Starting /dee2/code/volunteer_pipeline.sh ERR3317467 current disk space = 1524778418176 free memory = 1599151528 ERR3317467 SRAfilesize dbbecc9b3e6c4297013b54b88adf4bee ERR3317467.sra ERR3317467.sra file validated ERR3317467 is paired end ERR3317467 is conventional basespace ERR3317467 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3317467_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 49 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.57125 34.0 31.0 34.0 31.0 34.0 2 32.35225 34.0 31.0 34.0 31.0 34.0 3 32.93225 34.0 31.0 34.0 31.0 34.0 4 36.42625 37.0 37.0 37.0 35.0 37.0 5 36.46275 37.0 37.0 37.0 35.0 37.0 6 36.275 37.0 37.0 37.0 35.0 37.0 7 36.39025 37.0 37.0 37.0 35.0 37.0 8 36.438 37.0 37.0 37.0 35.0 37.0 9 38.2425 39.0 39.0 39.0 37.0 39.0 10-11 38.177375 39.0 39.0 39.0 37.0 39.0 12-13 38.183 39.0 39.0 39.0 37.0 39.0 14-15 39.81675 41.0 40.0 41.0 38.0 41.0 16-17 39.7785 41.0 40.0 41.0 37.5 41.0 18-19 39.73675 41.0 40.0 41.0 37.0 41.0 20-21 39.722624999999994 41.0 40.0 41.0 37.0 41.0 22-23 39.5585 41.0 40.0 41.0 37.0 41.0 24-25 39.429874999999996 41.0 39.0 41.0 37.0 41.0 26-27 39.35325 41.0 39.0 41.0 36.0 41.0 28-29 39.24375 41.0 39.0 41.0 36.0 41.0 30-31 39.0545 40.0 39.0 41.0 35.0 41.0 32-33 38.822500000000005 40.0 38.5 41.0 35.0 41.0 34-35 38.593875 40.0 38.0 41.0 34.5 41.0 36-37 38.413125 40.0 38.0 41.0 34.5 41.0 38-39 38.155 40.0 38.0 41.0 33.5 41.0 40-41 38.024375 40.0 38.0 41.0 33.0 41.0 42-43 37.93625 40.0 37.5 41.0 33.0 41.0 44-45 37.71325 40.0 37.0 41.0 33.0 41.0 46-47 37.524375 40.0 36.5 41.0 32.5 41.0 48-49 37.2115 39.5 35.5 41.0 31.5 41.0 50-51 37.49125 40.0 36.0 41.0 33.0 41.0 52-53 37.314750000000004 40.0 35.5 41.0 33.0 41.0 54-55 36.979875 39.0 35.0 41.0 32.5 41.0 56-57 36.772125 39.0 35.0 41.0 32.5 41.0 58-59 36.41725 38.5 35.0 41.0 31.0 41.0 60-61 36.002125 37.5 35.0 40.5 31.0 41.0 62-63 35.6535 37.0 35.0 40.0 30.5 41.0 64-65 35.41525 36.5 35.0 39.5 30.5 41.0 66-67 34.950125 36.0 35.0 39.0 29.5 41.0 68-69 34.55775 35.0 34.0 39.0 29.5 41.0 70-71 34.166875 35.0 34.0 37.5 29.0 40.0 72-73 33.78275 35.0 34.0 37.0 29.0 39.5 74-75 33.41475 35.0 34.0 37.0 29.0 39.0 76-77 32.072375 34.5 32.0 35.5 26.5 37.0 78-79 32.653125 35.0 33.0 36.0 27.0 37.0 80-81 32.442375 35.0 33.0 35.0 27.0 37.0 82-83 32.1085 35.0 33.0 35.0 26.0 36.5 84-85 31.902875 35.0 33.0 35.0 25.5 36.0 86-87 31.588625 35.0 33.0 35.0 25.0 36.0 88-89 31.3275 35.0 33.0 35.0 23.5 36.0 90-91 31.037125 35.0 32.5 35.0 21.5 35.0 92-93 30.749125 35.0 32.0 35.0 19.5 35.0 94-95 30.57875 35.0 32.0 35.0 18.5 35.0 96-97 30.209125 35.0 32.0 35.0 6.0 35.0 98-99 29.799750000000003 35.0 31.0 35.0 2.0 35.0 100-101 27.340125 32.0 27.0 34.5 2.0 35.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 1.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 6.0 10 2.0 11 4.0 12 7.0 13 5.0 14 8.0 15 10.0 16 11.0 17 13.0 18 11.0 19 14.0 20 11.0 21 22.0 22 16.0 23 19.0 24 25.0 25 24.0 26 26.0 27 27.0 28 43.0 29 51.0 30 59.0 31 68.0 32 78.0 33 156.0 34 201.0 35 341.0 36 616.0 37 968.0 38 1014.0 39 143.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 26.409651193286127 27.45869394177813 18.33202202989772 27.79963283503803 2 24.7 25.825 18.4 31.075000000000003 3 24.575 25.974999999999998 19.475 29.975 4 24.875 25.525 17.724999999999998 31.874999999999996 5 27.650000000000002 25.45 17.349999999999998 29.549999999999997 6 27.075 28.375 19.1 25.45 7 29.15 24.375 22.25 24.224999999999998 8 29.875 25.1 26.0 19.025 9 29.65 27.35 26.375 16.625 10-11 31.0125 26.450000000000003 23.65 18.8875 12-13 29.549999999999997 26.2125 23.599999999999998 20.6375 14-15 27.650000000000002 26.474999999999998 24.5 21.375 16-17 26.700000000000003 25.9875 24.4 22.912499999999998 18-19 25.8 26.424999999999997 25.35 22.425 20-21 26.400000000000002 25.775 24.7375 23.0875 22-23 25.7375 25.7875 25.337500000000002 23.1375 24-25 24.85 26.2125 26.025 22.912499999999998 26-27 25.7 27.0875 24.0625 23.150000000000002 28-29 26.375 25.137500000000003 25.162499999999998 23.325000000000003 30-31 25.637500000000003 27.3375 24.4125 22.6125 32-33 25.35 26.2875 25.0625 23.3 34-35 24.775 25.837500000000002 26.275 23.1125 36-37 26.1125 25.374999999999996 26.450000000000003 22.0625 38-39 24.8125 26.150000000000002 25.624999999999996 23.4125 40-41 26.4625 26.2125 24.75 22.575 42-43 25.4 26.55 25.174999999999997 22.875 44-45 25.924999999999997 25.974999999999998 25.1 23.0 46-47 26.5125 25.074999999999996 24.4125 24.0 48-49 26.2875 26.087500000000002 24.887500000000003 22.7375 50-51 24.925 26.2125 25.8125 23.05 52-53 25.687500000000004 25.8625 25.662499999999998 22.787499999999998 54-55 24.675 26.637499999999996 25.45 23.2375 56-57 25.174999999999997 26.75 24.7875 23.2875 58-59 25.912499999999998 25.412499999999998 25.6125 23.0625 60-61 26.187500000000004 26.224999999999998 25.2 22.3875 62-63 24.875 27.0625 24.1625 23.9 64-65 25.8125 25.95 24.9875 23.25 66-67 24.4125 26.875 25.662499999999998 23.05 68-69 25.424999999999997 25.887500000000003 24.9 23.7875 70-71 25.412499999999998 25.75 25.074999999999996 23.7625 72-73 25.162499999999998 26.224999999999998 26.0 22.6125 74-75 25.275 27.125 24.462500000000002 23.1375 76-77 25.662499999999998 26.650000000000002 24.224999999999998 23.4625 78-79 25.2 26.625 25.2125 22.9625 80-81 25.0625 26.5625 24.65 23.724999999999998 82-83 24.637500000000003 26.4625 25.162499999999998 23.7375 84-85 25.8625 26.1125 24.9 23.125 86-87 24.6125 26.8 24.6875 23.9 88-89 25.587500000000002 27.05 24.3 23.0625 90-91 25.2625 26.174999999999997 24.9375 23.625 92-93 24.9875 27.725 23.4125 23.875 94-95 25.1 26.450000000000003 24.525 23.925 96-97 25.7375 26.4625 24.175 23.625 98-99 25.224999999999998 27.675 24.4 22.7 100-101 25.95 25.687500000000004 23.625 24.7375 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.5 4 0.5 5 0.5 6 0.5 7 0.0 8 0.5 9 1.0 10 0.5 11 1.0 12 1.5 13 2.5 14 2.0 15 0.5 16 0.5 17 0.0 18 0.5 19 1.0 20 1.5 21 1.5 22 1.0 23 1.5 24 1.5 25 4.0 26 6.0 27 4.0 28 4.5 29 11.0 30 12.5 31 11.5 32 19.5 33 28.0 34 28.0 35 34.5 36 43.0 37 58.0 38 75.5 39 96.0 40 133.5 41 151.5 42 163.5 43 173.0 44 180.5 45 196.5 46 198.0 47 199.0 48 202.5 49 192.0 50 176.5 51 154.0 52 138.5 53 129.5 54 115.0 55 100.0 56 91.5 57 78.0 58 66.5 59 66.5 60 64.0 61 61.0 62 49.5 63 47.0 64 47.0 65 41.5 66 36.5 67 41.0 68 42.5 69 32.5 70 29.0 71 25.5 72 20.0 73 16.5 74 15.5 75 12.5 76 8.5 77 7.5 78 8.0 79 7.5 80 5.0 81 4.0 82 3.0 83 2.0 84 2.5 85 1.0 86 0.5 87 2.0 88 2.5 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 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 4.675 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 97.275 #Duplication Level Percentage of deduplicated Percentage of total 1 98.02107427396555 95.35 2 1.6191210485736314 3.15 3 0.1285016705217168 0.375 4 0.1285016705217168 0.5 5 0.02570033410434336 0.125 6 0.02570033410434336 0.15 7 0.05140066820868672 0.35000000000000003 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences warn #Sequence Count Percentage Possible Source ACTTAACTGGGGGATTCACCGCAAATACTACTTTGGCTCATTATTGCCGC 7 0.17500000000000002 No Hit ATGCCAGCTCTGACCGAAATCTTTGGGGATGATTCTGTATTACAATTTGG 7 0.17500000000000002 No Hit TATGTACCTTTTTCACACGTTTGTTTCATGTTGTATTTATGCATGTGATC 6 0.15 No Hit AGACCTTGTTATTGTGAGAATTCTTAATTCAAGAGTTGTAAGGAGGGACT 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 0.025 0.0 0.0 0.0 0.0 3 0.025 0.0 0.0 0.0 0.0 4 0.025 0.0 0.0 0.0 0.0 5 0.025 0.0 0.0 0.0 0.0 6 0.025 0.0 0.0 0.0 0.0 7 0.075 0.0 0.0 0.0 0.0 8 0.1 0.0 0.0 0.0 0.0 9 0.1 0.0 0.0 0.0 0.0 10-11 0.1 0.0 0.0 0.0 0.0 12-13 0.1 0.0 0.0 0.0 0.0 14-15 0.1 0.0 0.0 0.0 0.0 16-17 0.1 0.0 0.0 0.0 0.0 18-19 0.1 0.0 0.0 0.0 0.0 20-21 0.1125 0.0 0.0 0.0 0.0 22-23 0.125 0.0 0.0 0.0 0.0 24-25 0.125 0.0 0.0 0.0 0.0 26-27 0.15 0.0 0.0 0.0 0.0 28-29 0.1875 0.0 0.0 0.0 0.0 30-31 0.2 0.0 0.0 0.0 0.0 32-33 0.2875 0.0 0.0 0.0 0.0 34-35 0.42500000000000004 0.0 0.0 0.0 0.0 36-37 0.4625 0.0 0.0 0.0 0.0 38-39 0.5 0.0 0.0 0.0 0.0 40-41 0.6 0.0 0.0 0.0 0.0 42-43 0.7 0.0 0.0 0.0 0.0 44-45 0.8 0.0 0.0 0.0 0.0 46-47 0.9125000000000001 0.0 0.0 0.0 0.0 48-49 1.025 0.0 0.0 0.0 0.0 50-51 1.2000000000000002 0.0 0.0 0.0 0.0 52-53 1.4 0.0 0.0 0.0 0.0 54-55 1.5 0.0 0.0 0.0 0.0 56-57 1.675 0.0 0.0 0.0 0.0 58-59 1.8375 0.0 0.0 0.0 0.0 60-61 2.0375 0.0 0.0 0.0 0.0 62-63 2.2875 0.0 0.0 0.0 0.0 64-65 2.5 0.0 0.0 0.0 0.0 66-67 2.8625 0.0 0.0 0.0 0.0 68-69 3.05 0.0 0.0 0.0 0.0 70-71 3.3625 0.0 0.0 0.0 0.0 72-73 3.7125 0.0 0.0 0.0 0.0 74-75 4.3125 0.0 0.0 0.0 0.0 76-77 4.6 0.0 0.0 0.0 0.0 78-79 5.025 0.0 0.0 0.0 0.0 80-81 5.574999999999999 0.0 0.0 0.0 0.0 82-83 5.9875 0.0 0.0 0.0 0.0 84-85 6.75 0.0 0.0 0.0 0.0 86-87 7.4 0.0 0.0 0.0 0.0 88-89 8.1 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE ERR3317467 read2 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3317467_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 46 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.973 33.0 31.0 34.0 30.0 34.0 2 32.03 34.0 31.0 34.0 30.0 34.0 3 32.11025 34.0 31.0 34.0 30.0 34.0 4 35.334 37.0 35.0 37.0 35.0 37.0 5 35.45675 37.0 35.0 37.0 33.0 37.0 6 35.65475 37.0 36.0 37.0 35.0 37.0 7 35.69275 37.0 37.0 37.0 35.0 37.0 8 35.69225 37.0 37.0 37.0 35.0 37.0 9 37.338 39.0 38.0 39.0 35.0 39.0 10-11 37.43575 39.0 39.0 39.0 35.0 39.0 12-13 37.420249999999996 39.0 38.0 39.0 35.0 39.0 14-15 38.946125 41.0 40.0 41.0 36.0 41.0 16-17 38.8815 41.0 39.5 41.0 36.0 41.0 18-19 38.798874999999995 41.0 39.5 41.0 35.0 41.0 20-21 38.6975 41.0 39.0 41.0 35.0 41.0 22-23 38.709999999999994 41.0 39.0 41.0 35.0 41.0 24-25 38.591499999999996 41.0 39.0 41.0 35.0 41.0 26-27 38.497749999999996 41.0 39.0 41.0 35.0 41.0 28-29 38.414249999999996 41.0 39.0 41.0 35.0 41.0 30-31 38.289125 40.5 38.5 41.0 34.5 41.0 32-33 38.22175 40.0 38.0 41.0 34.5 41.0 34-35 37.976 40.0 38.0 41.0 33.5 41.0 36-37 37.836875 40.0 38.0 41.0 33.0 41.0 38-39 37.730999999999995 40.0 38.0 41.0 33.0 41.0 40-41 37.867875 40.0 38.0 41.0 33.5 41.0 42-43 37.8635 40.0 38.0 41.0 33.5 41.0 44-45 37.705375000000004 40.0 38.0 41.0 33.0 41.0 46-47 37.417125 40.0 37.0 41.0 33.0 41.0 48-49 37.244625 40.0 37.0 41.0 33.0 41.0 50-51 36.214375000000004 39.0 35.5 40.5 30.5 40.5 52-53 36.24125 39.0 35.0 40.5 30.5 41.0 54-55 36.585750000000004 39.0 35.0 41.0 31.0 41.0 56-57 36.3965 39.0 35.0 41.0 31.0 41.0 58-59 36.200874999999996 39.0 35.0 41.0 31.0 41.0 60-61 35.83225 39.0 35.0 41.0 30.0 41.0 62-63 35.553625 38.0 35.0 40.5 30.0 41.0 64-65 35.27975 37.0 35.0 40.0 29.0 41.0 66-67 35.3065 37.0 35.0 40.0 30.5 41.0 68-69 34.858000000000004 36.5 35.0 39.0 29.5 41.0 70-71 34.650125 36.0 35.0 39.0 30.0 41.0 72-73 34.254875 35.5 35.0 39.0 29.0 40.5 74-75 33.924375 35.0 34.0 37.0 29.0 39.5 76-77 33.547875000000005 35.0 34.0 37.0 29.0 39.0 78-79 33.272999999999996 35.0 34.0 36.5 29.0 39.0 80-81 32.989125 35.0 34.0 36.0 29.0 37.0 82-83 32.651375 35.0 34.0 36.0 28.0 37.0 84-85 32.399375000000006 35.0 34.0 35.0 27.0 37.0 86-87 32.101749999999996 35.0 33.5 35.0 26.5 36.0 88-89 31.938375 35.0 33.0 35.0 26.5 36.0 90-91 31.719375 35.0 33.0 35.0 25.0 36.0 92-93 31.552625 35.0 33.0 35.0 25.0 35.5 94-95 31.457 35.0 33.0 35.0 24.5 35.0 96-97 31.0825 35.0 33.0 35.0 21.5 35.0 98-99 30.81175 35.0 33.0 35.0 19.0 35.0 100-101 28.761499999999998 33.0 29.0 34.5 2.0 35.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 51.0 3 4.0 4 6.0 5 4.0 6 5.0 7 3.0 8 3.0 9 4.0 10 10.0 11 9.0 12 13.0 13 4.0 14 9.0 15 8.0 16 6.0 17 9.0 18 9.0 19 5.0 20 6.0 21 13.0 22 8.0 23 11.0 24 11.0 25 21.0 26 20.0 27 26.0 28 31.0 29 30.0 30 53.0 31 61.0 32 90.0 33 102.0 34 195.0 35 254.0 36 461.0 37 898.0 38 1272.0 39 275.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 29.5 12.1 29.049999999999997 29.349999999999998 2 25.724999999999998 10.725 27.025 36.525 3 23.799999999999997 12.325 30.225 33.650000000000006 4 24.525 11.25 28.675 35.55 5 25.45 13.8 24.675 36.075 6 25.674999999999997 19.1 29.799999999999997 25.424999999999997 7 20.375 23.425 38.125 18.075 8 18.0 25.25 36.65 20.1 9 19.2 28.925 34.050000000000004 17.825 10-11 19.5125 27.8625 32.1125 20.5125 12-13 19.6125 28.475 31.474999999999998 20.4375 14-15 20.325 26.8625 30.5 22.3125 16-17 20.775 26.5125 28.712500000000002 24.0 18-19 20.974999999999998 26.5375 29.9625 22.525000000000002 20-21 20.4625 26.075 29.1875 24.275 22-23 20.4625 25.7375 29.425 24.375 24-25 20.5375 26.775 29.1125 23.575 26-27 21.075 25.7625 28.512500000000003 24.65 28-29 20.5125 25.474999999999998 27.762500000000003 26.25 30-31 21.0375 26.4125 28.475 24.075 32-33 22.412499999999998 25.5125 27.35 24.725 34-35 20.8875 25.5 28.262500000000003 25.35 36-37 21.175 25.387500000000003 28.599999999999998 24.837500000000002 38-39 22.8125 24.887500000000003 26.987499999999997 25.3125 40-41 21.8625 24.55 27.5125 26.075 42-43 21.775 25.9625 28.15 24.1125 44-45 22.900000000000002 26.487500000000004 25.8125 24.8 46-47 21.85 25.7 26.987499999999997 25.4625 48-49 20.5875 27.6625 27.700000000000003 24.05 50-51 22.5625 26.137500000000003 27.224999999999998 24.075 52-53 21.637500000000003 26.375 26.5375 25.45 54-55 22.037499999999998 26.2625 27.85 23.849999999999998 56-57 22.162499999999998 25.5375 27.5125 24.7875 58-59 22.125 25.137500000000003 26.775 25.9625 60-61 21.55 25.9625 28.5625 23.925 62-63 22.8 26.0 26.400000000000002 24.8 64-65 22.425 24.825 27.712500000000002 25.0375 66-67 21.475 27.35 27.5125 23.6625 68-69 22.375 25.374999999999996 26.5875 25.662499999999998 70-71 21.775 26.3625 26.5375 25.324999999999996 72-73 22.475 26.25 26.5 24.775 74-75 23.125 25.974999999999998 26.5125 24.3875 76-77 22.775000000000002 26.237500000000004 26.437500000000004 24.55 78-79 22.825 25.937500000000004 26.525 24.712500000000002 80-81 22.9625 25.4875 27.200000000000003 24.349999999999998 82-83 23.9875 25.124999999999996 25.7375 25.15 84-85 23.549999999999997 25.637500000000003 26.5125 24.3 86-87 25.2875 25.2125 26.1 23.400000000000002 88-89 23.4125 24.9125 25.900000000000002 25.775 90-91 24.4875 26.887499999999996 25.95 22.675 92-93 23.8125 26.6125 25.362499999999997 24.212500000000002 94-95 23.549999999999997 25.874999999999996 26.125 24.45 96-97 25.087500000000002 26.0125 26.1625 22.7375 98-99 24.2875 26.5125 25.112499999999997 24.087500000000002 100-101 25.162499999999998 25.575 24.725 24.5375 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 23.0 1 15.5 2 5.5 3 3.0 4 1.5 5 1.5 6 3.5 7 2.5 8 1.5 9 1.0 10 1.0 11 3.0 12 4.0 13 2.5 14 2.0 15 1.5 16 3.5 17 4.5 18 2.0 19 1.0 20 1.0 21 2.5 22 1.5 23 1.5 24 3.0 25 4.0 26 6.0 27 10.0 28 11.0 29 10.0 30 12.0 31 19.0 32 28.5 33 33.0 34 38.5 35 51.5 36 67.0 37 74.0 38 101.0 39 131.5 40 140.5 41 164.5 42 196.5 43 198.0 44 188.0 45 206.5 46 202.5 47 183.5 48 174.5 49 161.5 50 154.0 51 151.0 52 146.0 53 123.5 54 87.5 55 74.5 56 83.0 57 76.0 58 65.5 59 54.5 60 48.5 61 50.0 62 44.5 63 42.5 64 43.0 65 37.5 66 34.0 67 30.5 68 23.5 69 20.5 70 18.5 71 15.5 72 17.5 73 15.5 74 8.0 75 6.0 76 7.5 77 7.0 78 4.0 79 2.5 80 4.0 81 3.5 82 1.0 83 0.5 84 0.5 85 0.0 86 0.5 87 0.5 88 0.0 89 0.0 90 0.5 91 1.0 92 1.0 93 0.5 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 10-11 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 97.125 #Duplication Level Percentage of deduplicated Percentage of total 1 98.84169884169884 96.0 2 0.7464607464607464 1.4500000000000002 3 0.18018018018018017 0.525 4 0.05148005148005148 0.2 5 0.02574002574002574 0.125 6 0.05148005148005148 0.3 7 0.05148005148005148 0.35000000000000003 8 0.02574002574002574 0.2 9 0.0 0.0 >10 0.02574002574002574 0.8500000000000001 >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 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 34 0.8500000000000001 No Hit TGGGGATGAAAAATAGAAAACTCAAAGCAATGTCAGAGTTGACAAAACTG 8 0.2 No Hit TCTTCATATTTAGTTTTATCTATTAATCGATAGTATCTACCGGCGCGAAC 7 0.17500000000000002 No Hit CCACCGAATTGTAATACAGAATCATCCCCAAAGATTTCGGTCAGAGCTGG 7 0.17500000000000002 No Hit TGGGGGTGAAAAATAGAAAACTCAAAGCAATGTCAGAGTTGACAAAACTG 6 0.15 No Hit CCACCAAATTGTAATACAGAATCATCCCCAAAGATTTCGGTCAGAGCTGG 6 0.15 No Hit ATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 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 0.025 0.0 0.0 0.0 0.0 3 0.025 0.0 0.0 0.0 0.0 4 0.025 0.0 0.0 0.0 0.0 5 0.025 0.0 0.0 0.0 0.0 6 0.025 0.0 0.0 0.0 0.0 7 0.075 0.0 0.0 0.0 0.0 8 0.1 0.0 0.0 0.0 0.0 9 0.1 0.0 0.0 0.0 0.0 10-11 0.1 0.0 0.0 0.0 0.0 12-13 0.1 0.0 0.0 0.0 0.0 14-15 0.1 0.0 0.0 0.0 0.0 16-17 0.1 0.0 0.0 0.0 0.0 18-19 0.1 0.0 0.0 0.0 0.0 20-21 0.1125 0.0 0.0 0.0 0.0 22-23 0.125 0.0 0.0 0.0 0.0 24-25 0.125 0.0 0.0 0.0 0.0 26-27 0.15 0.0 0.0 0.0 0.0 28-29 0.15 0.0 0.0 0.0 0.0 30-31 0.15 0.0 0.0 0.0 0.0 32-33 0.23750000000000002 0.0 0.0 0.0 0.0 34-35 0.375 0.0 0.0 0.0 0.0 36-37 0.4125 0.0 0.0 0.0 0.0 38-39 0.45 0.0 0.0 0.0 0.0 40-41 0.55 0.0 0.0 0.0 0.0 42-43 0.6499999999999999 0.0 0.0 0.0 0.0 44-45 0.75 0.0 0.0 0.0 0.0 46-47 0.8625 0.0 0.0 0.0 0.0 48-49 0.975 0.0 0.0 0.0 0.0 50-51 1.15 0.0 0.0 0.0 0.0 52-53 1.35 0.0 0.0 0.0 0.0 54-55 1.4500000000000002 0.0 0.0 0.0 0.0 56-57 1.625 0.0 0.0 0.0 0.0 58-59 1.7875 0.0 0.0 0.0 0.0 60-61 1.9874999999999998 0.0 0.0 0.0 0.0 62-63 2.2249999999999996 0.0 0.0 0.0 0.0 64-65 2.4875 0.0 0.0 0.0 0.0 66-67 2.8375000000000004 0.0 0.0 0.0 0.0 68-69 3.0125 0.0 0.0 0.0 0.0 70-71 3.2875 0.0 0.0 0.0 0.0 72-73 3.6375 0.0 0.0 0.0 0.0 74-75 4.2375 0.0 0.0 0.0 0.0 76-77 4.525 0.0 0.0 0.0 0.0 78-79 4.9625 0.0 0.0 0.0 0.0 80-81 5.4625 0.0 0.0 0.0 0.0 82-83 5.9 0.0 0.0 0.0 0.0 84-85 6.675000000000001 0.0 0.0 0.0 0.0 86-87 7.3375 0.0 0.0 0.0 0.0 88-89 8.075 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 1874589 spots for ERR3317467.sra Written 1874589 spots for ERR3317467.sra Read 1874589 spots for ERR3317467.sra Written 1874589 spots for ERR3317467.sra Read 1874589 spots for ERR3317467.sra Written 1874589 spots for ERR3317467.sra Read 1874589 spots for ERR3317467.sra Written 1874589 spots for ERR3317467.sra Read 1874593 spots for ERR3317467.sra Written 1874593 spots for ERR3317467.sra Read 1874589 spots for ERR3317467.sra Written 1874589 spots for ERR3317467.sra Read 1874589 spots for ERR3317467.sra Written 1874589 spots for ERR3317467.sra Read 1874589 spots for ERR3317467.sra Written 1874589 spots for ERR3317467.sra Read 1874589 spots for ERR3317467.sra Written 1874589 spots for ERR3317467.sra Read 1874589 spots for ERR3317467.sra Written 1874589 spots for ERR3317467.sra Read 1874589 spots for ERR3317467.sra Written 1874589 spots for ERR3317467.sra Read 1874589 spots for ERR3317467.sra Written 1874589 spots for ERR3317467.sra Read 1874589 spots for ERR3317467.sra Written 1874589 spots for ERR3317467.sra Read 1874589 spots for ERR3317467.sra Written 1874589 spots for ERR3317467.sra Read 1874589 spots for ERR3317467.sra Written 1874589 spots for ERR3317467.sra Read 1874589 spots for ERR3317467.sra Written 1874589 spots for ERR3317467.sra Read 1874589 spots for ERR3317467.sra Written 1874589 spots for ERR3317467.sra Read 1874589 spots for ERR3317467.sra Written 1874589 spots for ERR3317467.sra Read 1874589 spots for ERR3317467.sra Written 1874589 spots for ERR3317467.sra Read 1874589 spots for ERR3317467.sra Written 1874589 spots for ERR3317467.sra SRR ids: ['ERR3317467.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_m6fv7fsp ERR3317467.sra spots: 37491784 blocks: [[1, 1874589], [1874590, 3749178], [3749179, 5623767], [5623768, 7498356], [7498357, 9372945], [9372946, 11247534], [11247535, 13122123], [13122124, 14996712], [14996713, 16871301], [16871302, 18745890], [18745891, 20620479], [20620480, 22495068], [22495069, 24369657], [24369658, 26244246], [26244247, 28118835], [28118836, 29993424], [29993425, 31868013], [31868014, 33742602], [33742603, 35617191], [35617192, 37491784]] ERR3317467 file size 9021727 ERR3317467 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 ERR3317467 ERR3317467_1.fastq ERR3317467_2.fastq Input file: ERR3317467_1.fastq Paired file: ERR3317467_2.fastq trimmed: ERR3317467-trimmed-pair1.fastq, ERR3317467-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 10:12:30 2024 >> started Tue Dec 10 10:13:04 2024 >> done (34.191s) 37491784 read pairs processed; of these: 297201 ( 0.79%) short read pairs filtered out after trimming by size control 697738 ( 1.86%) empty read pairs filtered out after trimming by size control 36496845 (97.35%) read pairs available; of these: 11335318 (31.06%) trimmed read pairs available after processing 25161527 (68.94%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 753 0.00% 19 828 0.00% 20 1287 0.00% 21 1486 0.00% 22 1854 0.01% 23 2557 0.01% 24 3105 0.01% 25 3823 0.01% 26 4395 0.01% 27 5108 0.01% 28 5444 0.01% 29 6668 0.02% 30 7266 0.02% 31 10790 0.03% 32 9634 0.03% 33 10425 0.03% 34 12687 0.03% 35 12828 0.04% 36 14169 0.04% 37 15091 0.04% 38 17874 0.05% 39 18673 0.05% 40 18976 0.05% 41 20613 0.06% 42 21764 0.06% 43 23836 0.07% 44 25214 0.07% 45 25460 0.07% 46 27460 0.08% 47 31488 0.09% 48 31906 0.09% 49 33789 0.09% 50 37369 0.10% 51 37511 0.10% 52 38956 0.11% 53 42738 0.12% 54 47700 0.13% 55 50047 0.14% 56 51398 0.14% 57 54225 0.15% 58 58344 0.16% 59 76315 0.21% 60 86314 0.24% 61 94271 0.26% 62 100146 0.27% 63 105633 0.29% 64 113083 0.31% 65 124732 0.34% 66 131802 0.36% 67 132745 0.36% 68 132705 0.36% 69 133870 0.37% 70 137285 0.38% 71 143649 0.39% 72 150108 0.41% 73 159735 0.44% 74 158424 0.43% 75 157779 0.43% 76 156734 0.43% 77 164936 0.45% 78 180167 0.49% 79 176894 0.48% 80 182141 0.50% 81 184866 0.51% 82 186584 0.51% 83 193569 0.53% 84 200731 0.55% 85 217179 0.60% 86 224167 0.61% 87 230682 0.63% 88 231336 0.63% 89 251190 0.69% 90 243164 0.67% 91 249323 0.68% 92 264275 0.72% 93 276236 0.76% 94 302830 0.83% 95 345719 0.95% 96 370034 1.01% 97 424666 1.16% 98 523595 1.43% 99 716553 1.96% 100 1853612 5.08% 101 25161527 68.94% 36496845 reads passed initial QC criterion=sequence-density sequence-density=0.40 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=27 prefix-density=0.39 prefix-fanout=2.0 sequence=CAGGTGCTCAAGGAGCTGGAGGAGGTCAAGAAGGAGTACCC criterion=fanout-score sequence-density=0.10 sequence-density-rank=13 fanout-score=77.15 fanout-score-rank=1 prefix-density=0.66 prefix-fanout=11.7 sequence=GCCGCCGCCGCCA criterion=sequence-density sequence-density=0.35 sequence-density-rank=1 fanout-score=2.21 fanout-score-rank=27 prefix-density=0.37 prefix-fanout=2.1 sequence=GTGGCGTCGGTGCACCCGAACATGGGCAGCTTCCACATTGTCCAGTACCT criterion=fanout-score sequence-density=0.01 sequence-density-rank=40 fanout-score=60.97 fanout-score-rank=1 prefix-density=0.06 prefix-fanout=6.0 sequence=TTATATATATTACTGTTCACCAAATGAATATACTCAATATCTTTATATATGAACAAAAACTTTTCATGCCCAGCAATTGCTTGGATGCAATGCGGTACTTAGGTACAAAGAGTGAAACATCAGAATAATTAAAGTGGCATGCTTAAAAGGTGTAAAGGCAGCTGCCGTCGTCACTCCTTGCTGTTGGGTCGTAGTTCTCGGCATTCCGGTCAGTGCAACCTTCTGGGACGGGCAAATTACCTTGTTGTGCTCCTTTACCTCCTCCTATGCAGCTAGAGATGGTGTGTGTATGAAGAGTGTTCTAACCGTAGAAGGAACCAGTCTTCATGGCATCTGAGTTAGCATCTCCCAGAGCAGCCTCGCTCATGTACTTGTCAGCAAGCTGCACACGCTTGACATTGT ERR3317467 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 10 10:13:44 Started mapping on | Dec 10 10:13:45 Finished on | Dec 10 10:15:52 Mapping speed, Million of reads per hour | 1034.56 Number of input reads | 36496845 Average input read length | 191 UNIQUE READS: Uniquely mapped reads number | 32033708 Uniquely mapped reads % | 87.77% Average mapped length | 190.39 Number of splices: Total | 19344010 Number of splices: Annotated (sjdb) | 18339270 Number of splices: GT/AG | 19057488 Number of splices: GC/AG | 254464 Number of splices: AT/AC | 13356 Number of splices: Non-canonical | 18702 Mismatch rate per base, % | 0.42% Deletion rate per base | 0.00% Deletion average length | 1.23 Insertion rate per base | 0.00% Insertion average length | 1.27 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 2950284 % of reads mapped to multiple loci | 8.08% Number of reads mapped to too many loci | 92289 % of reads mapped to too many loci | 0.25% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.42% % of reads unmapped: other | 1.48% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1764371 1764371 1764371 N_multimapping 2950284 2950284 2950284 N_noFeature 1262039 2744810 29850220 N_ambiguous 968523 295283 16724 UnstrandedReadsAssigned:29803146 PositiveStrandReadsAssigned:28993615 NegativeStrandReadsAssigned:2166764 Dataset is classified positive stranded MeadianReadLen=101 20thPercentileLength=99 echo kmer=95 ERR3317467 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: ERR3317467-trimmed-pair1.fastq ERR3317467-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 36,496,845 reads, 31,249,451 reads pseudoaligned [quant] estimated average fragment length: 191.181 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,124 rounds 52973 ERR3317467.ke.tsv 35125 ERR3317467.se.tsv 88098 total ==> ERR3317467.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 746.037 0 0 PNS24247 1044 853.819 47.3238 2.67155 PNS24249 1928 1737.82 152.972 4.24285 PNS24246 1044 853.819 47.3238 2.67155 PNS24248 1044 853.819 47.3238 2.67155 PNS24244 1471 1280.82 173.056 6.51252 PNS24243 293 134.687 0 0 KQK14069 1603 1412.82 2208.76 75.3549 KQK14071 474 293.216 7.49162 1.23151 ==> ERR3317467.se.tsv <== BRADI_1g14170v3 2606 BRADI_1g53295v3 211 BRADI_1g59795v3 542 BRADI_1g07683v3 0 BRADI_1g00485v3 94 BRADI_1g20270v3 1732 BRADI_1g74790v3 615 BRADI_1g09890v3 8 BRADI_1g77505v3 369 BRADI_1g48960v3 0 ERR3317467 completed mapping pipeline successfully