Number of reads mapped to too many loci | 149926 % of reads mapped to too many loci | 1.29% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.16% % of reads unmapped: other | 5.31% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1136219 1136219 1136219 N_multimapping 666824 666824 666824 N_noFeature 275803 9499727 465626 N_ambiguous 193745 1587 44867 UnstrandedReadsAssigned:9372308 PositiveStrandReadsAssigned:340542 NegativeStrandReadsAssigned:9331363 Dataset is classified negative stranded MeadianReadLen=101 20thPercentileLength=101 echo kmer=97 ERR3450054 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: ERR3450054-trimmed-pair1.fastq ERR3450054-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 11,644,899 reads, 9,965,532 reads pseudoaligned [quant] estimated average fragment length: 187.861 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,179 rounds 52973 ERR3450054.ke.tsv 35125 ERR3450054.se.tsv 88098 total ==> ERR3450054.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 749.359 0 0 PNS24247 1044 857.139 23.5463 4.11806 PNS24249 1928 1741.14 54.9358 4.72982 PNS24246 1044 857.139 23.5463 4.11806 PNS24248 1044 857.139 23.5463 4.11806 PNS24244 1471 1284.14 35.4254 4.13548 PNS24243 293 128.932 0 0 KQK14069 1603 1416.14 3627.74 384.019 KQK14071 474 291.232 137.427 70.7385 ==> ERR3450054.se.tsv <== BRADI_1g14170v3 3852 BRADI_1g53295v3 15 BRADI_1g59795v3 90 BRADI_1g07683v3 0 BRADI_1g00485v3 15 BRADI_1g20270v3 934 BRADI_1g74790v3 138 BRADI_1g09890v3 7 BRADI_1g77505v3 124 BRADI_1g48960v3 0 ERR3450054 completed mapping pipeline successfully