Starting /dee2/code/volunteer_pipeline.sh ERR3450087 current disk space = 1542762258432 free memory = 1600065576 ERR3450087 SRAfilesize 50a06cdbdf7721fe967f613a253e7fc2 ERR3450087.sra ERR3450087.sra file validated ERR3450087 is paired end ERR3450087 is conventional basespace ERR3450087 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3450087_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 36.1395 37.0 37.0 37.0 37.0 37.0 2 36.251 37.0 37.0 37.0 37.0 37.0 3 36.3955 37.0 37.0 37.0 37.0 37.0 4 36.455 37.0 37.0 37.0 37.0 37.0 5 36.504 37.0 37.0 37.0 37.0 37.0 6 36.5335 37.0 37.0 37.0 37.0 37.0 7 36.4755 37.0 37.0 37.0 37.0 37.0 8 36.4835 37.0 37.0 37.0 37.0 37.0 9 36.522 37.0 37.0 37.0 37.0 37.0 10-11 36.47 37.0 37.0 37.0 37.0 37.0 12-13 36.56325 37.0 37.0 37.0 37.0 37.0 14-15 36.5095 37.0 37.0 37.0 37.0 37.0 16-17 36.4585 37.0 37.0 37.0 37.0 37.0 18-19 36.448750000000004 37.0 37.0 37.0 37.0 37.0 20-21 36.47825 37.0 37.0 37.0 37.0 37.0 22-23 36.5005 37.0 37.0 37.0 37.0 37.0 24-25 36.4525 37.0 37.0 37.0 37.0 37.0 26-27 36.43125 37.0 37.0 37.0 37.0 37.0 28-29 36.35125 37.0 37.0 37.0 37.0 37.0 30-31 36.3665 37.0 37.0 37.0 37.0 37.0 32-33 36.315250000000006 37.0 37.0 37.0 37.0 37.0 34-35 36.3575 37.0 37.0 37.0 37.0 37.0 36-37 36.37575 37.0 37.0 37.0 37.0 37.0 38-39 36.320750000000004 37.0 37.0 37.0 37.0 37.0 40-41 36.2795 37.0 37.0 37.0 37.0 37.0 42-43 36.27675 37.0 37.0 37.0 37.0 37.0 44-45 36.233000000000004 37.0 37.0 37.0 37.0 37.0 46-47 36.27175 37.0 37.0 37.0 37.0 37.0 48-49 36.2575 37.0 37.0 37.0 37.0 37.0 50-51 36.189499999999995 37.0 37.0 37.0 37.0 37.0 52-53 36.2325 37.0 37.0 37.0 37.0 37.0 54-55 36.147999999999996 37.0 37.0 37.0 37.0 37.0 56-57 36.1105 37.0 37.0 37.0 37.0 37.0 58-59 36.1335 37.0 37.0 37.0 37.0 37.0 60-61 36.135 37.0 37.0 37.0 37.0 37.0 62-63 36.15025 37.0 37.0 37.0 37.0 37.0 64-65 36.022000000000006 37.0 37.0 37.0 37.0 37.0 66-67 36.103 37.0 37.0 37.0 37.0 37.0 68-69 36.07175 37.0 37.0 37.0 37.0 37.0 70-71 35.951499999999996 37.0 37.0 37.0 37.0 37.0 72-73 36.091750000000005 37.0 37.0 37.0 37.0 37.0 74-75 36.15 37.0 37.0 37.0 37.0 37.0 76-77 36.111000000000004 37.0 37.0 37.0 37.0 37.0 78-79 36.10925 37.0 37.0 37.0 37.0 37.0 80-81 36.132000000000005 37.0 37.0 37.0 37.0 37.0 82-83 36.054 37.0 37.0 37.0 37.0 37.0 84-85 36.025999999999996 37.0 37.0 37.0 37.0 37.0 86-87 36.0235 37.0 37.0 37.0 37.0 37.0 88-89 36.006249999999994 37.0 37.0 37.0 37.0 37.0 90-91 35.9675 37.0 37.0 37.0 37.0 37.0 92-93 35.95375 37.0 37.0 37.0 37.0 37.0 94-95 35.78675 37.0 37.0 37.0 37.0 37.0 96-97 35.90525 37.0 37.0 37.0 37.0 37.0 98-99 35.828 37.0 37.0 37.0 37.0 37.0 100-101 35.801 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 23 1.0 24 3.0 25 9.0 26 13.0 27 13.0 28 27.0 29 30.0 30 39.0 31 64.0 32 66.0 33 93.0 34 115.0 35 204.0 36 1634.0 37 1689.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 39.93457473578258 11.273276295923502 10.820332159033718 37.97181680926019 2 23.275000000000002 13.075000000000001 29.575000000000003 34.075 3 21.675 17.675 23.674999999999997 36.975 4 26.974999999999998 23.849999999999998 19.45 29.725 5 26.875 27.450000000000003 20.9 24.775 6 23.05 31.4 23.400000000000002 22.15 7 20.025000000000002 23.9 36.525 19.55 8 21.725 23.150000000000002 27.925 27.200000000000003 9 21.525 21.45 31.525 25.5 10-11 23.8875 28.749999999999996 22.4875 24.875 12-13 23.6375 22.6875 25.275 28.4 14-15 23.0375 25.662499999999998 25.087500000000002 26.2125 16-17 24.0 24.4875 24.212500000000002 27.3 18-19 24.3125 25.0625 24.099999999999998 26.525 20-21 23.7875 25.937500000000004 24.725 25.55 22-23 24.762500000000003 24.637500000000003 23.625 26.974999999999998 24-25 24.7375 24.712500000000002 24.4375 26.1125 26-27 24.375 25.55 24.25 25.825 28-29 24.675 24.2625 23.65 27.4125 30-31 23.7 24.1375 24.45 27.712500000000002 32-33 24.9875 24.525 24.45 26.0375 34-35 24.8 23.799999999999997 24.5 26.900000000000002 36-37 23.799999999999997 24.875 24.1125 27.212500000000002 38-39 23.5 24.8625 24.2 27.437499999999996 40-41 23.8125 24.75 24.275 27.1625 42-43 23.599999999999998 24.762500000000003 24.7875 26.85 44-45 24.712500000000002 23.6625 25.7875 25.837500000000002 46-47 24.65 24.85 23.375 27.125 48-49 23.9875 23.8125 24.05 28.15 50-51 23.775 25.224999999999998 23.9375 27.0625 52-53 25.362499999999997 25.087500000000002 22.925 26.625 54-55 24.1375 24.5625 24.0625 27.237499999999997 56-57 23.849999999999998 24.212500000000002 24.275 27.6625 58-59 23.625 24.6125 24.0375 27.725 60-61 25.05 23.8125 23.7125 27.425 62-63 24.0625 25.1875 24.2 26.55 64-65 25.0625 24.175 24.962500000000002 25.8 66-67 24.1375 24.0125 23.95 27.900000000000002 68-69 24.887500000000003 24.675 23.400000000000002 27.037499999999998 70-71 24.962500000000002 24.5625 24.875 25.6 72-73 24.55 24.0125 24.099999999999998 27.3375 74-75 24.8625 24.05 23.599999999999998 27.487499999999997 76-77 26.575 23.849999999999998 23.5125 26.0625 78-79 24.6875 24.4125 23.8125 27.0875 80-81 24.5125 24.462500000000002 24.087500000000002 26.937499999999996 82-83 25.575 25.224999999999998 21.925 27.275 84-85 24.887500000000003 24.5625 23.7875 26.7625 86-87 24.75 23.799999999999997 23.6625 27.787499999999998 88-89 24.9875 24.325 23.8125 26.875 90-91 25.2 25.162499999999998 23.1125 26.525 92-93 24.762500000000003 25.4625 23.4875 26.2875 94-95 25.650000000000002 24.175 23.05 27.125 96-97 24.325 24.2875 23.425 27.962500000000002 98-99 23.825 24.575 24.0375 27.5625 100-101 25.6 24.3125 23.6375 26.450000000000003 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 10.0 1 6.5 2 2.5 3 1.5 4 1.0 5 1.5 6 2.0 7 2.0 8 2.0 9 1.0 10 0.0 11 0.5 12 0.5 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.5 19 0.5 20 0.5 21 0.5 22 1.0 23 1.5 24 1.0 25 0.5 26 0.0 27 1.0 28 2.0 29 3.5 30 6.0 31 5.5 32 5.0 33 6.5 34 10.5 35 14.5 36 35.5 37 47.5 38 50.0 39 66.0 40 74.5 41 98.5 42 117.0 43 132.0 44 148.5 45 159.0 46 185.5 47 197.0 48 188.0 49 180.5 50 172.5 51 163.0 52 156.5 53 155.5 54 136.0 55 121.0 56 128.0 57 115.5 58 98.5 59 92.5 60 91.5 61 78.0 62 67.0 63 69.0 64 61.0 65 63.0 66 67.5 67 58.5 68 49.5 69 41.0 70 41.5 71 45.0 72 36.5 73 25.5 74 18.0 75 17.0 76 18.0 77 14.5 78 9.0 79 5.5 80 5.5 81 4.5 82 3.0 83 2.5 84 1.5 85 1.0 86 0.5 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.65 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 84.375 #Duplication Level Percentage of deduplicated Percentage of total 1 85.83703703703704 72.425 2 11.525925925925925 19.45 3 1.7777777777777777 4.5 4 0.5629629629629629 1.9 5 0.14814814814814814 0.625 6 0.05925925925925926 0.3 7 0.02962962962962963 0.17500000000000002 8 0.0 0.0 9 0.0 0.0 >10 0.05925925925925926 0.625 >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 15 0.375 No Hit GCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGC 10 0.25 No Hit CCGAAGGCCAACACAATAGGACCGGAATCCTATGATGTTATCCCATGCTA 7 0.17500000000000002 No Hit CCCGTGTCAGGATTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTG 6 0.15 No Hit CCCGACTGTCCCTATTAATCATTACTCCGATCCCGAAGGCCAACACAATA 6 0.15 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGCTCATTATCTCGTAT 5 0.125 TruSeq Adapter, Index 2 (97% over 37bp) GCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCC 5 0.125 No Hit GTTACGACTTCTCCTTCCTCTAAATGATAAGGTTCAATGGACTTCTCGCG 5 0.125 No Hit CCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAA 5 0.125 No Hit GCCGCAGGCTCCACGCCTGGTGGTGCCCTTCCGTCAATTCCTTTAAGTTT 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 0.025 0.0 0.0 0.0 0.0 32-33 0.05 0.0 0.0 0.0 0.0 34-35 0.0625 0.0 0.0 0.0 0.0 36-37 0.1125 0.0 0.0 0.0 0.0 38-39 0.1375 0.0 0.0 0.0 0.0 40-41 0.16249999999999998 0.0 0.0 0.0 0.0 42-43 0.225 0.0 0.0 0.0 0.0 44-45 0.2625 0.0 0.0 0.0 0.0 46-47 0.3 0.0 0.0 0.0 0.0 48-49 0.325 0.0 0.0 0.0 0.0 50-51 0.4 0.0 0.0 0.0 0.0 52-53 0.475 0.0 0.0 0.0 0.0 54-55 0.525 0.0 0.0 0.0 0.0 56-57 0.55 0.0 0.0 0.0 0.0 58-59 0.55 0.0 0.0 0.0 0.0 60-61 0.6499999999999999 0.0 0.0 0.0 0.0 62-63 0.8125 0.0 0.0 0.0 0.0 64-65 1.0625 0.0 0.0 0.0 0.0 66-67 1.2375 0.0 0.0 0.0 0.0 68-69 1.2875 0.0 0.0 0.0 0.0 70-71 1.475 0.0 0.0 0.0 0.0 72-73 1.7999999999999998 0.0 0.0 0.0 0.0 74-75 2.1375 0.0 0.0 0.0 0.0 76-77 2.575 0.0 0.0 0.0 0.0 78-79 2.95 0.0 0.0 0.0 0.0 80-81 3.375 0.0 0.0 0.0 0.0 82-83 3.8375000000000004 0.0 0.0 0.0 0.0 84-85 4.475 0.0 0.0 0.0 0.0 86-87 4.95 0.0 0.0 0.0 0.0 88-89 5.375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TGATCTC 15 0.009957196 47.5 50-51 >>END_MODULE ERR3450087 read2 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3450087_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 35.967 37.0 37.0 37.0 37.0 37.0 2 35.8405 37.0 37.0 37.0 37.0 37.0 3 35.847 37.0 37.0 37.0 37.0 37.0 4 35.946 37.0 37.0 37.0 37.0 37.0 5 35.957 37.0 37.0 37.0 37.0 37.0 6 36.0405 37.0 37.0 37.0 37.0 37.0 7 35.9795 37.0 37.0 37.0 37.0 37.0 8 36.1295 37.0 37.0 37.0 37.0 37.0 9 36.0535 37.0 37.0 37.0 37.0 37.0 10-11 36.0895 37.0 37.0 37.0 37.0 37.0 12-13 36.07325 37.0 37.0 37.0 37.0 37.0 14-15 36.08775 37.0 37.0 37.0 37.0 37.0 16-17 36.122 37.0 37.0 37.0 37.0 37.0 18-19 36.06375 37.0 37.0 37.0 37.0 37.0 20-21 36.105999999999995 37.0 37.0 37.0 37.0 37.0 22-23 36.08175 37.0 37.0 37.0 37.0 37.0 24-25 36.061 37.0 37.0 37.0 37.0 37.0 26-27 36.00375 37.0 37.0 37.0 37.0 37.0 28-29 36.039249999999996 37.0 37.0 37.0 37.0 37.0 30-31 36.0185 37.0 37.0 37.0 37.0 37.0 32-33 35.944500000000005 37.0 37.0 37.0 37.0 37.0 34-35 35.9645 37.0 37.0 37.0 37.0 37.0 36-37 35.93425 37.0 37.0 37.0 37.0 37.0 38-39 36.001 37.0 37.0 37.0 37.0 37.0 40-41 35.95875 37.0 37.0 37.0 37.0 37.0 42-43 35.931 37.0 37.0 37.0 37.0 37.0 44-45 35.9225 37.0 37.0 37.0 37.0 37.0 46-47 35.91925 37.0 37.0 37.0 37.0 37.0 48-49 35.90275 37.0 37.0 37.0 37.0 37.0 50-51 35.8785 37.0 37.0 37.0 37.0 37.0 52-53 35.945499999999996 37.0 37.0 37.0 37.0 37.0 54-55 35.8515 37.0 37.0 37.0 37.0 37.0 56-57 35.916 37.0 37.0 37.0 37.0 37.0 58-59 35.90425 37.0 37.0 37.0 37.0 37.0 60-61 35.842 37.0 37.0 37.0 37.0 37.0 62-63 35.87775 37.0 37.0 37.0 37.0 37.0 64-65 35.813 37.0 37.0 37.0 37.0 37.0 66-67 35.855999999999995 37.0 37.0 37.0 37.0 37.0 68-69 35.789 37.0 37.0 37.0 37.0 37.0 70-71 35.79175 37.0 37.0 37.0 37.0 37.0 72-73 35.838 37.0 37.0 37.0 37.0 37.0 74-75 35.6805 37.0 37.0 37.0 37.0 37.0 76-77 35.71325 37.0 37.0 37.0 37.0 37.0 78-79 35.5935 37.0 37.0 37.0 37.0 37.0 80-81 35.817750000000004 37.0 37.0 37.0 37.0 37.0 82-83 35.748000000000005 37.0 37.0 37.0 37.0 37.0 84-85 35.79025 37.0 37.0 37.0 37.0 37.0 86-87 35.75675 37.0 37.0 37.0 37.0 37.0 88-89 35.65425 37.0 37.0 37.0 37.0 37.0 90-91 35.68375 37.0 37.0 37.0 37.0 37.0 92-93 35.629999999999995 37.0 37.0 37.0 37.0 37.0 94-95 35.65175 37.0 37.0 37.0 37.0 37.0 96-97 35.641 37.0 37.0 37.0 37.0 37.0 98-99 35.57775 37.0 37.0 37.0 37.0 37.0 100-101 35.601749999999996 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 14 2.0 15 7.0 16 3.0 17 3.0 18 3.0 19 7.0 20 7.0 21 6.0 22 12.0 23 18.0 24 13.0 25 12.0 26 14.0 27 23.0 28 16.0 29 39.0 30 33.0 31 49.0 32 56.0 33 65.0 34 122.0 35 229.0 36 2113.0 37 1148.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 41.4 16.25 11.975 30.375000000000004 2 27.1 23.325000000000003 25.974999999999998 23.599999999999998 3 25.650000000000002 23.1 26.85 24.4 4 30.475 25.575 19.0 24.95 5 28.95 28.95 20.150000000000002 21.95 6 24.4 32.95 20.65 22.0 7 25.575 20.349999999999998 29.925 24.15 8 24.375 22.075 23.75 29.799999999999997 9 25.8 21.75 24.8 27.650000000000002 10-11 27.6 26.887499999999996 21.05 24.462500000000002 12-13 28.6875 21.15 23.525 26.637499999999996 14-15 26.275 24.85 23.5875 25.2875 16-17 27.250000000000004 25.6125 21.837500000000002 25.3 18-19 27.537499999999998 24.2625 23.4625 24.7375 20-21 26.55 24.837500000000002 23.025000000000002 25.587500000000002 22-23 28.349999999999998 24.25 22.6 24.8 24-25 27.187499999999996 25.3 23.05 24.462500000000002 26-27 26.9125 24.212500000000002 23.775 25.1 28-29 27.0 24.8625 22.975 25.162499999999998 30-31 27.85 24.8625 22.5875 24.7 32-33 26.275 24.762500000000003 23.6625 25.3 34-35 27.125 24.4 22.475 26.0 36-37 27.375 25.525 23.1625 23.9375 38-39 25.9875 24.325 23.225 26.4625 40-41 27.212500000000002 24.2375 23.9 24.65 42-43 27.6 24.825 23.575 24.0 44-45 26.4125 24.8125 23.2375 25.5375 46-47 27.425 24.2625 22.85 25.4625 48-49 27.5625 24.3875 22.7 25.35 50-51 26.887499999999996 24.9875 23.974999999999998 24.15 52-53 27.6125 25.0375 22.275 25.074999999999996 54-55 27.775 24.462500000000002 22.875 24.887500000000003 56-57 27.85 23.7625 23.849999999999998 24.5375 58-59 27.55 24.675 23.275000000000002 24.5 60-61 28.0875 24.0375 23.075000000000003 24.8 62-63 28.15 24.637500000000003 23.525 23.6875 64-65 28.325 23.95 22.775000000000002 24.95 66-67 27.712500000000002 24.587500000000002 23.2125 24.4875 68-69 27.187499999999996 25.0625 23.225 24.525 70-71 28.025 24.65 23.200000000000003 24.125 72-73 26.5375 24.65 23.3 25.5125 74-75 28.299999999999997 23.875 23.075000000000003 24.75 76-77 27.825 23.7125 22.625 25.837500000000002 78-79 27.900000000000002 23.6375 23.8875 24.575 80-81 27.700000000000003 24.65 23.075000000000003 24.575 82-83 27.35 23.799999999999997 24.2875 24.5625 84-85 28.050000000000004 24.6875 23.0125 24.25 86-87 27.425 24.1625 23.625 24.7875 88-89 28.212500000000002 23.925 23.575 24.2875 90-91 27.6 24.587500000000002 23.724999999999998 24.087500000000002 92-93 27.975 24.712500000000002 22.6125 24.7 94-95 28.9 24.5375 22.9625 23.599999999999998 96-97 29.25 24.087500000000002 23.1625 23.5 98-99 28.4 24.275 23.4875 23.8375 100-101 28.9125 24.1625 23.4375 23.4875 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.5 3 1.0 4 0.5 5 0.5 6 0.5 7 1.0 8 2.0 9 2.5 10 2.5 11 2.0 12 1.5 13 1.5 14 3.5 15 3.0 16 1.0 17 1.5 18 1.5 19 1.0 20 2.0 21 1.5 22 1.0 23 1.5 24 2.0 25 3.0 26 3.5 27 2.5 28 0.5 29 0.5 30 3.5 31 4.5 32 4.0 33 3.5 34 8.0 35 17.5 36 34.0 37 41.5 38 48.5 39 58.5 40 74.0 41 100.0 42 114.0 43 133.0 44 144.5 45 149.5 46 163.5 47 185.0 48 188.0 49 175.0 50 160.5 51 157.5 52 157.0 53 138.0 54 139.5 55 130.0 56 105.0 57 101.0 58 102.5 59 88.5 60 76.5 61 76.0 62 77.5 63 76.0 64 70.0 65 68.5 66 63.0 67 64.0 68 67.5 69 57.5 70 49.0 71 49.0 72 41.0 73 39.5 74 38.5 75 24.0 76 18.5 77 14.0 78 8.5 79 9.0 80 6.0 81 3.5 82 2.5 83 1.5 84 2.0 85 1.0 86 0.0 87 0.5 88 1.0 89 0.5 90 0.0 91 1.0 92 2.0 93 1.5 94 1.0 95 1.0 96 0.5 97 0.0 98 0.0 99 2.5 100 6.0 >>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 85.975 #Duplication Level Percentage of deduplicated Percentage of total 1 86.50770572840942 74.375 2 11.51497528351265 19.8 3 1.4539110206455363 3.75 4 0.37801686536783946 1.3 5 0.05815644082582146 0.25 6 0.05815644082582146 0.3 7 0.0 0.0 8 0.0 0.0 9 0.02907822041291073 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 AGACGAACAACTGCGAAAGCATTTGCCAAGGATGTTTTCATTAATCAAGA 6 0.15 No Hit CGCCGTTTAGGCGACGGAAGTTTGAGGCAATAACAGGTCTGTGATGCCCT 6 0.15 No Hit CCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGCAA 5 0.125 No Hit ACCAGGTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAT 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 0.025 0.0 0.0 0.0 0.0 32-33 0.05 0.0 0.0 0.0 0.0 34-35 0.0625 0.0 0.0 0.0 0.0 36-37 0.1125 0.0 0.0 0.0 0.0 38-39 0.1375 0.0 0.0 0.0 0.0 40-41 0.16249999999999998 0.0 0.0 0.0 0.0 42-43 0.21250000000000002 0.0 0.0 0.0 0.0 44-45 0.225 0.0 0.0 0.0 0.0 46-47 0.25 0.0 0.0 0.0 0.0 48-49 0.275 0.0 0.0 0.0 0.0 50-51 0.35 0.0 0.0 0.0 0.0 52-53 0.42500000000000004 0.0 0.0 0.0 0.0 54-55 0.475 0.0 0.0 0.0 0.0 56-57 0.5 0.0 0.0 0.0 0.0 58-59 0.5 0.0 0.0 0.0 0.0 60-61 0.6000000000000001 0.0 0.0 0.0 0.0 62-63 0.7625 0.0 0.0 0.0 0.0 64-65 1.0125000000000002 0.0 0.0 0.0 0.0 66-67 1.1875 0.0 0.0 0.0 0.0 68-69 1.2375 0.0 0.0 0.0 0.0 70-71 1.4500000000000002 0.0 0.0 0.0 0.0 72-73 1.775 0.0 0.0 0.0 0.0 74-75 2.1375 0.0 0.0 0.0 0.0 76-77 2.575 0.0 0.0 0.0 0.0 78-79 2.95 0.0 0.0 0.0 0.0 80-81 3.375 0.0 0.0 0.0 0.0 82-83 3.8375000000000004 0.0 0.0 0.0 0.0 84-85 4.475 0.0 0.0 0.0 0.0 86-87 4.95 0.0 0.0 0.0 0.0 88-89 5.4 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 2660796 spots for ERR3450087.sra Written 2660796 spots for ERR3450087.sra Read 2660806 spots for ERR3450087.sra Written 2660806 spots for ERR3450087.sra Read 2660796 spots for ERR3450087.sra Written 2660796 spots for ERR3450087.sra Read 2660796 spots for ERR3450087.sra Written 2660796 spots for ERR3450087.sra Read 2660796 spots for ERR3450087.sra Written 2660796 spots for ERR3450087.sra Read 2660796 spots for ERR3450087.sra Written 2660796 spots for ERR3450087.sra Read 2660796 spots for ERR3450087.sra Written 2660796 spots for ERR3450087.sra Read 2660796 spots for ERR3450087.sra Written 2660796 spots for ERR3450087.sra Read 2660796 spots for ERR3450087.sra Written 2660796 spots for ERR3450087.sra Read 2660796 spots for ERR3450087.sra Written 2660796 spots for ERR3450087.sra Read 2660796 spots for ERR3450087.sra Written 2660796 spots for ERR3450087.sra Read 2660796 spots for ERR3450087.sra Written 2660796 spots for ERR3450087.sra Read 2660796 spots for ERR3450087.sra Written 2660796 spots for ERR3450087.sra Read 2660796 spots for ERR3450087.sra Written 2660796 spots for ERR3450087.sra Read 2660796 spots for ERR3450087.sra Written 2660796 spots for ERR3450087.sra Read 2660796 spots for ERR3450087.sra Written 2660796 spots for ERR3450087.sra Read 2660796 spots for ERR3450087.sra Written 2660796 spots for ERR3450087.sra Read 2660796 spots for ERR3450087.sra Written 2660796 spots for ERR3450087.sra Read 2660796 spots for ERR3450087.sra Written 2660796 spots for ERR3450087.sra Read 2660796 spots for ERR3450087.sra Written 2660796 spots for ERR3450087.sra SRR ids: ['ERR3450087.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_bi8h0yed ERR3450087.sra spots: 53215930 blocks: [[1, 2660796], [2660797, 5321592], [5321593, 7982388], [7982389, 10643184], [10643185, 13303980], [13303981, 15964776], [15964777, 18625572], [18625573, 21286368], [21286369, 23947164], [23947165, 26607960], [26607961, 29268756], [29268757, 31929552], [31929553, 34590348], [34590349, 37251144], [37251145, 39911940], [39911941, 42572736], [42572737, 45233532], [45233533, 47894328], [47894329, 50555124], [50555125, 53215930]] ERR3450087 file size 12814563 ERR3450087 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 ERR3450087 ERR3450087_1.fastq ERR3450087_2.fastq Input file: ERR3450087_1.fastq Paired file: ERR3450087_2.fastq trimmed: ERR3450087-trimmed-pair1.fastq, ERR3450087-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 15:05:52 2024 >> started Sat Dec 7 15:06:46 2024 >> done (53.659s) 53215930 read pairs processed; of these: 435 ( 0.00%) short read pairs filtered out after trimming by size control 61682 ( 0.12%) empty read pairs filtered out after trimming by size control 53153813 (99.88%) read pairs available; of these: 5120886 ( 9.63%) trimmed read pairs available after processing 48032927 (90.37%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 52 0.00% 19 100 0.00% 20 308 0.00% 21 769 0.00% 22 958 0.00% 23 541 0.00% 24 502 0.00% 25 695 0.00% 26 1083 0.00% 27 1334 0.00% 28 2030 0.00% 29 2614 0.00% 30 3332 0.01% 31 3899 0.01% 32 4061 0.01% 33 3961 0.01% 34 4200 0.01% 35 4139 0.01% 36 4682 0.01% 37 5145 0.01% 38 6182 0.01% 39 7162 0.01% 40 8557 0.02% 41 9866 0.02% 42 11124 0.02% 43 11616 0.02% 44 10632 0.02% 45 10608 0.02% 46 11483 0.02% 47 12628 0.02% 48 14056 0.03% 49 15421 0.03% 50 17138 0.03% 51 19413 0.04% 52 21010 0.04% 53 22541 0.04% 54 23763 0.04% 55 24787 0.05% 56 25585 0.05% 57 27491 0.05% 58 29992 0.06% 59 32655 0.06% 60 35322 0.07% 61 39371 0.07% 62 43015 0.08% 63 46048 0.09% 64 48294 0.09% 65 50077 0.09% 66 52426 0.10% 67 55280 0.10% 68 58394 0.11% 69 60307 0.11% 70 65162 0.12% 71 69097 0.13% 72 75079 0.14% 73 79775 0.15% 74 83310 0.16% 75 86795 0.16% 76 90214 0.17% 77 92384 0.17% 78 96816 0.18% 79 102743 0.19% 80 105286 0.20% 81 110521 0.21% 82 116585 0.22% 83 121320 0.23% 84 126950 0.24% 85 133318 0.25% 86 135179 0.25% 87 141712 0.27% 88 146444 0.28% 89 151303 0.28% 90 157266 0.30% 91 166012 0.31% 92 171802 0.32% 93 176859 0.33% 94 183501 0.35% 95 188241 0.35% 96 192936 0.36% 97 199915 0.38% 98 203273 0.38% 99 205372 0.39% 100 239067 0.45% 101 48032927 90.37% 53153813 reads passed initial QC criterion=sequence-density sequence-density=0.31 sequence-density-rank=1 fanout-score=2.09 fanout-score-rank=22 prefix-density=0.32 prefix-fanout=2.0 sequence=TTCGCTATCGGTC criterion=fanout-score sequence-density=0.08 sequence-density-rank=16 fanout-score=156.28 fanout-score-rank=1 prefix-density=0.59 prefix-fanout=20.6 sequence=CGCCGCCGCCGC criterion=sequence-density sequence-density=0.23 sequence-density-rank=1 fanout-score=1.95 fanout-score-rank=32 prefix-density=0.23 prefix-fanout=1.9 sequence=CAAGTGTTGGATTTAAAGCTGGTGTTAAAGATTATAGATTGACTTACTACACCCCGGAGTATGAAACCAAGGATACTGATATCTTGGCAGCATTCCGAGTATCTCCTCAACCTGGGGTTCCGCCCGAAGAAGCAGGGGCTGCAGTAGCTGCCGAATCTTCTACTGGTACATGGACAACTGTTTGGACTGATGGACTTACTAGTCTTGATCGTTACAAAGGACGATGCTATCACATCGAGCCTGTTCCTGGGGAAGACAGTCAATGGATCTGTTATGTAGCTTATCCATTAGATCTATTTGAAGAGGGTTCCGTTACTAACATGTTTACTTCCATTGTAGGTAACGTATTTGGTTTCAAAGCCCTACGTGCTCTACGTCTGGAGGATCTACGAATTCCCCCTACTTATTCAAAAACTTTCCAAGGCCCGCCTCACGGTATCCAAGTGGAAAGAGATAAGTTGAACAAGTATGGTCGTCCTTTATTGGGATGTACTATTAAGCCAAAATTGGG criterion=fanout-score sequence-density=0.08 sequence-density-rank=21 fanout-score=213.98 fanout-score-rank=1 prefix-density=0.73 prefix-fanout=22.2 sequence=CGGCGGCGGCGC ERR3450087 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 15:07:21 Started mapping on | Dec 07 15:07:22 Finished on | Dec 07 15:11:52 Mapping speed, Million of reads per hour | 708.72 Number of input reads | 53153813 Average input read length | 198 UNIQUE READS: Uniquely mapped reads number | 39658325 Uniquely mapped reads % | 74.61% Average mapped length | 198.01 Number of splices: Total | 24996183 Number of splices: Annotated (sjdb) | 23667862 Number of splices: GT/AG | 24669341 Number of splices: GC/AG | 282398 Number of splices: AT/AC | 15404 Number of splices: Non-canonical | 29040 Mismatch rate per base, % | 0.23% Deletion rate per base | 0.01% Deletion average length | 2.12 Insertion rate per base | 0.01% Insertion average length | 1.92 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 2643519 % of reads mapped to multiple loci | 4.97% Number of reads mapped to too many loci | 1860356 % of reads mapped to too many loci | 3.50% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.99% % of reads unmapped: other | 13.93% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 10851969 10851969 10851969 N_multimapping 2643519 2643519 2643519 N_noFeature 1360728 38246533 2181658 N_ambiguous 715709 5863 130405 UnstrandedReadsAssigned:37581888 PositiveStrandReadsAssigned:1405929 NegativeStrandReadsAssigned:37346262 Dataset is classified negative stranded MeadianReadLen=101 20thPercentileLength=101 echo kmer=97 ERR3450087 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: ERR3450087-trimmed-pair1.fastq ERR3450087-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 53,153,813 reads, 39,365,841 reads pseudoaligned [quant] estimated average fragment length: 184.866 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,255 rounds 52973 ERR3450087.ke.tsv 35125 ERR3450087.se.tsv 88098 total ==> ERR3450087.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 752.432 0 0 PNS24247 1044 860.134 90.2355 4.0529 PNS24249 1928 1744.13 436.027 9.65801 PNS24246 1044 860.134 90.2355 4.0529 PNS24248 1044 860.134 90.2355 4.0529 PNS24244 1471 1287.13 119.266 3.57971 PNS24243 293 129.746 0 0 KQK14069 1603 1419.13 10811.7 294.322 KQK14071 474 294.073 488.187 64.1335 ==> ERR3450087.se.tsv <== BRADI_1g14170v3 11757 BRADI_1g53295v3 48 BRADI_1g59795v3 466 BRADI_1g07683v3 0 BRADI_1g00485v3 130 BRADI_1g20270v3 4880 BRADI_1g74790v3 380 BRADI_1g09890v3 42 BRADI_1g77505v3 519 BRADI_1g48960v3 3 ERR3450087 completed mapping pipeline successfully