Starting /dee2/code/volunteer_pipeline.sh SRR13165347 current disk space = 1542265479168 free memory = 1600010352 SRR13165347 SRAfilesize e95493168cd37fad0bfedbeb23b9adbd SRR13165347.sra SRR13165347.sra file validated SRR13165347 is paired end SRR13165347 is conventional basespace SRR13165347 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR13165347_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 49 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.583 37.0 37.0 37.0 37.0 37.0 2 36.041 37.0 37.0 37.0 37.0 37.0 3 36.3675 37.0 37.0 37.0 37.0 37.0 4 36.4675 37.0 37.0 37.0 37.0 37.0 5 36.5585 37.0 37.0 37.0 37.0 37.0 6 36.4805 37.0 37.0 37.0 37.0 37.0 7 36.3745 37.0 37.0 37.0 37.0 37.0 8 36.4855 37.0 37.0 37.0 37.0 37.0 9 36.4935 37.0 37.0 37.0 37.0 37.0 10-14 36.544799999999995 37.0 37.0 37.0 37.0 37.0 15-19 36.4713 37.0 37.0 37.0 37.0 37.0 20-24 36.4449 37.0 37.0 37.0 37.0 37.0 25-29 36.4568 37.0 37.0 37.0 37.0 37.0 30-34 36.3782 37.0 37.0 37.0 37.0 37.0 35-39 36.3391 37.0 37.0 37.0 37.0 37.0 40-44 36.318799999999996 37.0 37.0 37.0 37.0 37.0 45-49 36.2328 37.0 37.0 37.0 37.0 37.0 50-54 36.2951 37.0 37.0 37.0 37.0 37.0 55-59 36.2005 37.0 37.0 37.0 37.0 37.0 60-64 36.2236 37.0 37.0 37.0 37.0 37.0 65-69 36.193 37.0 37.0 37.0 37.0 37.0 70-74 36.1912 37.0 37.0 37.0 37.0 37.0 75-79 36.1882 37.0 37.0 37.0 37.0 37.0 80-84 36.1202 37.0 37.0 37.0 37.0 37.0 85-89 36.183499999999995 37.0 37.0 37.0 37.0 37.0 90-94 36.0805 37.0 37.0 37.0 37.0 37.0 95-99 36.057900000000004 37.0 37.0 37.0 37.0 37.0 100-104 35.9716 37.0 37.0 37.0 37.0 37.0 105-109 36.0163 37.0 37.0 37.0 37.0 37.0 110-114 35.97089999999999 37.0 37.0 37.0 37.0 37.0 115-119 35.9891 37.0 37.0 37.0 37.0 37.0 120-124 35.823299999999996 37.0 37.0 37.0 37.0 37.0 125-129 35.86729999999999 37.0 37.0 37.0 37.0 37.0 130-134 35.779199999999996 37.0 37.0 37.0 37.0 37.0 135-139 35.6303 37.0 37.0 37.0 37.0 37.0 140-144 35.549800000000005 37.0 37.0 37.0 37.0 37.0 145-149 35.2656 37.0 37.0 37.0 34.6 37.0 150-151 35.10825 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 1.0 21 2.0 22 1.0 23 2.0 24 4.0 25 2.0 26 7.0 27 10.0 28 19.0 29 28.0 30 40.0 31 40.0 32 49.0 33 126.0 34 154.0 35 320.0 36 2792.0 37 403.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 57.225 11.5 5.1499999999999995 26.125 2 25.1386787695411 9.78315683308119 31.038830055471507 34.039334341906205 3 18.224999999999998 16.175 26.474999999999998 39.125 4 23.724999999999998 22.400000000000002 22.925 30.95 5 25.624999999999996 26.625 22.900000000000002 24.85 6 25.1 30.875000000000004 20.674999999999997 23.35 7 17.150000000000002 27.975 35.275 19.6 8 21.925 24.675 28.175 25.224999999999998 9 21.425 21.175 33.324999999999996 24.075 10-14 23.615 26.87 25.185000000000002 24.33 15-19 23.0 25.330000000000002 25.66 26.009999999999998 20-24 23.080000000000002 25.759999999999998 25.335 25.825 25-29 23.54 26.51 24.765 25.185000000000002 30-34 23.505000000000003 25.900000000000002 24.805 25.790000000000003 35-39 23.625 26.045 25.235000000000003 25.095 40-44 23.200000000000003 25.865 25.665 25.27 45-49 23.044999999999998 26.22 25.474999999999998 25.259999999999998 50-54 22.939999999999998 26.005 24.610000000000003 26.445 55-59 23.265 25.755 25.21 25.77 60-64 23.13 25.705 25.365 25.8 65-69 24.025 25.575 24.87 25.53 70-74 23.919999999999998 26.715 24.295 25.069999999999997 75-79 23.849999999999998 25.7 24.7 25.75 80-84 23.78 25.27 24.725 26.224999999999998 85-89 24.165 25.380000000000003 24.6 25.855 90-94 24.025 25.435000000000002 24.41 26.13 95-99 24.26 25.2 24.47 26.07 100-104 24.45 25.3 24.175 26.075 105-109 25.124999999999996 25.15 23.89 25.835 110-114 23.855 25.805 24.345 25.995 115-119 25.095 25.34 24.65 24.915000000000003 120-124 23.56 26.295 24.055 26.090000000000003 125-129 24.765 25.64 23.28 26.314999999999998 130-134 24.89 25.295 23.64 26.174999999999997 135-139 24.22 25.19 24.335 26.255 140-144 24.415 25.635 23.544999999999998 26.405 145-149 24.615000000000002 25.27 24.07 26.045 150-151 25.337500000000002 25.2875 24.0375 25.337500000000002 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.5 2 1.5 3 1.0 4 0.0 5 0.5 6 0.5 7 0.5 8 0.5 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 0.5 19 0.5 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.0 26 0.5 27 1.0 28 1.0 29 1.5 30 3.0 31 9.0 32 14.0 33 25.0 34 30.0 35 24.0 36 32.5 37 50.0 38 73.0 39 107.5 40 129.5 41 145.5 42 169.5 43 183.0 44 190.5 45 196.5 46 196.5 47 185.0 48 189.0 49 186.0 50 179.0 51 175.0 52 155.0 53 137.0 54 132.5 55 113.5 56 101.5 57 95.0 58 76.0 59 69.0 60 53.5 61 48.0 62 52.0 63 53.5 64 39.5 65 36.5 66 40.0 67 34.5 68 34.5 69 37.5 70 34.0 71 28.0 72 30.5 73 24.5 74 15.5 75 12.5 76 13.5 77 11.0 78 7.0 79 4.5 80 2.5 81 2.0 82 1.0 83 0.5 84 0.0 85 0.5 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 0.0 2 0.8500000000000001 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 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 71.825 #Duplication Level Percentage of deduplicated Percentage of total 1 73.82526975287156 53.025 2 17.855899756352244 25.650000000000002 3 5.325443786982249 11.475 4 2.018795683954055 5.800000000000001 5 0.6961364427427775 2.5 6 0.034806822137138885 0.15 7 0.06961364427427777 0.35000000000000003 8 0.10442046641141664 0.6 9 0.06961364427427777 0.44999999999999996 >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 GGCAAGACAGAAAATTTTAAGCCCTGATGGGGTGCAACAAAAATTGTCTT 9 0.22499999999999998 No Hit GGGCTTCCTTGATCTCATCACCACCATCCTCATTGGTGTCAGATGTCCAT 9 0.22499999999999998 No Hit AGCAGGGATAGCAGCTGAGATTTCTTTCAGGTCTTCGTTGCTCAGCTTTA 8 0.2 No Hit GTTACAAAAATGATAACTGAAGAGTAACATTACGATACACCAGAGCCAAA 8 0.2 No Hit TCTGCATGCATGGATGGATCCATCGATTTGCTCAAGTTGAGTTTCACTTG 8 0.2 No Hit GGCAAGTATACATAGTTAACCTGGCAAGTAGGCATGGTTAATCTGACAAT 7 0.17500000000000002 No Hit GCTGAATCTTTACTTGGGATGCAATACAACTTTCTGCCAACTTTCGTAGT 7 0.17500000000000002 No Hit CTTCTCTTCAAACTCAGGAGTATAACCCACTTCATCATTGTCCACAAAAG 6 0.15 No Hit GTAGGGGTTGATCCGTCCATGAGCACGGTAGGTCCGACGCCGCTGTTTCT 5 0.125 No Hit GCACTGTCACTGTTCCAAGTTTCTTCAACCCGTGGGCGAAAGTACCAGCC 5 0.125 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGCCATAATCTCGTTT 5 0.125 TruSeq Adapter, Index 20 (97% over 38bp) CTCGCTGTGGAGCTGCGCGAAGCAGTCGCTGCTGTGGAGGTCGGTGTCGA 5 0.125 No Hit GCCCCAGTGAACCCTTCCAATAAACTGCCAGGGTGTTTCTGTGCTGGAGC 5 0.125 No Hit GTCACAAATGTTACGTTTGAAAAGCCTCAAGCTGCGATCATCAAAATACA 5 0.125 No Hit GTCTGGACGAACTTGGTGAGATTAAGCCTGACGCTCTGCTTGTCAAGGTA 5 0.125 No Hit CTGCGAAACGGCTCTGGAAAAAGCCCTCAAATGATGGCTCCCTCTTGGTC 5 0.125 No Hit GGTTGTTTTCTTTGTCACCTTGTCGCGGTAGAGCTGCCAGCATCTTCCAG 5 0.125 No Hit GCCAGGGAACCTCAGGCAGCAAGTAACACCACTCATGGTAGCAGAGATAA 5 0.125 No Hit GCCTCCAAAAGGAAAGTTTCTGGATTACTTGAAGCTTCTGCAAGCTCGGC 5 0.125 No Hit GGTTGCAGCAGTACATAGGAGGTAAAACAAAAGGGGCGGCGACTCAATGT 5 0.125 No Hit GCTCAAATCTTGGGTGACCGATCCACTTCTTCAGGTTGTCTTTTGAACCA 5 0.125 No Hit CCTGGCTGTCCTGCCGTTTGGCATCCTGTAGTACCAAGGTACACCTGAGT 5 0.125 No Hit GGCATAAGAAAACAGTTCATCATAAGCAGAATAGGCTTCATCATCAAACC 5 0.125 No Hit GTTCTTTTCATGACTGACTCTTCACGTCCATCAGGCAATGTCATTGTCAA 5 0.125 No Hit GCCTACTGCGTAGCTAGTGGGGGAGGCGAGCAGATCAGGCGCGCAGAAGG 5 0.125 No Hit GGCATTCCCTTCGTCTGCCTCTTGTCATGCCAGTAATCATGTATCAATTC 5 0.125 No Hit CGATCACATGCGCGTGCACACACCAACCGAACAAATACAAGAAAAATGAA 5 0.125 No Hit CCCACGCCTAACCATCGATTGCATATTATAGAATTATACAAAGTAGTAAT 5 0.125 No Hit >>END_MODULE >>Adapter Content fail #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 0.0125 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.037500000000000006 0.0 0.0 0.0 0.0 34-35 0.05 0.0 0.0 0.0 0.0 36-37 0.0625 0.0 0.0 0.0 0.0 38-39 0.125 0.0 0.0 0.0 0.0 40-41 0.175 0.0 0.0 0.0 0.0 42-43 0.175 0.0 0.0 0.0 0.0 44-45 0.175 0.0 0.0 0.0 0.0 46-47 0.2 0.0 0.0 0.0 0.0 48-49 0.2 0.0 0.0 0.0 0.0 50-51 0.2375 0.0 0.0 0.0 0.0 52-53 0.2625 0.0 0.0 0.0 0.0 54-55 0.275 0.0 0.0 0.0 0.0 56-57 0.275 0.0 0.0 0.0 0.0 58-59 0.275 0.0 0.0 0.0 0.0 60-61 0.275 0.0 0.0 0.0 0.0 62-63 0.35 0.0 0.0 0.0 0.0 64-65 0.4125 0.0 0.0 0.0 0.0 66-67 0.4625 0.0 0.0 0.0 0.0 68-69 0.5375000000000001 0.0 0.0 0.0 0.0 70-71 0.625 0.0 0.0 0.0 0.0 72-73 0.6875 0.0 0.0 0.0 0.0 74-75 0.8 0.0 0.0 0.0 0.0 76-77 0.8125 0.0 0.0 0.0 0.0 78-79 0.95 0.0 0.0 0.0 0.0 80-81 1.075 0.0 0.0 0.0 0.0 82-83 1.1875 0.0 0.0 0.0 0.0 84-85 1.4 0.0 0.0 0.0 0.0 86-87 1.5875 0.0 0.0 0.0 0.0 88-89 1.7375 0.0 0.0 0.0 0.0 90-91 1.8375 0.0 0.0 0.0 0.0 92-93 2.0875000000000004 0.0 0.0 0.0 0.0 94-95 2.25 0.0 0.0 0.0 0.0 96-97 2.65 0.0 0.0 0.0 0.0 98-99 3.0250000000000004 0.0 0.0 0.0 0.0 100-101 3.4000000000000004 0.0 0.0 0.0 0.0 102-103 3.6375 0.0 0.0 0.0 0.0 104-105 4.1375 0.0 0.0 0.0 0.0 106-107 4.574999999999999 0.0 0.0 0.0 0.0 108-109 5.1375 0.0 0.0 0.0 0.0 110-111 5.925 0.0 0.0 0.0 0.0 112-113 6.3125 0.0 0.0 0.0 0.0 114-115 6.8625 0.0 0.0 0.0 0.0 116-117 7.7125 0.0 0.0 0.0 0.0 118-119 8.5 0.0 0.0 0.0 0.0 120-121 9.075 0.0 0.0 0.0 0.0 122-123 9.775 0.0 0.0 0.0 0.0 124-125 10.35 0.0 0.0 0.0 0.0 126-127 11.05 0.0 0.0 0.0 0.0 128-129 11.912500000000001 0.0 0.0 0.0 0.0 130-131 12.524999999999999 0.0 0.0 0.0 0.0 132-133 13.0 0.0 0.0 0.0 0.0 134-135 13.65 0.0 0.0 0.0 0.0 136-137 14.3125 0.0 0.0 0.0 0.0 138-139 14.8625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GACACCA 10 0.006830828 145.0 1 >>END_MODULE SRR13165347 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR13165347_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 51 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.9175 37.0 37.0 37.0 37.0 37.0 2 35.923 37.0 37.0 37.0 37.0 37.0 3 35.961 37.0 37.0 37.0 37.0 37.0 4 35.9965 37.0 37.0 37.0 37.0 37.0 5 36.0355 37.0 37.0 37.0 37.0 37.0 6 36.08 37.0 37.0 37.0 37.0 37.0 7 36.081 37.0 37.0 37.0 37.0 37.0 8 36.087 37.0 37.0 37.0 37.0 37.0 9 36.137 37.0 37.0 37.0 37.0 37.0 10-14 36.0992 37.0 37.0 37.0 37.0 37.0 15-19 36.0105 37.0 37.0 37.0 37.0 37.0 20-24 36.078050000000005 37.0 37.0 37.0 37.0 37.0 25-29 35.980149999999995 37.0 37.0 37.0 37.0 37.0 30-34 35.92295 37.0 37.0 37.0 37.0 37.0 35-39 35.925349999999995 37.0 37.0 37.0 37.0 37.0 40-44 35.86905 37.0 37.0 37.0 37.0 37.0 45-49 35.961200000000005 37.0 37.0 37.0 37.0 37.0 50-54 35.85175 37.0 37.0 37.0 37.0 37.0 55-59 35.862350000000006 37.0 37.0 37.0 37.0 37.0 60-64 35.80575 37.0 37.0 37.0 37.0 37.0 65-69 35.7539 37.0 37.0 37.0 37.0 37.0 70-74 35.66755 37.0 37.0 37.0 37.0 37.0 75-79 35.73415 37.0 37.0 37.0 37.0 37.0 80-84 35.71489999999999 37.0 37.0 37.0 37.0 37.0 85-89 35.64065 37.0 37.0 37.0 37.0 37.0 90-94 35.64325 37.0 37.0 37.0 37.0 37.0 95-99 35.650850000000005 37.0 37.0 37.0 37.0 37.0 100-104 35.52695 37.0 37.0 37.0 37.0 37.0 105-109 35.56875 37.0 37.0 37.0 37.0 37.0 110-114 35.47775 37.0 37.0 37.0 37.0 37.0 115-119 35.36515 37.0 37.0 37.0 37.0 37.0 120-124 35.33725 37.0 37.0 37.0 37.0 37.0 125-129 35.307100000000005 37.0 37.0 37.0 37.0 37.0 130-134 35.16475 37.0 37.0 37.0 29.8 37.0 135-139 35.1425 37.0 37.0 37.0 32.2 37.0 140-144 34.95815 37.0 37.0 37.0 25.0 37.0 145-149 34.724 37.0 37.0 37.0 25.0 37.0 150-151 34.597750000000005 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 2.0 13 1.0 14 3.0 15 2.0 16 5.0 17 0.0 18 1.0 19 2.0 20 5.0 21 5.0 22 7.0 23 11.0 24 12.0 25 12.0 26 15.0 27 9.0 28 14.0 29 25.0 30 40.0 31 48.0 32 78.0 33 124.0 34 228.0 35 596.0 36 2546.0 37 209.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 51.432880844645545 21.669180492709906 6.510809451985923 20.38712921065862 2 31.5 22.575 23.525 22.400000000000002 3 23.9 26.075 27.975 22.05 4 28.275 30.025000000000002 19.400000000000002 22.3 5 28.749999999999996 33.324999999999996 17.5 20.424999999999997 6 24.725 35.375 17.9 22.0 7 24.9 19.900000000000002 33.1 22.1 8 24.3 23.3 22.15 30.25 9 22.325 23.849999999999998 26.875 26.950000000000003 10-14 26.834999999999997 25.355 22.39 25.419999999999998 15-19 27.029999999999998 24.740000000000002 23.505000000000003 24.725 20-24 26.516325816290813 24.72123606180309 24.201210060503026 24.56122806140307 25-29 26.25156289072268 24.72118029507377 24.14603650912728 24.88122030507627 30-34 26.949042356353452 24.078611791768765 24.368655298294744 24.60369055358304 35-39 26.63633181659083 24.846242312115603 23.71618580929046 24.8012400620031 40-44 25.718857828674302 24.90373556033405 24.333650047507128 25.04375656348452 45-49 26.21762176217622 25.272527252725276 24.132413241324134 24.377437743774376 50-54 25.83129156457823 24.591229561478073 24.496224811240563 25.081254062703135 55-59 27.24181045261315 24.82620655163791 24.17604401100275 23.755938984746187 60-64 26.536326816340818 25.02125106255313 23.941197059852993 24.501225061253063 65-69 26.82 25.224999999999998 24.04 23.915 70-74 26.851712928232057 24.391097774443608 24.256064016004 24.50112528132033 75-79 27.254088113216984 24.873731059658947 23.78356753513027 24.0886132919938 80-84 26.085 25.28 24.805 23.830000000000002 85-89 27.47186796699175 24.48112028007002 24.391097774443608 23.655913978494624 90-94 27.336366818340917 24.636231811590577 24.24621231061553 23.781189059452974 95-99 27.35136756837842 25.99629981499075 23.491174558727938 23.161158057902895 100-104 27.171792948237062 24.981245311327832 24.526131532883223 23.320830207551886 105-109 27.151787946986744 24.751187796949235 24.74118529632408 23.355838959739934 110-114 27.43637181859093 25.47127356367818 24.14620731036552 22.94614730736537 115-119 27.851962990747687 25.47136784196049 24.15603900975244 22.520630157539383 120-124 28.20205051262816 25.081270317579396 23.570892723180794 23.145786446611652 125-129 28.500700140028005 24.889977995599118 23.63972794558912 22.969593918783758 130-134 29.845445906067127 25.003751312959537 23.288150852798477 21.862651928174863 135-139 29.67890367110133 24.917475242572774 23.3370011003301 22.0666199859958 140-144 30.351517575878795 25.056252812640633 23.53117655882794 21.061053052652632 145-149 30.599179753926176 24.97249174752426 23.67710313093928 20.75122536761028 150-151 30.952976488244122 24.68734367183592 23.461730865432717 20.897948974487242 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.5 5 0.5 6 0.0 7 0.0 8 0.0 9 1.5 10 1.5 11 1.0 12 1.5 13 1.0 14 0.5 15 0.5 16 0.5 17 0.0 18 0.5 19 1.0 20 1.0 21 0.5 22 0.0 23 0.5 24 0.5 25 0.5 26 1.0 27 1.0 28 1.0 29 1.5 30 4.5 31 5.5 32 7.0 33 14.0 34 16.5 35 20.5 36 34.5 37 50.5 38 63.0 39 80.0 40 103.5 41 137.0 42 147.0 43 160.5 44 191.0 45 191.5 46 188.0 47 177.0 48 161.5 49 168.5 50 179.5 51 172.0 52 152.5 53 131.5 54 117.0 55 102.5 56 95.5 57 84.5 58 81.0 59 79.0 60 71.5 61 76.5 62 71.5 63 56.5 64 56.5 65 58.5 66 57.0 67 60.5 68 49.0 69 46.5 70 53.5 71 43.5 72 28.0 73 19.5 74 18.0 75 17.0 76 14.5 77 12.5 78 7.0 79 4.5 80 5.0 81 4.0 82 1.5 83 1.0 84 1.0 85 0.5 86 1.0 87 0.5 88 1.0 89 1.0 90 0.0 91 1.0 92 1.5 93 1.5 94 3.0 95 2.5 96 1.0 97 1.0 98 2.0 99 3.0 100 6.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.5499999999999999 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 0.005 25-29 0.025 30-34 0.015 35-39 0.005 40-44 0.015 45-49 0.01 50-54 0.005 55-59 0.025 60-64 0.005 65-69 0.0 70-74 0.025 75-79 0.015 80-84 0.0 85-89 0.025 90-94 0.005 95-99 0.005 100-104 0.025 105-109 0.025 110-114 0.005 115-119 0.025 120-124 0.025 125-129 0.02 130-134 0.034999999999999996 135-139 0.03 140-144 0.005 145-149 0.03 150-151 0.05 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 73.075 #Duplication Level Percentage of deduplicated Percentage of total 1 75.2651385562778 55.00000000000001 2 17.105713308244955 25.0 3 4.823811152925077 10.575 4 1.9842627437564146 5.800000000000001 5 0.5131713992473486 1.875 6 0.10263427984946973 0.44999999999999996 7 0.0 0.0 8 0.10263427984946973 0.6 9 0.06842285323297981 0.44999999999999996 >10 0.034211426616489904 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 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 10 0.25 No Hit GGTCTAAGTCGGTCCATCTTGTTGTCATCTGGACCGTTCTGTTTGAGCAA 9 0.22499999999999998 No Hit GCTCCGACTCACCCCATAAGGCTTGGGCTTGCACTTAACTTCTCTGTGTT 9 0.22499999999999998 No Hit GGAGCCGAGAACGGAGGCTGCAAGTGCGGGGACAACTGCACCTGCAACCC 8 0.2 No Hit GCCCACTTGGTCGTGGTTTCTTTGCTGGCAGGGCAGCCGTAGAGAGCATA 8 0.2 No Hit GAGCGAGCACCCCGGCGCCTTCGAGTGATCGGCGACGGCCGGCTTCGTCT 8 0.2 No Hit GAGCGATTTTAGCAGTAAAATGAACCATCTCCTGTTAGCAATCTTGCAGA 6 0.15 No Hit TATGCCTGTGTGACAGGCATCTCGCCTTGTAGCGGTTAACTATGAATACT 6 0.15 No Hit GGGGGCTCCATTTGATGAAACTGATCAAGACATCACCCATCAGATTGTTG 6 0.15 No Hit GCAAGCCCGCGCTCCGCATGGCGATGCAGACCAGGGAGCAGCACATCCGG 5 0.125 No Hit GCTAAGAATGGCATGGCTGGTGCATGATGGGAGCAAACCCAACCAGAAGC 5 0.125 No Hit GCAAGGCCGTCGGCGAGCTCGACAGCACCGGCGCGTTCAGCATCCCCCTC 5 0.125 No Hit GTTCAAGGACCCGGCCAAGGACATGGACGTGAACTACATGGAGTACAACG 5 0.125 No Hit GGAGTACTTCCTCCGTCTCATGTTAAATGTCGAAATATTACATGTATCTA 5 0.125 No Hit GAGTACCCTGACAGAATGATGTTGACCTTCTCCGTTTTCCCATCACCAAA 5 0.125 No Hit GAAACATTGGGTGCCACTCAGCTGTTGAAGAAGTTGGCCTTTACAACCAC 5 0.125 No Hit AATTCTGCTTTATATTCTGAAGTATAAGCAGTACCATCAGAAATCTCCTC 5 0.125 No Hit CTCTCCTGCCAATCCCCTCATCGCCTCCGCCGCCGAATCCGAGACCCCGA 5 0.125 No Hit GGAGGAGGAGAGGGGGGAGGAGGTCGAGGAGGACGAAGAGGAGCCTAGGG 5 0.125 No Hit GTCTAATCCGATTCAAACGCATCGCTTCCTCGTGTCCAAACTAAGCCCGA 5 0.125 No Hit ACGGGAGACAGCGTTTGCCCTGAGGAAGATGCCACTGGGCAAGGCTAAAA 5 0.125 No Hit GGGGACGCCGTGCCTCGTCGCTGGAGTAATTTGTTTGCTATTGTATTCAT 5 0.125 No Hit GTTGTGCACACCTGACGTTTGCTCAAAACTTGGTGGAAGAGTCATAGCTT 5 0.125 No Hit GGAAACGGAGCAGCCGATGAGGATAAGCTGCAAGGCGAACAGGAGCTTGA 5 0.125 No Hit >>END_MODULE >>Adapter Content fail #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 0.0125 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.037500000000000006 0.0 0.0 0.0 0.0 34-35 0.05 0.0 0.0 0.0 0.0 36-37 0.0625 0.0 0.0 0.0 0.0 38-39 0.125 0.0 0.0 0.0 0.0 40-41 0.175 0.0 0.0 0.0 0.0 42-43 0.175 0.0 0.0 0.0 0.0 44-45 0.175 0.0 0.0 0.0 0.0 46-47 0.2 0.0 0.0 0.0 0.0 48-49 0.2 0.0 0.0 0.0 0.0 50-51 0.2375 0.0 0.0 0.0 0.0 52-53 0.2625 0.0 0.0 0.0 0.0 54-55 0.275 0.0 0.0 0.0 0.0 56-57 0.275 0.0 0.0 0.0 0.0 58-59 0.275 0.0 0.0 0.0 0.0 60-61 0.275 0.0 0.0 0.0 0.0 62-63 0.35 0.0 0.0 0.0 0.0 64-65 0.4125 0.0 0.0 0.0 0.0 66-67 0.4625 0.0 0.0 0.0 0.0 68-69 0.5375000000000001 0.0 0.0 0.0 0.0 70-71 0.625 0.0 0.0 0.0 0.0 72-73 0.6875 0.0 0.0 0.0 0.0 74-75 0.8 0.0 0.0 0.0 0.0 76-77 0.8125 0.0 0.0 0.0 0.0 78-79 0.9750000000000001 0.0 0.0 0.0 0.0 80-81 1.1 0.0 0.0 0.0 0.0 82-83 1.2125 0.0 0.0 0.0 0.0 84-85 1.425 0.0 0.0 0.0 0.0 86-87 1.6125 0.0 0.0 0.0 0.0 88-89 1.7625 0.0 0.0 0.0 0.0 90-91 1.8624999999999998 0.0 0.0 0.0 0.0 92-93 2.1125 0.0 0.0 0.0 0.0 94-95 2.2750000000000004 0.0 0.0 0.0 0.0 96-97 2.6624999999999996 0.0 0.0 0.0 0.0 98-99 3.0250000000000004 0.0 0.0 0.0 0.0 100-101 3.3875 0.0 0.0 0.0 0.0 102-103 3.6125 0.0 0.0 0.0 0.0 104-105 4.125 0.0 0.0 0.0 0.0 106-107 4.574999999999999 0.0 0.0 0.0 0.0 108-109 5.1375 0.0 0.0 0.0 0.0 110-111 5.9375 0.0 0.0 0.0 0.0 112-113 6.35 0.0 0.0 0.0 0.0 114-115 6.9375 0.0 0.0 0.0 0.0 116-117 7.7875 0.0 0.0 0.0 0.0 118-119 8.575 0.0 0.0 0.0 0.0 120-121 9.1375 0.0 0.0 0.0 0.0 122-123 9.825 0.0 0.0 0.0 0.0 124-125 10.425 0.0 0.0 0.0 0.0 126-127 11.1375 0.0 0.0 0.0 0.0 128-129 12.0125 0.0 0.0 0.0 0.0 130-131 12.6375 0.0 0.0 0.0 0.0 132-133 13.1125 0.0 0.0 0.0 0.0 134-135 13.7375 0.0 0.0 0.0 0.0 136-137 14.3875 0.0 0.0 0.0 0.0 138-139 14.9375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AGGACGT 10 0.006830828 145.0 1 GGGAGAG 10 0.006830828 145.0 145 >>END_MODULE Read 1584497 spots for SRR13165347.sra Written 1584497 spots for SRR13165347.sra Read 1584497 spots for SRR13165347.sra Written 1584497 spots for SRR13165347.sra Read 1584497 spots for SRR13165347.sra Written 1584497 spots for SRR13165347.sra Read 1584497 spots for SRR13165347.sra Written 1584497 spots for SRR13165347.sra Read 1584497 spots for SRR13165347.sra Written 1584497 spots for SRR13165347.sra Read 1584497 spots for SRR13165347.sra Written 1584497 spots for SRR13165347.sra Read 1584497 spots for SRR13165347.sra Written 1584497 spots for SRR13165347.sra Read 1584497 spots for SRR13165347.sra Written 1584497 spots for SRR13165347.sra Read 1584497 spots for SRR13165347.sra Written 1584497 spots for SRR13165347.sra Read 1584497 spots for SRR13165347.sra Written 1584497 spots for SRR13165347.sra Read 1584516 spots for SRR13165347.sra Written 1584516 spots for SRR13165347.sra Read 1584497 spots for SRR13165347.sra Written 1584497 spots for SRR13165347.sra Read 1584497 spots for SRR13165347.sra Written 1584497 spots for SRR13165347.sra Read 1584497 spots for SRR13165347.sra Written 1584497 spots for SRR13165347.sra Read 1584497 spots for SRR13165347.sra Written 1584497 spots for SRR13165347.sra Read 1584497 spots for SRR13165347.sra Written 1584497 spots for SRR13165347.sra Read 1584497 spots for SRR13165347.sra Written 1584497 spots for SRR13165347.sra Read 1584497 spots for SRR13165347.sra Written 1584497 spots for SRR13165347.sra Read 1584497 spots for SRR13165347.sra Written 1584497 spots for SRR13165347.sra Read 1584497 spots for SRR13165347.sra Written 1584497 spots for SRR13165347.sra SRR ids: ['SRR13165347.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_5sflxk97 SRR13165347.sra spots: 31689959 blocks: [[1, 1584497], [1584498, 3168994], [3168995, 4753491], [4753492, 6337988], [6337989, 7922485], [7922486, 9506982], [9506983, 11091479], [11091480, 12675976], [12675977, 14260473], [14260474, 15844970], [15844971, 17429467], [17429468, 19013964], [19013965, 20598461], [20598462, 22182958], [22182959, 23767455], [23767456, 25351952], [25351953, 26936449], [26936450, 28520946], [28520947, 30105443], [30105444, 31689959]] SRR13165347 file size 10747934 SRR13165347 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 SRR13165347 SRR13165347_1.fastq SRR13165347_2.fastq Input file: SRR13165347_1.fastq Paired file: SRR13165347_2.fastq trimmed: SRR13165347-trimmed-pair1.fastq, SRR13165347-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 15:43:23 2024 >> started Sat Dec 7 15:44:10 2024 >> done (47.021s) 31689959 read pairs processed; of these: 917 ( 0.00%) short read pairs filtered out after trimming by size control 87344 ( 0.28%) empty read pairs filtered out after trimming by size control 31601698 (99.72%) read pairs available; of these: 5992547 (18.96%) trimmed read pairs available after processing 25609151 (81.04%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 113 0.00% 19 141 0.00% 20 186 0.00% 21 333 0.00% 22 462 0.00% 23 654 0.00% 24 821 0.00% 25 1138 0.00% 26 1310 0.00% 27 1698 0.01% 28 1981 0.01% 29 2192 0.01% 30 2531 0.01% 31 2680 0.01% 32 2935 0.01% 33 3071 0.01% 34 3180 0.01% 35 3268 0.01% 36 3500 0.01% 37 3506 0.01% 38 3734 0.01% 39 3809 0.01% 40 3701 0.01% 41 3668 0.01% 42 3557 0.01% 43 3655 0.01% 44 3559 0.01% 45 3509 0.01% 46 3452 0.01% 47 3513 0.01% 48 3512 0.01% 49 3649 0.01% 50 3632 0.01% 51 3605 0.01% 52 3438 0.01% 53 3394 0.01% 54 3304 0.01% 55 3505 0.01% 56 3459 0.01% 57 3659 0.01% 58 3827 0.01% 59 4122 0.01% 60 4361 0.01% 61 4502 0.01% 62 4366 0.01% 63 4720 0.01% 64 4974 0.02% 65 5229 0.02% 66 5494 0.02% 67 5840 0.02% 68 6392 0.02% 69 6929 0.02% 70 7618 0.02% 71 7930 0.03% 72 8928 0.03% 73 9584 0.03% 74 10481 0.03% 75 11198 0.04% 76 12146 0.04% 77 12972 0.04% 78 14315 0.05% 79 15629 0.05% 80 16754 0.05% 81 18565 0.06% 82 19756 0.06% 83 21760 0.07% 84 23628 0.07% 85 25400 0.08% 86 27868 0.09% 87 29685 0.09% 88 31124 0.10% 89 32889 0.10% 90 34173 0.11% 91 36887 0.12% 92 39385 0.12% 93 41982 0.13% 94 44896 0.14% 95 47799 0.15% 96 50150 0.16% 97 52137 0.16% 98 54558 0.17% 99 56463 0.18% 100 58140 0.18% 101 59317 0.19% 102 61092 0.19% 103 63872 0.20% 104 66293 0.21% 105 68049 0.22% 106 71313 0.23% 107 72284 0.23% 108 74499 0.24% 109 76399 0.24% 110 77610 0.25% 111 79370 0.25% 112 81016 0.26% 113 82042 0.26% 114 84382 0.27% 115 87621 0.28% 116 89076 0.28% 117 91111 0.29% 118 92440 0.29% 119 93446 0.30% 120 95623 0.30% 121 95751 0.30% 122 96588 0.31% 123 98479 0.31% 124 101174 0.32% 125 102123 0.32% 126 103298 0.33% 127 103824 0.33% 128 106126 0.34% 129 108648 0.34% 130 107005 0.34% 131 108108 0.34% 132 110147 0.35% 133 111801 0.35% 134 111927 0.35% 135 113412 0.36% 136 114110 0.36% 137 114880 0.36% 138 117212 0.37% 139 118174 0.37% 140 117831 0.37% 141 118720 0.38% 142 120481 0.38% 143 120262 0.38% 144 122421 0.39% 145 122223 0.39% 146 121992 0.39% 147 123334 0.39% 148 122566 0.39% 149 124561 0.39% 150 125944 0.40% 151 25609151 81.04% 31601698 reads passed initial QC criterion=sequence-density sequence-density=0.13 sequence-density-rank=1 fanout-score=9.91 fanout-score-rank=23 prefix-density=0.09 prefix-fanout=9.9 sequence=GGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGCCATAATCTCGTATGCCGTCTTCTGCTTGAAAA criterion=fanout-score sequence-density=0.10 sequence-density-rank=2 fanout-score=342.67 fanout-score-rank=1 prefix-density=1.04 prefix-fanout=31.9 sequence=CTTCTTCTTGTC criterion=sequence-density sequence-density=0.17 sequence-density-rank=1 fanout-score=2.91 fanout-score-rank=34 prefix-density=0.20 prefix-fanout=2.5 sequence=CGGTTCCGGTTC criterion=fanout-score sequence-density=0.01 sequence-density-rank=34 fanout-score=1076.51 fanout-score-rank=1 prefix-density=0.78 prefix-fanout=19.7 sequence=GCCGCCGCCCCTCGTCCTCTGTGTTCCTTCTCCGAGTTTCAGCCATGGGTAAGGAGAAGACTCACATCAACATCGTGGTCATTGGCCATGTCGACTCTGGCAAGTCGACCACCACTGGCCACCTGATCTACAAGCTTGGAGGTATTGACAAGCGTGTGATCGAGAGGTTCGAGAAGGAGGCTGCTGAGATGAACAAGAGGTCATTCAAGTACGCGTGGGTGCTTGACAAGCTGAAGGCTGAGCGTGAGAGAGGTATCACCATCGATATTGCCTTGTGGAAGTTCGAGACCACCAAGTACTACTGCACCGTCATTGATGCCCCTGGACACCGTGACTTCATCAAGAACATGATTACCGGTACCTCCCAGGCTGA SRR13165347 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 15:46:01 Started mapping on | Dec 07 15:46:01 Finished on | Dec 07 15:49:01 Mapping speed, Million of reads per hour | 632.03 Number of input reads | 31601698 Average input read length | 290 UNIQUE READS: Uniquely mapped reads number | 29179935 Uniquely mapped reads % | 92.34% Average mapped length | 290.07 Number of splices: Total | 27424764 Number of splices: Annotated (sjdb) | 25716144 Number of splices: GT/AG | 27069349 Number of splices: GC/AG | 292017 Number of splices: AT/AC | 19130 Number of splices: Non-canonical | 44268 Mismatch rate per base, % | 0.24% Deletion rate per base | 0.01% Deletion average length | 2.50 Insertion rate per base | 0.01% Insertion average length | 2.26 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 415310 % of reads mapped to multiple loci | 1.31% Number of reads mapped to too many loci | 133665 % of reads mapped to too many loci | 0.42% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.91% % of reads unmapped: other | 2.01% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 2006822 2006822 2006822 N_multimapping 415310 415310 415310 N_noFeature 831407 28433508 1050253 N_ambiguous 603344 4513 76212 UnstrandedReadsAssigned:27745184 PositiveStrandReadsAssigned:741914 NegativeStrandReadsAssigned:28053470 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR13165347 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: SRR13165347-trimmed-pair1.fastq SRR13165347-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 31,601,698 reads, 28,584,491 reads pseudoaligned [quant] estimated average fragment length: 239.281 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,277 rounds 52973 SRR13165347.ke.tsv 35125 SRR13165347.se.tsv 88098 total ==> SRR13165347.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 698.153 0 0 PNS24247 1044 805.719 39.2125 2.49336 PNS24249 1928 1689.72 220.943 6.69901 PNS24246 1044 805.719 39.2125 2.49336 PNS24248 1044 805.719 39.2125 2.49336 PNS24244 1471 1232.72 159.419 6.62555 PNS24243 293 109.6 0 0 KQK14069 1603 1364.72 3 0.112622 KQK14071 474 254.34 0 0 ==> SRR13165347.se.tsv <== BRADI_1g14170v3 3 BRADI_1g53295v3 30 BRADI_1g59795v3 624 BRADI_1g07683v3 0 BRADI_1g00485v3 376 BRADI_1g20270v3 7349 BRADI_1g74790v3 24 BRADI_1g09890v3 8 BRADI_1g77505v3 364 BRADI_1g48960v3 0 SRR13165347 completed mapping pipeline successfully