Starting /dee2/code/volunteer_pipeline.sh ERR3450055 current disk space = 1543154913280 free memory = 1603228268 ERR3450055 SRAfilesize 6247ba465852a4a9972b3fa90ada9ba8 ERR3450055.sra ERR3450055.sra file validated ERR3450055 is paired end ERR3450055 is conventional basespace ERR3450055 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3450055_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 52 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.11975 37.0 37.0 37.0 37.0 37.0 2 36.3935 37.0 37.0 37.0 37.0 37.0 3 36.421 37.0 37.0 37.0 37.0 37.0 4 36.4305 37.0 37.0 37.0 37.0 37.0 5 36.5075 37.0 37.0 37.0 37.0 37.0 6 36.449 37.0 37.0 37.0 37.0 37.0 7 36.535 37.0 37.0 37.0 37.0 37.0 8 36.468 37.0 37.0 37.0 37.0 37.0 9 36.5035 37.0 37.0 37.0 37.0 37.0 10-11 36.5535 37.0 37.0 37.0 37.0 37.0 12-13 36.51475 37.0 37.0 37.0 37.0 37.0 14-15 36.47525 37.0 37.0 37.0 37.0 37.0 16-17 36.536500000000004 37.0 37.0 37.0 37.0 37.0 18-19 36.5525 37.0 37.0 37.0 37.0 37.0 20-21 36.457499999999996 37.0 37.0 37.0 37.0 37.0 22-23 36.54575 37.0 37.0 37.0 37.0 37.0 24-25 36.401250000000005 37.0 37.0 37.0 37.0 37.0 26-27 36.441 37.0 37.0 37.0 37.0 37.0 28-29 36.3835 37.0 37.0 37.0 37.0 37.0 30-31 36.413250000000005 37.0 37.0 37.0 37.0 37.0 32-33 36.3935 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 36.40325 37.0 37.0 37.0 37.0 37.0 38-39 36.2955 37.0 37.0 37.0 37.0 37.0 40-41 36.34775 37.0 37.0 37.0 37.0 37.0 42-43 36.272999999999996 37.0 37.0 37.0 37.0 37.0 44-45 36.21625 37.0 37.0 37.0 37.0 37.0 46-47 36.118 37.0 37.0 37.0 37.0 37.0 48-49 36.198 37.0 37.0 37.0 37.0 37.0 50-51 36.17375 37.0 37.0 37.0 37.0 37.0 52-53 36.13975 37.0 37.0 37.0 37.0 37.0 54-55 36.15275 37.0 37.0 37.0 37.0 37.0 56-57 36.12325 37.0 37.0 37.0 37.0 37.0 58-59 36.084500000000006 37.0 37.0 37.0 37.0 37.0 60-61 36.1055 37.0 37.0 37.0 37.0 37.0 62-63 36.058 37.0 37.0 37.0 37.0 37.0 64-65 36.09075 37.0 37.0 37.0 37.0 37.0 66-67 36.11725 37.0 37.0 37.0 37.0 37.0 68-69 36.133750000000006 37.0 37.0 37.0 37.0 37.0 70-71 36.12 37.0 37.0 37.0 37.0 37.0 72-73 36.0815 37.0 37.0 37.0 37.0 37.0 74-75 36.07125 37.0 37.0 37.0 37.0 37.0 76-77 36.17100000000001 37.0 37.0 37.0 37.0 37.0 78-79 36.18775 37.0 37.0 37.0 37.0 37.0 80-81 36.133250000000004 37.0 37.0 37.0 37.0 37.0 82-83 35.999 37.0 37.0 37.0 37.0 37.0 84-85 36.1065 37.0 37.0 37.0 37.0 37.0 86-87 36.08625000000001 37.0 37.0 37.0 37.0 37.0 88-89 36.1385 37.0 37.0 37.0 37.0 37.0 90-91 36.0905 37.0 37.0 37.0 37.0 37.0 92-93 36.079499999999996 37.0 37.0 37.0 37.0 37.0 94-95 36.08625 37.0 37.0 37.0 37.0 37.0 96-97 36.02275 37.0 37.0 37.0 37.0 37.0 98-99 35.985749999999996 37.0 37.0 37.0 37.0 37.0 100-101 36.021249999999995 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 1.0 21 2.0 22 2.0 23 4.0 24 6.0 25 7.0 26 12.0 27 14.0 28 23.0 29 30.0 30 53.0 31 40.0 32 56.0 33 83.0 34 77.0 35 179.0 36 1671.0 37 1740.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 39.10208176573865 10.057687484324052 10.534236267870579 40.305994482066716 2 22.175 13.900000000000002 30.475 33.45 3 21.525 17.4 24.575 36.5 4 29.475 22.525000000000002 17.5 30.5 5 28.675 26.924999999999997 21.325 23.075000000000003 6 23.5 31.35 22.975 22.175 7 20.275000000000002 22.45 36.85 20.424999999999997 8 21.75 20.775 30.099999999999998 27.375 9 23.200000000000003 21.425 29.175 26.200000000000003 10-11 24.4 27.9375 22.175 25.4875 12-13 23.1 22.6875 25.7875 28.425 14-15 23.75 24.5625 25.7125 25.974999999999998 16-17 25.112499999999997 23.799999999999997 24.587500000000002 26.5 18-19 25.45 24.4875 23.9 26.1625 20-21 24.4875 23.962500000000002 24.825 26.724999999999998 22-23 25.0 23.8375 24.775 26.387500000000003 24-25 25.525 23.45 24.474999999999998 26.55 26-27 24.425 23.8875 24.775 26.9125 28-29 25.674999999999997 23.6625 24.1875 26.474999999999998 30-31 24.637500000000003 23.0375 24.0625 28.262500000000003 32-33 23.8875 23.6125 25.587500000000002 26.9125 34-35 24.6625 24.7875 24.025 26.525 36-37 23.875 23.4375 24.5125 28.175 38-39 24.525 23.4875 25.2875 26.700000000000003 40-41 24.925 22.9875 24.8625 27.224999999999998 42-43 24.9 23.925 24.025 27.150000000000002 44-45 24.5625 24.3625 24.4875 26.5875 46-47 25.3125 23.45 24.8625 26.375 48-49 24.725 23.8625 24.175 27.237499999999997 50-51 24.75 23.7 24.325 27.224999999999998 52-53 25.362499999999997 23.7375 23.95 26.950000000000003 54-55 25.2 23.962500000000002 24.2625 26.575 56-57 25.4375 23.1625 24.5125 26.887499999999996 58-59 24.85 24.4375 23.1875 27.525 60-61 24.675 23.849999999999998 24.6 26.875 62-63 24.675 24.15 24.3 26.875 64-65 25.374999999999996 23.6625 24.474999999999998 26.487500000000004 66-67 25.374999999999996 23.4375 23.150000000000002 28.037499999999998 68-69 25.1875 24.025 23.5625 27.224999999999998 70-71 25.324999999999996 23.849999999999998 24.1625 26.6625 72-73 26.200000000000003 23.8125 22.650000000000002 27.3375 74-75 25.5625 24.462500000000002 22.3375 27.6375 76-77 25.900000000000002 24.275 23.3875 26.437500000000004 78-79 25.637500000000003 23.625 23.4375 27.3 80-81 24.7875 24.175 23.6625 27.375 82-83 25.3 23.474999999999998 24.0375 27.187499999999996 84-85 25.0 24.462500000000002 22.7 27.8375 86-87 25.162499999999998 24.275 23.6875 26.875 88-89 25.4875 24.05 23.4625 27.0 90-91 25.35 24.637500000000003 23.3125 26.700000000000003 92-93 25.2625 24.2625 23.875 26.6 94-95 25.074999999999996 24.9125 23.150000000000002 26.8625 96-97 25.45 23.849999999999998 22.875 27.825 98-99 25.15 24.175 23.974999999999998 26.700000000000003 100-101 25.4 25.224999999999998 22.4375 26.937499999999996 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 8.0 1 4.5 2 0.5 3 0.0 4 0.0 5 1.5 6 2.0 7 3.0 8 2.5 9 0.0 10 1.0 11 3.0 12 2.5 13 0.5 14 0.0 15 0.5 16 0.5 17 0.0 18 0.0 19 0.5 20 2.0 21 2.0 22 1.5 23 2.0 24 1.0 25 0.0 26 2.0 27 4.0 28 3.0 29 2.0 30 2.0 31 6.0 32 6.5 33 10.5 34 13.5 35 13.0 36 20.5 37 35.5 38 46.5 39 55.0 40 72.0 41 88.0 42 115.0 43 148.0 44 158.5 45 157.5 46 170.0 47 177.0 48 170.0 49 161.5 50 165.5 51 173.0 52 157.5 53 141.0 54 132.5 55 127.0 56 126.0 57 120.0 58 118.0 59 100.5 60 79.5 61 81.0 62 72.5 63 66.0 64 68.0 65 71.5 66 61.5 67 57.0 68 65.5 69 54.5 70 44.0 71 42.0 72 37.5 73 36.0 74 30.0 75 21.5 76 15.5 77 14.0 78 16.5 79 9.5 80 5.0 81 6.0 82 6.0 83 2.0 84 0.0 85 0.5 86 0.5 87 0.0 88 0.5 89 1.0 90 0.5 91 0.0 92 0.0 93 0.5 94 0.5 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 0.325 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 89.7 #Duplication Level Percentage of deduplicated Percentage of total 1 90.66332218506132 81.325 2 7.94314381270903 14.249999999999998 3 1.0590858416945375 2.85 4 0.16722408026755853 0.6 5 0.055741360089186176 0.25 6 0.055741360089186176 0.3 7 0.027870680044593088 0.17500000000000002 8 0.0 0.0 9 0.0 0.0 >10 0.027870680044593088 0.25 >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 10 0.25 No Hit GTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCC 7 0.17500000000000002 No Hit GTCGAGTTATCATGAATCATCGGATCAGCGAGCAAAGCCCGCGTCAGCCT 6 0.15 No Hit GCCGCAGGCTCCACGCCTGGTGGTGCCCTTCCGTCAATTCCTTTAAGTTT 6 0.15 No Hit GCTGGAATTACCGCGGCTGCTGGCACCAGACTTGCCCTCCAATGGATCCT 5 0.125 No Hit CCGGAACCCAAAGACTTTGATTTCTCATAAGGTGCCGGCGGAGTCCTATA 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 0.0875 0.0 0.0 0.0 0.0 36-37 0.125 0.0 0.0 0.0 0.0 38-39 0.15 0.0 0.0 0.0 0.0 40-41 0.225 0.0 0.0 0.0 0.0 42-43 0.30000000000000004 0.0 0.0 0.0 0.0 44-45 0.325 0.0 0.0 0.0 0.0 46-47 0.35 0.0 0.0 0.0 0.0 48-49 0.4375 0.0 0.0 0.0 0.0 50-51 0.4625 0.0 0.0 0.0 0.0 52-53 0.5375 0.0 0.0 0.0 0.0 54-55 0.5874999999999999 0.0 0.0 0.0 0.0 56-57 0.625 0.0 0.0 0.0 0.0 58-59 0.7 0.0 0.0 0.0 0.0 60-61 0.875 0.0 0.0 0.0 0.0 62-63 1.0499999999999998 0.0 0.0 0.0 0.0 64-65 1.2375 0.0 0.0 0.0 0.0 66-67 1.4 0.0 0.0 0.0 0.0 68-69 1.6625 0.0 0.0 0.0 0.0 70-71 1.8875000000000002 0.0 0.0 0.0 0.0 72-73 2.2 0.0 0.0 0.0 0.0 74-75 2.575 0.0 0.0 0.0 0.0 76-77 3.0375 0.0 0.0 0.0 0.0 78-79 3.3499999999999996 0.0 0.0 0.0 0.0 80-81 3.6624999999999996 0.0 0.0 0.0 0.0 82-83 4.075 0.0 0.0 0.0 0.0 84-85 4.5375 0.0 0.0 0.0 0.0 86-87 5.0375 0.0 0.0 0.0 0.0 88-89 5.6875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE ERR3450055 read2 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3450055_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 36.0025 37.0 37.0 37.0 37.0 37.0 2 35.9225 37.0 37.0 37.0 37.0 37.0 3 35.8725 37.0 37.0 37.0 37.0 37.0 4 36.1285 37.0 37.0 37.0 37.0 37.0 5 36.1345 37.0 37.0 37.0 37.0 37.0 6 36.181 37.0 37.0 37.0 37.0 37.0 7 36.0585 37.0 37.0 37.0 37.0 37.0 8 36.0215 37.0 37.0 37.0 37.0 37.0 9 36.0525 37.0 37.0 37.0 37.0 37.0 10-11 36.136750000000006 37.0 37.0 37.0 37.0 37.0 12-13 36.10325 37.0 37.0 37.0 37.0 37.0 14-15 36.0975 37.0 37.0 37.0 37.0 37.0 16-17 36.064 37.0 37.0 37.0 37.0 37.0 18-19 36.105000000000004 37.0 37.0 37.0 37.0 37.0 20-21 36.06375 37.0 37.0 37.0 37.0 37.0 22-23 36.047250000000005 37.0 37.0 37.0 37.0 37.0 24-25 36.05675 37.0 37.0 37.0 37.0 37.0 26-27 35.983000000000004 37.0 37.0 37.0 37.0 37.0 28-29 35.93675 37.0 37.0 37.0 37.0 37.0 30-31 35.9855 37.0 37.0 37.0 37.0 37.0 32-33 35.8155 37.0 37.0 37.0 37.0 37.0 34-35 35.884249999999994 37.0 37.0 37.0 37.0 37.0 36-37 35.91375 37.0 37.0 37.0 37.0 37.0 38-39 35.879 37.0 37.0 37.0 37.0 37.0 40-41 35.858999999999995 37.0 37.0 37.0 37.0 37.0 42-43 35.9155 37.0 37.0 37.0 37.0 37.0 44-45 35.825 37.0 37.0 37.0 37.0 37.0 46-47 35.73225 37.0 37.0 37.0 37.0 37.0 48-49 35.81125 37.0 37.0 37.0 37.0 37.0 50-51 35.7785 37.0 37.0 37.0 37.0 37.0 52-53 35.849999999999994 37.0 37.0 37.0 37.0 37.0 54-55 35.798 37.0 37.0 37.0 37.0 37.0 56-57 35.7175 37.0 37.0 37.0 37.0 37.0 58-59 35.7455 37.0 37.0 37.0 37.0 37.0 60-61 35.70025 37.0 37.0 37.0 37.0 37.0 62-63 35.6875 37.0 37.0 37.0 37.0 37.0 64-65 35.65325 37.0 37.0 37.0 37.0 37.0 66-67 35.623999999999995 37.0 37.0 37.0 37.0 37.0 68-69 35.53575 37.0 37.0 37.0 37.0 37.0 70-71 35.59825 37.0 37.0 37.0 37.0 37.0 72-73 35.5715 37.0 37.0 37.0 37.0 37.0 74-75 35.5975 37.0 37.0 37.0 37.0 37.0 76-77 35.702749999999995 37.0 37.0 37.0 37.0 37.0 78-79 35.531000000000006 37.0 37.0 37.0 37.0 37.0 80-81 35.562749999999994 37.0 37.0 37.0 37.0 37.0 82-83 35.59125 37.0 37.0 37.0 37.0 37.0 84-85 35.57275 37.0 37.0 37.0 37.0 37.0 86-87 35.706 37.0 37.0 37.0 37.0 37.0 88-89 35.8095 37.0 37.0 37.0 37.0 37.0 90-91 35.757 37.0 37.0 37.0 37.0 37.0 92-93 35.698 37.0 37.0 37.0 37.0 37.0 94-95 35.77575 37.0 37.0 37.0 37.0 37.0 96-97 35.709500000000006 37.0 37.0 37.0 37.0 37.0 98-99 35.732 37.0 37.0 37.0 37.0 37.0 100-101 35.66175 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 14 3.0 15 3.0 16 1.0 17 2.0 18 7.0 19 7.0 20 10.0 21 13.0 22 14.0 23 19.0 24 10.0 25 14.0 26 19.0 27 18.0 28 27.0 29 24.0 30 37.0 31 49.0 32 55.0 33 83.0 34 93.0 35 279.0 36 2114.0 37 1099.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 40.525 16.7 12.375 30.4 2 26.875 21.725 27.150000000000002 24.25 3 25.35 24.7 25.650000000000002 24.3 4 30.975 25.775 18.325 24.925 5 29.775000000000002 29.275000000000002 17.275 23.674999999999997 6 23.5 33.900000000000006 19.950000000000003 22.650000000000002 7 23.5 19.425 31.2 25.874999999999996 8 26.150000000000002 20.424999999999997 23.35 30.075000000000003 9 26.0 21.725 23.549999999999997 28.725 10-11 28.6125 26.7125 19.3125 25.362499999999997 12-13 29.1125 22.075 22.287499999999998 26.525 14-15 26.187500000000004 25.025 24.212500000000002 24.575 16-17 28.050000000000004 23.7875 21.9375 26.224999999999998 18-19 27.625 24.7375 22.4375 25.2 20-21 27.1 24.6 21.8875 26.4125 22-23 28.3625 23.200000000000003 23.225 25.2125 24-25 27.4125 24.525 23.0375 25.025 26-27 27.8125 24.962500000000002 22.05 25.174999999999997 28-29 28.1 24.4 22.1375 25.362499999999997 30-31 28.287499999999998 24.7375 22.55 24.425 32-33 26.575 24.175 23.400000000000002 25.85 34-35 27.250000000000004 23.8875 23.150000000000002 25.7125 36-37 27.075 24.212500000000002 23.225 25.4875 38-39 26.224999999999998 25.074999999999996 22.9375 25.7625 40-41 27.750000000000004 24.337500000000002 22.85 25.0625 42-43 26.387500000000003 24.9375 23.3625 25.3125 44-45 27.400000000000002 24.2 23.7875 24.6125 46-47 27.5625 24.55 22.537499999999998 25.35 48-49 26.787499999999998 24.025 23.400000000000002 25.7875 50-51 26.075 24.8625 23.7375 25.324999999999996 52-53 26.937499999999996 24.4 22.625 26.0375 54-55 27.3875 24.462500000000002 22.900000000000002 25.25 56-57 26.450000000000003 24.3125 24.0375 25.2 58-59 26.9625 24.05 23.5125 25.474999999999998 60-61 27.6125 24.6125 22.8 24.975 62-63 28.212500000000002 24.15 23.2625 24.375 64-65 27.025 23.9875 23.1875 25.8 66-67 26.937499999999996 25.1875 22.8 25.074999999999996 68-69 26.5625 25.7875 22.900000000000002 24.75 70-71 27.9375 25.8 22.275 23.9875 72-73 26.974999999999998 25.3125 22.85 24.8625 74-75 26.950000000000003 24.525 22.875 25.650000000000002 76-77 28.4375 24.075 22.55 24.9375 78-79 27.187499999999996 24.8625 23.7375 24.212500000000002 80-81 27.700000000000003 24.725 23.2875 24.2875 82-83 27.85 23.9125 22.925 25.3125 84-85 28.849999999999998 23.65 22.975 24.525 86-87 28.575 24.575 23.0125 23.8375 88-89 28.8625 24.3 22.425 24.4125 90-91 28.575 24.125 22.75 24.55 92-93 29.549999999999997 25.137500000000003 21.7 23.6125 94-95 28.875 24.95 22.15 24.025 96-97 27.9125 24.337500000000002 23.474999999999998 24.275 98-99 29.0875 24.587500000000002 22.8 23.525 100-101 30.062499999999996 25.337500000000002 21.6625 22.9375 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.5 4 1.0 5 1.5 6 2.0 7 2.0 8 1.0 9 0.5 10 1.5 11 2.5 12 1.5 13 0.0 14 2.5 15 3.0 16 1.0 17 2.0 18 3.5 19 4.5 20 2.5 21 0.5 22 1.5 23 2.0 24 4.5 25 4.0 26 2.5 27 4.0 28 4.5 29 5.5 30 4.0 31 1.5 32 4.0 33 6.0 34 7.5 35 14.0 36 22.0 37 35.0 38 47.5 39 61.5 40 73.0 41 93.5 42 122.0 43 138.5 44 148.5 45 145.5 46 139.0 47 142.0 48 152.5 49 169.5 50 165.5 51 149.5 52 136.0 53 137.5 54 147.5 55 144.5 56 131.0 57 113.5 58 116.0 59 110.5 60 86.5 61 80.0 62 77.0 63 67.0 64 74.5 65 75.0 66 71.0 67 68.0 68 54.5 69 49.0 70 56.5 71 55.5 72 46.5 73 41.0 74 26.5 75 23.5 76 24.0 77 15.0 78 15.5 79 13.0 80 8.0 81 6.5 82 5.0 83 4.0 84 2.0 85 0.5 86 1.0 87 1.0 88 1.0 89 1.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.5 95 0.5 96 0.0 97 0.0 98 0.0 99 1.0 100 4.5 >>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 10-11 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 90.35 #Duplication Level Percentage of deduplicated Percentage of total 1 91.28389596015495 82.475 2 7.44327614831212 13.450000000000001 3 0.9684560044272275 2.625 4 0.1936912008854455 0.7000000000000001 5 0.02767017155506364 0.125 6 0.0 0.0 7 0.0 0.0 8 0.05534034311012728 0.4 9 0.02767017155506364 0.22499999999999998 >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 9 0.22499999999999998 No Hit CCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGCAA 8 0.2 No Hit CTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGCAAG 8 0.2 No Hit ATTTGAACTGTGAAACTGCGAATGGCTCATTAAATCAGTTATAGTTTGTT 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 0.0875 0.0 0.0 0.0 0.0 36-37 0.125 0.0 0.0 0.0 0.0 38-39 0.15 0.0 0.0 0.0 0.0 40-41 0.225 0.0 0.0 0.0 0.0 42-43 0.30000000000000004 0.0 0.0 0.0 0.0 44-45 0.325 0.0 0.0 0.0 0.0 46-47 0.35 0.0 0.0 0.0 0.0 48-49 0.4375 0.0 0.0 0.0 0.0 50-51 0.4625 0.0 0.0 0.0 0.0 52-53 0.5375 0.0 0.0 0.0 0.0 54-55 0.5874999999999999 0.0 0.0 0.0 0.0 56-57 0.625 0.0 0.0 0.0 0.0 58-59 0.7 0.0 0.0 0.0 0.0 60-61 0.875 0.0 0.0 0.0 0.0 62-63 1.0499999999999998 0.0 0.0 0.0 0.0 64-65 1.2375 0.0 0.0 0.0 0.0 66-67 1.4 0.0 0.0 0.0 0.0 68-69 1.6625 0.0 0.0 0.0 0.0 70-71 1.875 0.0 0.0 0.0 0.0 72-73 2.175 0.0 0.0 0.0 0.0 74-75 2.5250000000000004 0.0 0.0 0.0 0.0 76-77 2.9875 0.0 0.0 0.0 0.0 78-79 3.3 0.0 0.0 0.0 0.0 80-81 3.6125 0.0 0.0 0.0 0.0 82-83 4.025 0.0 0.0 0.0 0.0 84-85 4.4875 0.0 0.0 0.0 0.0 86-87 4.9875 0.0 0.0 0.0 0.0 88-89 5.6375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 1317472 spots for ERR3450055.sra Written 1317472 spots for ERR3450055.sra Read 1317472 spots for ERR3450055.sra Written 1317472 spots for ERR3450055.sra Read 1317472 spots for ERR3450055.sra Written 1317472 spots for ERR3450055.sra Read 1317490 spots for ERR3450055.sra Written 1317490 spots for ERR3450055.sra Read 1317472 spots for ERR3450055.sra Written 1317472 spots for ERR3450055.sra Read 1317472 spots for ERR3450055.sra Written 1317472 spots for ERR3450055.sra Read 1317472 spots for ERR3450055.sra Written 1317472 spots for ERR3450055.sra Read 1317472 spots for ERR3450055.sra Written 1317472 spots for ERR3450055.sra Read 1317472 spots for ERR3450055.sra Written 1317472 spots for ERR3450055.sra Read 1317472 spots for ERR3450055.sra Written 1317472 spots for ERR3450055.sra Read 1317472 spots for ERR3450055.sra Written 1317472 spots for ERR3450055.sra Read 1317472 spots for ERR3450055.sra Written 1317472 spots for ERR3450055.sra Read 1317472 spots for ERR3450055.sra Written 1317472 spots for ERR3450055.sra Read 1317472 spots for ERR3450055.sra Written 1317472 spots for ERR3450055.sra Read 1317472 spots for ERR3450055.sra Written 1317472 spots for ERR3450055.sra Read 1317472 spots for ERR3450055.sra Written 1317472 spots for ERR3450055.sra Read 1317472 spots for ERR3450055.sra Written 1317472 spots for ERR3450055.sra Read 1317472 spots for ERR3450055.sra Written 1317472 spots for ERR3450055.sra Read 1317472 spots for ERR3450055.sra Written 1317472 spots for ERR3450055.sra Read 1317472 spots for ERR3450055.sra Written 1317472 spots for ERR3450055.sra SRR ids: ['ERR3450055.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_3kv3f8x6 ERR3450055.sra spots: 26349458 blocks: [[1, 1317472], [1317473, 2634944], [2634945, 3952416], [3952417, 5269888], [5269889, 6587360], [6587361, 7904832], [7904833, 9222304], [9222305, 10539776], [10539777, 11857248], [11857249, 13174720], [13174721, 14492192], [14492193, 15809664], [15809665, 17127136], [17127137, 18444608], [18444609, 19762080], [19762081, 21079552], [21079553, 22397024], [22397025, 23714496], [23714497, 25031968], [25031969, 26349458]] ERR3450055 file size 6334077 ERR3450055 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 ERR3450055 ERR3450055_1.fastq ERR3450055_2.fastq Input file: ERR3450055_1.fastq Paired file: ERR3450055_2.fastq trimmed: ERR3450055-trimmed-pair1.fastq, ERR3450055-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 14:07:38 2024 >> started Sat Dec 7 14:08:04 2024 >> done (25.451s) 26349458 read pairs processed; of these: 249 ( 0.00%) short read pairs filtered out after trimming by size control 42155 ( 0.16%) empty read pairs filtered out after trimming by size control 26307054 (99.84%) read pairs available; of these: 2694945 (10.24%) trimmed read pairs available after processing 23612109 (89.76%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 31 0.00% 19 63 0.00% 20 196 0.00% 21 447 0.00% 22 620 0.00% 23 311 0.00% 24 293 0.00% 25 418 0.00% 26 606 0.00% 27 829 0.00% 28 1260 0.00% 29 1530 0.01% 30 2049 0.01% 31 2514 0.01% 32 2524 0.01% 33 2476 0.01% 34 2547 0.01% 35 2604 0.01% 36 2788 0.01% 37 3245 0.01% 38 3801 0.01% 39 4413 0.02% 40 5264 0.02% 41 6156 0.02% 42 6817 0.03% 43 7042 0.03% 44 6468 0.02% 45 6149 0.02% 46 6743 0.03% 47 7585 0.03% 48 8159 0.03% 49 9258 0.04% 50 10354 0.04% 51 11629 0.04% 52 12620 0.05% 53 13143 0.05% 54 13755 0.05% 55 14493 0.06% 56 15481 0.06% 57 16066 0.06% 58 17596 0.07% 59 18518 0.07% 60 20154 0.08% 61 22639 0.09% 62 24126 0.09% 63 25760 0.10% 64 27345 0.10% 65 28117 0.11% 66 29461 0.11% 67 31005 0.12% 68 32273 0.12% 69 33450 0.13% 70 35258 0.13% 71 38379 0.15% 72 40985 0.16% 73 42968 0.16% 74 44452 0.17% 75 46219 0.18% 76 48384 0.18% 77 49760 0.19% 78 51627 0.20% 79 54296 0.21% 80 55821 0.21% 81 58471 0.22% 82 61849 0.24% 83 64092 0.24% 84 66330 0.25% 85 69355 0.26% 86 70761 0.27% 87 73331 0.28% 88 75350 0.29% 89 78317 0.30% 90 80076 0.30% 91 84567 0.32% 92 87384 0.33% 93 89681 0.34% 94 92584 0.35% 95 95127 0.36% 96 96195 0.37% 97 100176 0.38% 98 100759 0.38% 99 102305 0.39% 100 116895 0.44% 101 23612109 89.76% 26307054 reads passed initial QC criterion=sequence-density sequence-density=0.26 sequence-density-rank=1 fanout-score=2.01 fanout-score-rank=29 prefix-density=0.26 prefix-fanout=2.0 sequence=GTATTTAGCCTTG criterion=fanout-score sequence-density=0.11 sequence-density-rank=15 fanout-score=62.44 fanout-score-rank=1 prefix-density=1.12 prefix-fanout=6.0 sequence=GGCGGCGGCGGCCTCGCCGTCGCTGGTGTACTTCCCCAGCTGCGCCAGGGAGTTTGCCTTGGCGCGCAGCAGCAGTGCCTCCTGGGCCGCCGCCACG criterion=sequence-density sequence-density=0.17 sequence-density-rank=1 fanout-score=1.93 fanout-score-rank=31 prefix-density=0.16 prefix-fanout=1.9 sequence=GTCCGCATCATCGGCTTCGACAACACCCGGCAGGTGCAGTGCATCAGCTTCATCGCCTTCAAGCCACCGGGCTGCGAGGAATCCGGCAAGGCATAAACAACCAAGGACAGCTCCGTATTAAGATGGACCATATATAAAGTGTCAGCTCAGTTTTGTCAACTCTGACATTGCTTTGAGTTTTCTATTTTTCATCCCCAAGATTGTTGTTGTGTGTAGCAACCTGGCTCTCGATCGAGGAGCTAGCTTGCATATGTGAATTCC criterion=fanout-score sequence-density=0.10 sequence-density-rank=18 fanout-score=209.24 fanout-score-rank=1 prefix-density=0.85 prefix-fanout=23.5 sequence=CGGCGGCGGCGA ERR3450055 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 14:08:53 Started mapping on | Dec 07 14:08:53 Finished on | Dec 07 14:10:40 Mapping speed, Million of reads per hour | 885.10 Number of input reads | 26307054 Average input read length | 198 UNIQUE READS: Uniquely mapped reads number | 20546842 Uniquely mapped reads % | 78.10% Average mapped length | 197.62 Number of splices: Total | 12797891 Number of splices: Annotated (sjdb) | 12136905 Number of splices: GT/AG | 12629498 Number of splices: GC/AG | 146343 Number of splices: AT/AC | 7551 Number of splices: Non-canonical | 14499 Mismatch rate per base, % | 0.24% Deletion rate per base | 0.01% Deletion average length | 2.19 Insertion rate per base | 0.01% Insertion average length | 1.92 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1592952 % of reads mapped to multiple loci | 6.06% Number of reads mapped to too many loci | 670039 % of reads mapped to too many loci | 2.55% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.27% % of reads unmapped: other | 10.02% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 4167260 4167260 4167260 N_multimapping 1592952 1592952 1592952 N_noFeature 648815 19756507 1127968 N_ambiguous 387803 3062 81714 UnstrandedReadsAssigned:19510224 PositiveStrandReadsAssigned:787273 NegativeStrandReadsAssigned:19337160 Dataset is classified negative stranded MeadianReadLen=101 20thPercentileLength=101 echo kmer=97 ERR3450055 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: ERR3450055-trimmed-pair1.fastq ERR3450055-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 26,307,054 reads, 20,639,097 reads pseudoaligned [quant] estimated average fragment length: 185.514 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,194 rounds 52973 ERR3450055.ke.tsv 35125 ERR3450055.se.tsv 88098 total ==> ERR3450055.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 751.611 0 0 PNS24247 1044 859.486 46.4329 3.85426 PNS24249 1928 1743.49 315.54 12.9119 PNS24246 1044 859.486 46.4329 3.85426 PNS24248 1044 859.486 46.4329 3.85426 PNS24244 1471 1286.49 12.1611 0.67441 PNS24243 293 130.241 0 0 KQK14069 1603 1418.49 7141.55 359.188 KQK14071 474 293.13 244.597 59.5312 ==> ERR3450055.se.tsv <== BRADI_1g14170v3 7513 BRADI_1g53295v3 29 BRADI_1g59795v3 206 BRADI_1g07683v3 0 BRADI_1g00485v3 47 BRADI_1g20270v3 2336 BRADI_1g74790v3 196 BRADI_1g09890v3 12 BRADI_1g77505v3 260 BRADI_1g48960v3 2 ERR3450055 completed mapping pipeline successfully