Starting /dee2/code/volunteer_pipeline.sh SRR21835921 current disk space = 3088502751232 free memory = 1477286032 SRR21835921 SRAfilesize 0be3680ece69c0a8336e1774bf5472a7 SRR21835921.sra SRR21835921.sra file validated SRR21835921 is paired end SRR21835921 is conventional basespace SRR21835921 read1 length is 100-150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR21835921_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 100-150 %GC 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.647 37.0 37.0 37.0 37.0 37.0 2 36.5585 37.0 37.0 37.0 37.0 37.0 3 36.67925 37.0 37.0 37.0 37.0 37.0 4 36.701 37.0 37.0 37.0 37.0 37.0 5 36.7535 37.0 37.0 37.0 37.0 37.0 6 36.689 37.0 37.0 37.0 37.0 37.0 7 36.6585 37.0 37.0 37.0 37.0 37.0 8 36.7935 37.0 37.0 37.0 37.0 37.0 9 36.642 37.0 37.0 37.0 37.0 37.0 10-14 36.6792 37.0 37.0 37.0 37.0 37.0 15-19 36.6822 37.0 37.0 37.0 37.0 37.0 20-24 36.626000000000005 37.0 37.0 37.0 37.0 37.0 25-29 36.6145 37.0 37.0 37.0 37.0 37.0 30-34 36.60680000000001 37.0 37.0 37.0 37.0 37.0 35-39 36.5313 37.0 37.0 37.0 37.0 37.0 40-44 36.4762 37.0 37.0 37.0 37.0 37.0 45-49 36.447900000000004 37.0 37.0 37.0 37.0 37.0 50-54 36.4971 37.0 37.0 37.0 37.0 37.0 55-59 36.4342 37.0 37.0 37.0 37.0 37.0 60-64 36.3877 37.0 37.0 37.0 37.0 37.0 65-69 36.43050000000001 37.0 37.0 37.0 37.0 37.0 70-74 36.424 37.0 37.0 37.0 37.0 37.0 75-79 36.3297 37.0 37.0 37.0 37.0 37.0 80-84 36.339299999999994 37.0 37.0 37.0 37.0 37.0 85-89 36.229200000000006 37.0 37.0 37.0 37.0 37.0 90-94 36.177499999999995 37.0 37.0 37.0 37.0 37.0 95-99 36.207899999999995 37.0 37.0 37.0 37.0 37.0 100-104 36.07823951995889 37.0 37.0 37.0 37.0 37.0 105-109 36.150754942627245 37.0 37.0 37.0 37.0 37.0 110-114 36.08905197170652 37.0 37.0 37.0 37.0 37.0 115-119 35.99671038355932 37.0 37.0 37.0 37.0 37.0 120-124 35.895445741367084 37.0 37.0 37.0 37.0 37.0 125-129 35.89186782310264 37.0 37.0 37.0 37.0 37.0 130-134 35.8927468615044 37.0 37.0 37.0 37.0 37.0 135-139 35.7977355441736 37.0 37.0 37.0 37.0 37.0 140-144 35.780593927914964 37.0 37.0 37.0 37.0 37.0 145-149 35.739735136105686 37.0 37.0 37.0 37.0 37.0 150 35.68260292164675 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 23 1.0 24 1.0 25 3.0 26 3.0 27 7.0 28 10.0 29 12.0 30 19.0 31 32.0 32 33.0 33 58.0 34 96.0 35 324.0 36 3161.0 37 240.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 38.06306306306306 16.09109109109109 13.038038038038039 32.80780780780781 2 19.525000000000002 22.900000000000002 36.075 21.5 3 22.53063265816454 25.331332833208304 26.9567391847962 25.18129532383096 4 24.15 31.900000000000002 21.3 22.650000000000002 5 25.3 33.4 21.975 19.325 6 18.45 39.4 24.2 17.95 7 18.099999999999998 20.8 42.9 18.2 8 19.55 24.825 30.725 24.9 9 19.825 25.1 31.15 23.925 10-14 20.925 29.945 26.805 22.325 15-19 21.66 28.115000000000002 28.08 22.145 20-24 20.89 28.34 28.34 22.43 25-29 21.22 27.839999999999996 28.139999999999997 22.8 30-34 20.965 27.944999999999997 28.32 22.770000000000003 35-39 21.085 28.165000000000003 28.185 22.564999999999998 40-44 21.72 28.62 27.250000000000004 22.41 45-49 20.95 27.32 29.26 22.470000000000002 50-54 21.325 28.33 27.825 22.52 55-59 21.65 28.360000000000003 26.96 23.03 60-64 21.395 27.66 28.970000000000002 21.975 65-69 21.46 28.26 28.499999999999996 21.78 70-74 21.65 28.144999999999996 27.83 22.375 75-79 21.29 28.125 27.87 22.715 80-84 21.9 27.625 28.044999999999998 22.43 85-89 22.06 28.494999999999997 27.365000000000002 22.08 90-94 21.78 27.529999999999998 28.060000000000002 22.63 95-99 21.965 28.625 26.57 22.84 100-104 21.672260908772106 28.184960673312958 27.628876308802162 22.51390210911277 105-109 21.560255186617773 27.96001406540413 28.231275430753 22.248455317225098 110-114 21.459508460918613 28.011684125705077 27.805197421434325 22.72360999194198 115-119 22.312711821538773 28.524457483939504 27.02210531640447 22.140725378117253 120-124 20.918910695268522 29.03291241949389 27.587605862366242 22.460571022871342 125-129 22.063314332247558 27.692385993485342 28.379478827361567 21.864820846905538 130-134 22.363775901765155 27.838321821437706 27.270401637247378 22.527500639549757 135-139 21.78024462945832 27.238153972659063 28.45616198992702 22.5254394079556 140-144 21.856086079354405 27.582639284051524 28.5706895659821 21.99058507061197 145-149 21.687381504107858 28.07562671160733 27.606909627132925 22.630082157151886 150 20.823373173970783 28.207171314741036 29.00398406374502 21.965471447543162 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 2.0 22 2.0 23 1.5 24 3.5 25 2.0 26 2.5 27 4.5 28 9.0 29 15.5 30 16.0 31 21.0 32 26.0 33 27.5 34 43.0 35 70.0 36 83.5 37 113.5 38 150.5 39 174.0 40 203.0 41 229.5 42 249.0 43 263.5 44 284.0 45 290.5 46 270.0 47 263.5 48 232.5 49 180.5 50 153.5 51 139.0 52 107.5 53 70.0 54 67.0 55 66.5 56 50.0 57 27.5 58 17.0 59 14.5 60 12.0 61 10.0 62 13.0 63 8.5 64 2.0 65 1.5 66 0.5 67 2.0 68 1.5 69 0.5 70 1.5 71 1.0 72 0.0 73 0.0 74 0.0 75 0.0 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.1 2 0.0 3 0.025 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 100-101 9.0 102-103 6.0 104-105 3.0 106-107 2.0 108-109 3.0 110-111 6.0 112-113 6.0 114-115 9.0 116-117 5.0 118-119 3.0 120-121 3.0 122-123 8.0 124-125 1.0 126-127 11.0 128-129 10.0 130-131 7.0 132-133 7.0 134-135 6.0 136-137 7.0 138-139 7.0 140-141 10.0 142-143 32.0 144-145 20.0 146-147 38.0 148-149 16.0 150-151 3765.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 74.95 #Duplication Level Percentage of deduplicated Percentage of total 1 75.41694462975317 56.525000000000006 2 18.0787191460974 27.1 3 5.036691127418279 11.325000000000001 4 0.867244829886591 2.6 5 0.40026684456304207 1.5 6 0.13342228152101399 0.6 7 0.06671114076050699 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 GAAGGATGCATTTTGGCAGAAAAATGGGAAATTGCGAACATACTCAAGCT 7 0.17500000000000002 No Hit ATCATAGTACCCTGGTGAGCTGTGGTGCTCACGGTAGACCCAACCTTTCT 7 0.17500000000000002 No Hit GTGCAGTTGTAGATGGGTTGAAGTATGCATCTTCACATGAGTGGGTGAAG 6 0.15 No Hit GTACAATTGTCTGGGCTTGCTGGAAATTATGACCACTCTTCCAATCCCAG 6 0.15 No Hit CGGGTTAGATGCATCTGGAAGGAAGCCCAGGGTTAGTGTGTAGTGCTTTA 6 0.15 No Hit GTGAAAAAAGTGGGATGAAATAGTAAGTGAGTGATTGTTGCAATTGTAAC 6 0.15 No Hit AAGGGTCAGACCCTCCGCTTGCCTTCTGCCTCCATTGTCCGGTGCCGCTC 5 0.125 No Hit ATTATATCTCCCCTAAATCATGTTGAGCTACCACTTGAGGGTGCAAGCCC 5 0.125 No Hit GCCAGTTAAAATATCCCCAAAACCACCTGCTTTGAAGACTTTAGCAGCTT 5 0.125 No Hit ATTTGATTGTGCTCTGCTAGTATCTTCTTCCACCAGCCAGCCTCCCTGTG 5 0.125 No Hit AGAACATACATGCATTTCAAGAATATCATTCCAAAAAAAATCAATTGCTG 5 0.125 No Hit CTGGGAATTACATGCACCTTTAATTTGAAGCGTTTGTTTCACAGTACCAC 5 0.125 No Hit CTTCGTTTGCTAGCATCCTAACTTGAGGACTCCACCCCACCACACAACCC 5 0.125 No Hit CACCACTTTGACCATTGAGAACAATAACATTCCCATCAGAATCAACATCT 5 0.125 No Hit GCTTCAATGAAAGTAGAACATCCATGGAGAAATTTGTTGCAAAGAAAGTA 5 0.125 No Hit TGGGAAGGACATTATTTGCATTACATTACTATTTTTGAAAAAGGTTTCAG 5 0.125 No Hit GCTGGGTCCAAATATGCTGGTAATGTGTCCTTAATTCCCAATTCTTTAGC 5 0.125 No Hit CCTATGATCATCAGAGTAATATTTCATCCTTTCATTCTCTGGTAACTTGA 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.0 0.0 0.0 0.0 0.0 82-83 0.0 0.0 0.0 0.0 0.0 84-85 0.0 0.0 0.0 0.0 0.0 86-87 0.0 0.0 0.0 0.0 0.0 88-89 0.0 0.0 0.0 0.0 0.0 90-91 0.0 0.0 0.0 0.0 0.0 92-93 0.0 0.0 0.0 0.0 0.0 94-95 0.0 0.0 0.0 0.0 0.0 96-97 0.0 0.0 0.0 0.0 0.0 98-99 0.0 0.0 0.0 0.0 0.0 100-101 0.0 0.0 0.0 0.0 0.0 102-103 0.0 0.0 0.0 0.0 0.0 104-105 0.0 0.0 0.0 0.0 0.0 106-107 0.0 0.0 0.0 0.0 0.0 108-109 0.0 0.0 0.0 0.0 0.0 110-111 0.0 0.0 0.0 0.0 0.0 112-113 0.0 0.0 0.0 0.025 0.0 114-115 0.0 0.0 0.0 0.025 0.0 116-117 0.0 0.0 0.0 0.025 0.0 118-119 0.0 0.0 0.0 0.025 0.0 120-121 0.0 0.0 0.0 0.025 0.0 122-123 0.0 0.0 0.0 0.025 0.0 124-125 0.0 0.0 0.0 0.025 0.0 126-127 0.0 0.0 0.0 0.025 0.0 128-129 0.0 0.0 0.0 0.025 0.0 130-131 0.0 0.0 0.0 0.025 0.0 132-133 0.0 0.0 0.0 0.025 0.0 134-135 0.0 0.0 0.0 0.025 0.0 136-137 0.0 0.0 0.0 0.025 0.0 138 0.0 0.0 0.0 0.025 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AGTATTC 10 0.0070282277 143.625 5 >>END_MODULE SRR21835921 read2 length is 100-150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR21835921_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 100-150 %GC 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.4555 37.0 37.0 37.0 37.0 37.0 2 36.502 37.0 37.0 37.0 37.0 37.0 3 36.471 37.0 37.0 37.0 37.0 37.0 4 36.5945 37.0 37.0 37.0 37.0 37.0 5 36.3985 37.0 37.0 37.0 37.0 37.0 6 36.4995 37.0 37.0 37.0 37.0 37.0 7 36.4805 37.0 37.0 37.0 37.0 37.0 8 36.4725 37.0 37.0 37.0 37.0 37.0 9 36.44 37.0 37.0 37.0 37.0 37.0 10-14 36.4578 37.0 37.0 37.0 37.0 37.0 15-19 36.46810000000001 37.0 37.0 37.0 37.0 37.0 20-24 36.4327 37.0 37.0 37.0 37.0 37.0 25-29 36.2813 37.0 37.0 37.0 37.0 37.0 30-34 36.3777 37.0 37.0 37.0 37.0 37.0 35-39 36.3206 37.0 37.0 37.0 37.0 37.0 40-44 36.3005 37.0 37.0 37.0 37.0 37.0 45-49 36.2083 37.0 37.0 37.0 37.0 37.0 50-54 36.2584 37.0 37.0 37.0 37.0 37.0 55-59 36.221900000000005 37.0 37.0 37.0 37.0 37.0 60-64 36.1476 37.0 37.0 37.0 37.0 37.0 65-69 36.148999999999994 37.0 37.0 37.0 37.0 37.0 70-74 36.11899999999999 37.0 37.0 37.0 37.0 37.0 75-79 36.035000000000004 37.0 37.0 37.0 37.0 37.0 80-84 36.032300000000006 37.0 37.0 37.0 37.0 37.0 85-89 35.9794 37.0 37.0 37.0 37.0 37.0 90-94 35.995200000000004 37.0 37.0 37.0 37.0 37.0 95-99 35.8874 37.0 37.0 37.0 37.0 37.0 100-104 35.84493534592902 37.0 37.0 37.0 37.0 37.0 105-109 35.78481940458589 37.0 37.0 37.0 37.0 37.0 110-114 35.75819800331355 37.0 37.0 37.0 37.0 37.0 115-119 35.72469947142413 37.0 37.0 37.0 37.0 37.0 120-124 35.6333740751679 37.0 37.0 37.0 37.0 37.0 125-129 35.638909001981645 37.0 37.0 37.0 37.0 37.0 130-134 35.427786734871184 37.0 37.0 37.0 34.6 37.0 135-139 35.65820090622515 37.0 37.0 37.0 37.0 37.0 140-144 35.58760181181087 37.0 37.0 37.0 37.0 37.0 145-149 35.27184927394867 37.0 37.0 37.0 29.8 37.0 150 35.2199203187251 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 1.0 22 4.0 23 6.0 24 3.0 25 1.0 26 10.0 27 11.0 28 13.0 29 10.0 30 18.0 31 25.0 32 36.0 33 69.0 34 149.0 35 646.0 36 2871.0 37 127.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 37.1 13.700000000000001 14.124999999999998 35.075 2 20.9 22.8 32.525 23.775 3 21.45 26.224999999999998 28.199999999999996 24.125 4 26.55 30.55 21.3 21.6 5 25.775 33.7 23.5 17.025000000000002 6 18.9 37.65 24.55 18.9 7 15.875 18.875 44.800000000000004 20.45 8 18.3 23.400000000000002 30.825000000000003 27.474999999999998 9 19.725 23.875 31.7 24.7 10-14 21.37 28.915000000000003 27.450000000000003 22.264999999999997 15-19 21.755 28.435 27.72 22.09 20-24 21.22 29.575000000000003 27.345000000000002 21.86 25-29 21.215 28.88 27.87 22.035 30-34 22.065 28.194999999999997 28.144999999999996 21.595 35-39 21.279999999999998 27.575 28.055000000000003 23.09 40-44 21.575 27.415 28.015 22.994999999999997 45-49 21.77 28.535 27.950000000000003 21.745 50-54 22.32 27.834999999999997 28.415000000000003 21.43 55-59 21.89 28.08 27.884999999999998 22.145 60-64 21.92 27.944999999999997 28.015 22.12 65-69 21.975 28.665000000000003 27.189999999999998 22.17 70-74 21.755 28.345 27.57 22.33 75-79 22.35 28.21 27.92 21.52 80-84 22.155 27.71 28.13 22.005 85-89 21.235 28.185 27.915 22.665 90-94 21.495 28.4 27.36 22.745 95-99 21.715 28.78 27.46 22.045 100-104 21.597114373027402 27.80922799458945 28.099794599468964 22.49386303291418 105-109 21.64062892449892 27.79424323102426 28.356859396192295 22.208268448284525 110-114 21.94298952457695 27.56345688960516 27.910958904109588 22.582594681708297 115-119 21.285851585816175 28.645859679295864 27.02210531640447 23.046183418483484 120-124 22.0954409452812 28.160657234139663 28.059232212586842 21.68466960799229 125-129 22.694421824104236 27.28521986970684 28.08428338762215 21.936074918566774 130-134 22.3074955231517 28.503453568687643 27.36249680225121 21.82655410590944 135-139 21.615787850755474 28.281426662555248 27.736663583102068 22.366121903587214 140-144 22.006104184987844 28.896590967875436 27.706792199058505 21.390512648078218 145-149 22.203496945439223 28.433747630082156 28.065093743416895 21.297661681061722 150 21.93891102257636 28.339973439575033 27.54316069057105 22.177954847277555 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 2.5 23 3.5 24 2.5 25 5.0 26 4.5 27 6.0 28 13.5 29 12.0 30 6.5 31 15.0 32 33.5 33 41.5 34 42.0 35 60.0 36 82.0 37 110.5 38 149.0 39 185.0 40 205.0 41 220.0 42 258.0 43 283.0 44 282.5 45 273.0 46 269.0 47 234.5 48 194.0 49 199.5 50 176.5 51 122.5 52 90.5 53 84.0 54 76.0 55 67.0 56 57.0 57 35.0 58 24.5 59 18.5 60 14.5 61 15.5 62 8.5 63 4.0 64 5.5 65 2.5 66 1.0 67 1.5 68 0.5 69 1.0 70 1.0 71 0.0 72 0.0 73 0.0 74 0.0 75 0.0 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 100-101 9.0 102-103 6.0 104-105 3.0 106-107 2.0 108-109 3.0 110-111 6.0 112-113 6.0 114-115 9.0 116-117 5.0 118-119 3.0 120-121 3.0 122-123 8.0 124-125 1.0 126-127 11.0 128-129 10.0 130-131 7.0 132-133 7.0 134-135 6.0 136-137 7.0 138-139 7.0 140-141 10.0 142-143 32.0 144-145 20.0 146-147 38.0 148-149 16.0 150-151 3765.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 76.125 #Duplication Level Percentage of deduplicated Percentage of total 1 76.94581280788178 58.575 2 16.912972085385878 25.75 3 4.761904761904762 10.875 4 0.8210180623973727 2.5 5 0.361247947454844 1.375 6 0.16420361247947454 0.75 7 0.03284072249589491 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 CTCATCGGCAGCCGTTGCCACCGTCAACCGCACCCCGGCACAAGCCAACA 7 0.17500000000000002 No Hit AAATTACAAAAGGATTTCATTCCATGCACCATATCCTTCGAATTGAAAGG 6 0.15 No Hit CATGACTCAACTATCAAGTTCTGGGATCTTAGATATGGTAAGACTATGTT 6 0.15 No Hit TGAGGATTGAGTTCGAGTACTCTATTTTTTGATCTATAACTTTTAGCTAA 6 0.15 No Hit CCTTGTTTAAGGCATGTAAGGGGAGCAGGAATTTCTCACAAGGCATAAAT 6 0.15 No Hit CCTTGGTCTTGCCCTTGAATGGTTTGGTGCTGTGCAATCCTAGACTATCA 6 0.15 No Hit TGAAAACCACCCTCAAGGAAAAGAAACCTTCTCCCCCACTTGTCGACGCC 5 0.125 No Hit CCCCAACATACTTGACACCTTCGTTGTGCTATTTGCCATGTATGTAAACC 5 0.125 No Hit CAAGAATTTAACTTCTGATTGATAATAACATGAGTTCCGATGTTAGGTAT 5 0.125 No Hit GTTTGACAGGAGGGAAGGGGAAAAAATTATGAATGATAGTGGGTGTCAAT 5 0.125 No Hit CTAAAGCCAAGCAAATCACCTACAAGGTGTTGGAAGGAAACATGATGCTT 5 0.125 No Hit GCCATCCTTCATTAACGTCCCTGGCTCGTATCCTGCTTACTTCAAGATGT 5 0.125 No Hit GTTAAGACAATGGCCTCGAAGAAATCTGCAATCGTATTACCTGGTTCAAA 5 0.125 No Hit CGTCGGTGCTCTTTCTCACTGTTGTCTGCACCGTCAGTTCCTTGGTAAAG 5 0.125 No Hit TGATTGTTTTCCGTCAACTTACCAAGCTGGAGGTCAAGGATATTGCTGAT 5 0.125 No Hit AACATTGCTCCTTTTAGTGAAGGAATGAGTGGCATTGAAGCTGAACGAAG 5 0.125 No Hit TGCCAGTCCCACAGCCTCTTTCCTTCTACAGATAGGGTCACAGAGGCAAC 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.0 0.0 0.0 0.0 0.0 82-83 0.0 0.0 0.0 0.0 0.0 84-85 0.0 0.0 0.0 0.0 0.0 86-87 0.0 0.0 0.0 0.0 0.0 88-89 0.0 0.0 0.0 0.0 0.0 90-91 0.0 0.0 0.0 0.0 0.0 92-93 0.0 0.0 0.0 0.0 0.0 94-95 0.0 0.0 0.0 0.0 0.0 96-97 0.0 0.0 0.0 0.0 0.0 98-99 0.0 0.0 0.0 0.0 0.0 100-101 0.0 0.0 0.0 0.0 0.0 102-103 0.0 0.0 0.0 0.0 0.0 104-105 0.0 0.0 0.0 0.0 0.0 106-107 0.0 0.0 0.0 0.0 0.0 108-109 0.0 0.0 0.0 0.0 0.0 110-111 0.0 0.0 0.0 0.0 0.0 112-113 0.0 0.0 0.0 0.0 0.0 114-115 0.0 0.0 0.0 0.0 0.0 116-117 0.0 0.0 0.0 0.0 0.0 118-119 0.0 0.0 0.0 0.0 0.0 120-121 0.0 0.0 0.0 0.0 0.0 122-123 0.0 0.0 0.0 0.0 0.0 124-125 0.0 0.0 0.0 0.0 0.0 126-127 0.0 0.0 0.0 0.0 0.0 128-129 0.0 0.0 0.0 0.0 0.0 130-131 0.0 0.0 0.0 0.0 0.0 132-133 0.0 0.0 0.0 0.0 0.0 134-135 0.0 0.0 0.0 0.0 0.0 136-137 0.0 0.0 0.0 0.0 0.0 138 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CCAGCGG 10 0.0070282277 143.625 7 >>END_MODULE Read 1362898 spots for SRR21835921.sra Written 1362898 spots for SRR21835921.sra Read 1362898 spots for SRR21835921.sra Written 1362898 spots for SRR21835921.sra Read 1362898 spots for SRR21835921.sra Written 1362898 spots for SRR21835921.sra Read 1362898 spots for SRR21835921.sra Written 1362898 spots for SRR21835921.sra Read 1362898 spots for SRR21835921.sra Written 1362898 spots for SRR21835921.sra Read 1362898 spots for SRR21835921.sra Written 1362898 spots for SRR21835921.sra Read 1362898 spots for SRR21835921.sra Written 1362898 spots for SRR21835921.sra Read 1362898 spots for SRR21835921.sra Written 1362898 spots for SRR21835921.sra Read 1362898 spots for SRR21835921.sra Written 1362898 spots for SRR21835921.sra Read 1362898 spots for SRR21835921.sra Written 1362898 spots for SRR21835921.sra Read 1362898 spots for SRR21835921.sra Written 1362898 spots for SRR21835921.sra Read 1362898 spots for SRR21835921.sra Written 1362898 spots for SRR21835921.sra Read 1362898 spots for SRR21835921.sra Written 1362898 spots for SRR21835921.sra Read 1362898 spots for SRR21835921.sra Written 1362898 spots for SRR21835921.sra Read 1362898 spots for SRR21835921.sra Written 1362898 spots for SRR21835921.sra Read 1362898 spots for SRR21835921.sra Written 1362898 spots for SRR21835921.sra Read 1362898 spots for SRR21835921.sra Written 1362898 spots for SRR21835921.sra Read 1362898 spots for SRR21835921.sra Written 1362898 spots for SRR21835921.sra Read 1362898 spots for SRR21835921.sra Written 1362898 spots for SRR21835921.sra Read 1362903 spots for SRR21835921.sra Written 1362903 spots for SRR21835921.sra SRR ids: ['SRR21835921.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_60hjg2cx SRR21835921.sra spots: 27257965 blocks: [[1, 1362898], [1362899, 2725796], [2725797, 4088694], [4088695, 5451592], [5451593, 6814490], [6814491, 8177388], [8177389, 9540286], [9540287, 10903184], [10903185, 12266082], [12266083, 13628980], [13628981, 14991878], [14991879, 16354776], [16354777, 17717674], [17717675, 19080572], [19080573, 20443470], [20443471, 21806368], [21806369, 23169266], [23169267, 24532164], [24532165, 25895062], [25895063, 27257965]] SRR21835921 file size 9133362 SRR21835921 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 SRR21835921 SRR21835921_1.fastq SRR21835921_2.fastq Input file: SRR21835921_1.fastq Paired file: SRR21835921_2.fastq trimmed: SRR21835921-trimmed-pair1.fastq, SRR21835921-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 Thu Feb 13 18:10:32 2025 >> started Thu Feb 13 18:11:16 2025 >> done (44.002s) 27257965 read pairs processed; of these: 0 ( 0.00%) short read pairs filtered out after trimming by size control 0 ( 0.00%) empty read pairs filtered out after trimming by size control 27257965 (100.00%) read pairs available; of these: 1206 ( 0.00%) trimmed read pairs available after processing 27256759 (100.00%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 23 2 0.00% 24 1 0.00% 25 0 0.00% 26 0 0.00% 27 2 0.00% 28 2 0.00% 29 1 0.00% 30 3 0.00% 31 0 0.00% 32 0 0.00% 33 0 0.00% 34 0 0.00% 35 0 0.00% 36 0 0.00% 37 0 0.00% 38 0 0.00% 39 0 0.00% 40 0 0.00% 41 0 0.00% 42 0 0.00% 43 0 0.00% 44 0 0.00% 45 0 0.00% 46 0 0.00% 47 0 0.00% 48 0 0.00% 49 0 0.00% 50 0 0.00% 51 0 0.00% 52 0 0.00% 53 0 0.00% 54 0 0.00% 55 0 0.00% 56 0 0.00% 57 0 0.00% 58 0 0.00% 59 0 0.00% 60 1 0.00% 61 0 0.00% 62 1 0.00% 63 0 0.00% 64 1 0.00% 65 0 0.00% 66 0 0.00% 67 1 0.00% 68 0 0.00% 69 0 0.00% 70 0 0.00% 71 0 0.00% 72 0 0.00% 73 0 0.00% 74 3 0.00% 75 1 0.00% 76 0 0.00% 77 2 0.00% 78 0 0.00% 79 0 0.00% 80 1 0.00% 81 1 0.00% 82 0 0.00% 83 0 0.00% 84 0 0.00% 85 0 0.00% 86 0 0.00% 87 0 0.00% 88 0 0.00% 89 0 0.00% 90 2 0.00% 91 5 0.00% 92 1 0.00% 93 0 0.00% 94 1 0.00% 95 0 0.00% 96 0 0.00% 97 1 0.00% 98 1 0.00% 99 1 0.00% 100 15705 0.06% 101 16143 0.06% 102 16574 0.06% 103 16694 0.06% 104 17232 0.06% 105 17405 0.06% 106 17125 0.06% 107 17500 0.06% 108 17537 0.06% 109 17958 0.07% 110 18229 0.07% 111 18498 0.07% 112 18627 0.07% 113 19237 0.07% 114 19620 0.07% 115 20105 0.07% 116 19749 0.07% 117 20262 0.07% 118 20022 0.07% 119 20114 0.07% 120 20594 0.08% 121 21365 0.08% 122 22079 0.08% 123 22640 0.08% 124 22867 0.08% 125 23109 0.08% 126 22793 0.08% 127 22995 0.08% 128 23458 0.09% 129 24308 0.09% 130 25031 0.09% 131 25427 0.09% 132 25917 0.10% 133 26070 0.10% 134 25705 0.09% 135 27266 0.10% 136 24706 0.09% 137 29017 0.11% 138 30845 0.11% 139 33145 0.12% 140 37410 0.14% 141 47161 0.17% 142 58599 0.21% 143 123535 0.45% 144 34344 0.13% 145 70906 0.26% 146 218497 0.80% 147 27572 0.10% 148 27862 0.10% 149 27890 0.10% 150 25720481 94.36% 27257965 reads passed initial QC criterion=sequence-density sequence-density=0.15 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=31 prefix-density=0.15 prefix-fanout=2.0 sequence=CTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGG criterion=fanout-score sequence-density=0.06 sequence-density-rank=20 fanout-score=245.76 fanout-score-rank=1 prefix-density=0.55 prefix-fanout=26.4 sequence=AGCAGCAGCAGC criterion=sequence-density sequence-density=0.16 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=33 prefix-density=0.16 prefix-fanout=2.0 sequence=CTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGG criterion=fanout-score sequence-density=0.06 sequence-density-rank=21 fanout-score=239.60 fanout-score-rank=1 prefix-density=0.55 prefix-fanout=26.1 sequence=TCATCATCAACAATGGTGGCATTGACACTGAAGATGACTATCCCTACCTTGGTCGTGATGGTAGATGTGACACGTACAGGAAAAATGCCAAAGTTGTTTCAATCGATTCTTATGAAGATGTTCCTGAAAATGATGAGACGGCATTGAAAAAGGCAGTGGCAAATCAGCCAGTGAGTGTTGCAATTGAAGGTGGTGGC SRR21835921 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 13 18:11:57 Started mapping on | Feb 13 18:11:57 Finished on | Feb 13 18:14:44 Mapping speed, Million of reads per hour | 587.60 Number of input reads | 27257965 Average input read length | 297 UNIQUE READS: Uniquely mapped reads number | 25401189 Uniquely mapped reads % | 93.19% Average mapped length | 295.70 Number of splices: Total | 25314215 Number of splices: Annotated (sjdb) | 24803058 Number of splices: GT/AG | 24869951 Number of splices: GC/AG | 369815 Number of splices: AT/AC | 17267 Number of splices: Non-canonical | 57182 Mismatch rate per base, % | 0.30% Deletion rate per base | 0.01% Deletion average length | 2.71 Insertion rate per base | 0.01% Insertion average length | 2.09 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 580576 % of reads mapped to multiple loci | 2.13% Number of reads mapped to too many loci | 78563 % of reads mapped to too many loci | 0.29% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.31% % of reads unmapped: other | 0.08% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1276200 1276200 1276200 N_multimapping 580576 580576 580576 N_noFeature 817496 13287655 12750777 N_ambiguous 325335 71865 73696 UnstrandedReadsAssigned:24258358 PositiveStrandReadsAssigned:12041669 NegativeStrandReadsAssigned:12576716 Dataset is classified unstranded MeadianReadLen=150 20thPercentileLength=150 echo kmer=145 SRR21835921 Starting Kallisto paired end mapping to ensembl reference transcriptome [quant] fragment length distribution will be estimated from the data [index] k-mer length: 31 [index] number of targets: 52,400 [index] number of k-mers: 62,057,036 [index] number of equivalence classes: 130,681 [quant] running in paired-end mode [quant] will process pair 1: SRR21835921-trimmed-pair1.fastq SRR21835921-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 27,257,965 reads, 24,774,871 reads pseudoaligned [quant] estimated average fragment length: 289.158 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,276 rounds 52401 SRR21835921.ke.tsv 34699 SRR21835921.se.tsv 87100 total ==> SRR21835921.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1729.84 1208 28.3025 Potri.005G024800.1.v4.1 1035 746.842 257 13.9466 Potri.004G059700.1.v4.1 961 672.847 69 4.15621 Potri.007G009000.2.v4.1 1416 1127.84 0 0 Potri.003G141000.2.v4.1 2943 2654.84 1025.56 15.6562 Potri.016G087400.1.v4.1 270 64.6106 1122 703.807 Potri.015G069301.1.v4.1 564 279.478 0 0 Potri.010G195200.1.v4.1 1773 1484.84 150.831 4.11694 Potri.012G127500.1.v4.1 977 688.847 1898 111.67 ==> SRR21835921.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 1905 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 378 Potri.001G212900.v4.1 33 Potri.001G182400.v4.1 3 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 155 Potri.001G416900.v4.1 8 Potri.001G452600.v4.1 33 SRR21835921 completed mapping pipeline successfully