Starting /dee2/code/volunteer_pipeline.sh SRR12671347 current disk space = 3052157792256 free memory = 1459753568 SRR12671347 SRAfilesize dfe5242385c2cb9c92753a47e2dd3a30 SRR12671347.sra SRR12671347.sra file validated SRR12671347 is paired end SRR12671347 is conventional basespace SRR12671347 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12671347_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 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.633 37.0 37.0 37.0 37.0 37.0 2 36.38 37.0 37.0 37.0 37.0 37.0 3 36.595 37.0 37.0 37.0 37.0 37.0 4 36.6455 37.0 37.0 37.0 37.0 37.0 5 36.659 37.0 37.0 37.0 37.0 37.0 6 36.6815 37.0 37.0 37.0 37.0 37.0 7 36.594 37.0 37.0 37.0 37.0 37.0 8 36.5735 37.0 37.0 37.0 37.0 37.0 9 36.6435 37.0 37.0 37.0 37.0 37.0 10-14 36.596000000000004 37.0 37.0 37.0 37.0 37.0 15-19 36.5997 37.0 37.0 37.0 37.0 37.0 20-24 36.55970000000001 37.0 37.0 37.0 37.0 37.0 25-29 36.535 37.0 37.0 37.0 37.0 37.0 30-34 36.5411 37.0 37.0 37.0 37.0 37.0 35-39 36.529399999999995 37.0 37.0 37.0 37.0 37.0 40-44 36.49159999999999 37.0 37.0 37.0 37.0 37.0 45-49 36.475100000000005 37.0 37.0 37.0 37.0 37.0 50-54 36.46990000000001 37.0 37.0 37.0 37.0 37.0 55-59 36.4572 37.0 37.0 37.0 37.0 37.0 60-64 36.405300000000004 37.0 37.0 37.0 37.0 37.0 65-69 36.4172 37.0 37.0 37.0 37.0 37.0 70-74 36.377300000000005 37.0 37.0 37.0 37.0 37.0 75-79 36.3966 37.0 37.0 37.0 37.0 37.0 80-84 36.376400000000004 37.0 37.0 37.0 37.0 37.0 85-89 36.304500000000004 37.0 37.0 37.0 37.0 37.0 90-94 36.3542 37.0 37.0 37.0 37.0 37.0 95-99 36.2941 37.0 37.0 37.0 37.0 37.0 100-104 36.29110000000001 37.0 37.0 37.0 37.0 37.0 105-109 36.3237 37.0 37.0 37.0 37.0 37.0 110-114 36.17979999999999 37.0 37.0 37.0 37.0 37.0 115-119 36.2045 37.0 37.0 37.0 37.0 37.0 120-124 36.1793 37.0 37.0 37.0 37.0 37.0 125-129 36.105399999999996 37.0 37.0 37.0 37.0 37.0 130-134 36.0773 37.0 37.0 37.0 37.0 37.0 135-139 36.0073 37.0 37.0 37.0 37.0 37.0 140-144 35.876099999999994 37.0 37.0 37.0 37.0 37.0 145-149 35.774899999999995 37.0 37.0 37.0 37.0 37.0 150-151 35.512249999999995 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 1.0 21 1.0 22 0.0 23 1.0 24 1.0 25 4.0 26 5.0 27 8.0 28 7.0 29 16.0 30 21.0 31 23.0 32 48.0 33 69.0 34 106.0 35 262.0 36 2924.0 37 503.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 47.825 12.225 5.35 34.599999999999994 2 19.939879759519037 13.126252505010019 35.49599198396793 31.437875751503007 3 17.625 17.825 27.675 36.875 4 22.875 24.75 23.875 28.499999999999996 5 24.25 31.974999999999998 22.85 20.925 6 20.674999999999997 34.65 24.224999999999998 20.45 7 14.799999999999999 27.05 41.375 16.775000000000002 8 15.475 26.400000000000002 33.225 24.9 9 16.55 24.0 35.099999999999994 24.349999999999998 10-14 19.035 29.59 28.565 22.81 15-19 19.855 27.575 28.310000000000002 24.26 20-24 19.75 28.439999999999998 28.349999999999998 23.46 25-29 19.79 28.37 27.855 23.985 30-34 20.380000000000003 28.16 27.185 24.275 35-39 19.865 28.225 27.884999999999998 24.025 40-44 20.345 28.64 27.735 23.28 45-49 20.605 28.749999999999996 27.060000000000002 23.585 50-54 19.6 28.215 28.185 24.0 55-59 20.615 28.78 27.425 23.18 60-64 20.285 28.799999999999997 27.32 23.595 65-69 20.055 28.449999999999996 27.450000000000003 24.044999999999998 70-74 20.41 28.384999999999998 26.96 24.245 75-79 19.384999999999998 28.560000000000002 27.845 24.21 80-84 20.57 28.04 27.384999999999998 24.005000000000003 85-89 20.525 27.97 27.12 24.385 90-94 20.330000000000002 28.625 27.415 23.630000000000003 95-99 20.380000000000003 28.015 27.275 24.33 100-104 20.555 27.400000000000002 28.305000000000003 23.74 105-109 20.995 28.610000000000003 27.115000000000002 23.28 110-114 20.51 28.13 27.694999999999997 23.665 115-119 20.66 28.115000000000002 27.650000000000002 23.575 120-124 20.935000000000002 28.705000000000002 26.915 23.445 125-129 20.46 27.76 27.625 24.154999999999998 130-134 20.745 28.29 26.82 24.145 135-139 21.11 28.349999999999998 26.8 23.74 140-144 21.62 27.339999999999996 26.83 24.21 145-149 20.93 27.805000000000003 26.615 24.65 150-151 23.05 27.200000000000003 26.1625 23.5875 >>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 0.5 9 0.5 10 0.0 11 0.0 12 0.5 13 0.5 14 0.0 15 1.0 16 1.0 17 0.5 18 1.0 19 0.5 20 1.5 21 2.5 22 1.5 23 0.5 24 2.0 25 3.0 26 7.5 27 11.5 28 9.5 29 12.0 30 19.0 31 29.5 32 39.5 33 43.0 34 46.5 35 63.5 36 83.0 37 108.0 38 137.5 39 159.5 40 182.0 41 202.0 42 215.5 43 228.0 44 250.5 45 264.0 46 252.5 47 228.0 48 221.5 49 217.5 50 195.0 51 156.5 52 125.0 53 117.0 54 92.5 55 64.0 56 61.5 57 49.0 58 26.5 59 16.0 60 12.0 61 11.5 62 9.0 63 8.0 64 4.5 65 1.0 66 0.5 67 0.5 68 0.0 69 0.0 70 0.0 71 0.5 72 0.5 73 0.0 74 0.5 75 0.5 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 0.2 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 84.625 #Duplication Level Percentage of deduplicated Percentage of total 1 85.52437223042836 72.375 2 11.905465288035451 20.150000000000002 3 1.742983751846381 4.425 4 0.5908419497784343 2.0 5 0.1772525849335303 0.75 6 0.059084194977843424 0.3 7 0.0 0.0 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 GCAGCTACTTGACTTTTCAACTCTGCTTCTTGGTTTGTCAAAGCTGCTTT 6 0.15 No Hit GTTATCAATATGTTACGCTCTGCTAATATGCGCTGAACATCATTCTTGCG 6 0.15 No Hit GAGTCATTCAAGAGCTTTGGATTTGAACTATCCAACTCTTCATTAGTCAT 5 0.125 No Hit GCCAAGGAGATACTATAAGTGCTTCTTTCGGGTCGGGGAGTGCCTGCCAT 5 0.125 No Hit GCCTTCTTTATTGCTTCATAGCCTCCTTCCTCCCTCATGGTCTTTGTGCT 5 0.125 No Hit CAGCTTAGAAACCACCGCGGAGACGAAGCACAAGGTGTAGAGTGGACTCC 5 0.125 No Hit GTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACC 5 0.125 No Hit CTCTAGCAACACTGGTCTCAAGAGTTGGAGGACCGCATATGATGACACCC 5 0.125 No Hit >>END_MODULE >>Adapter Content warn #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 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 0.0125 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.025 0.0 0.0 0.0 0.0 68-69 0.037500000000000006 0.0 0.0 0.0 0.0 70-71 0.0625 0.0 0.0 0.0 0.0 72-73 0.1 0.0 0.0 0.0 0.0 74-75 0.1375 0.0 0.0 0.0 0.0 76-77 0.15 0.0 0.0 0.0 0.0 78-79 0.1875 0.0 0.0 0.0 0.0 80-81 0.25 0.0 0.0 0.0 0.0 82-83 0.3 0.0 0.0 0.0 0.0 84-85 0.3625 0.0 0.0 0.0 0.0 86-87 0.45 0.0 0.0 0.0 0.0 88-89 0.5625 0.0 0.0 0.0 0.0 90-91 0.6 0.0 0.0 0.0 0.0 92-93 0.7375 0.0 0.0 0.0 0.0 94-95 0.9125 0.0 0.0 0.0 0.0 96-97 1.075 0.0 0.0 0.0 0.0 98-99 1.3 0.0 0.0 0.0 0.0 100-101 1.55 0.0 0.0 0.0 0.0 102-103 1.9125 0.0 0.0 0.0 0.0 104-105 2.1625 0.0 0.0 0.0 0.0 106-107 2.275 0.0 0.0 0.0 0.0 108-109 2.5 0.0 0.0 0.0 0.0 110-111 2.825 0.0 0.0 0.0 0.0 112-113 3.15 0.0 0.0 0.0 0.0 114-115 3.5 0.0 0.0 0.0 0.0 116-117 3.7750000000000004 0.0 0.0 0.0 0.0 118-119 4.0625 0.0 0.0 0.0 0.0 120-121 4.375 0.0 0.0 0.0 0.0 122-123 4.75 0.0 0.0 0.0 0.0 124-125 5.125 0.0 0.0 0.0 0.0 126-127 5.4125 0.0 0.0 0.0 0.0 128-129 5.725 0.0 0.0 0.0 0.0 130-131 6.225 0.0 0.0 0.0 0.0 132-133 6.699999999999999 0.0 0.0 0.0 0.0 134-135 7.2375 0.0 0.0 0.0 0.0 136-137 7.75 0.0 0.0 0.0 0.0 138-139 8.225 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AAAAAAA 70 7.343502E-4 14.5 50-54 >>END_MODULE SRR12671347 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12671347_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 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.2 37.0 37.0 37.0 37.0 37.0 2 36.143 37.0 37.0 37.0 37.0 37.0 3 36.025 37.0 37.0 37.0 37.0 37.0 4 36.333 37.0 37.0 37.0 37.0 37.0 5 36.3645 37.0 37.0 37.0 37.0 37.0 6 36.232 37.0 37.0 37.0 37.0 37.0 7 36.1925 37.0 37.0 37.0 37.0 37.0 8 36.2825 37.0 37.0 37.0 37.0 37.0 9 36.368 37.0 37.0 37.0 37.0 37.0 10-14 36.2362 37.0 37.0 37.0 37.0 37.0 15-19 36.2692 37.0 37.0 37.0 37.0 37.0 20-24 36.168400000000005 37.0 37.0 37.0 37.0 37.0 25-29 36.18620000000001 37.0 37.0 37.0 37.0 37.0 30-34 36.1257 37.0 37.0 37.0 37.0 37.0 35-39 36.0841 37.0 37.0 37.0 37.0 37.0 40-44 36.104 37.0 37.0 37.0 37.0 37.0 45-49 36.064499999999995 37.0 37.0 37.0 37.0 37.0 50-54 35.9869 37.0 37.0 37.0 37.0 37.0 55-59 36.021300000000004 37.0 37.0 37.0 37.0 37.0 60-64 35.973400000000005 37.0 37.0 37.0 37.0 37.0 65-69 36.009100000000004 37.0 37.0 37.0 37.0 37.0 70-74 36.015699999999995 37.0 37.0 37.0 37.0 37.0 75-79 35.978899999999996 37.0 37.0 37.0 37.0 37.0 80-84 35.898199999999996 37.0 37.0 37.0 37.0 37.0 85-89 35.920300000000005 37.0 37.0 37.0 37.0 37.0 90-94 35.9423 37.0 37.0 37.0 37.0 37.0 95-99 35.869299999999996 37.0 37.0 37.0 37.0 37.0 100-104 35.777100000000004 37.0 37.0 37.0 37.0 37.0 105-109 35.7804 37.0 37.0 37.0 37.0 37.0 110-114 35.713800000000006 37.0 37.0 37.0 37.0 37.0 115-119 35.7924 37.0 37.0 37.0 37.0 37.0 120-124 35.7419 37.0 37.0 37.0 37.0 37.0 125-129 35.62179999999999 37.0 37.0 37.0 37.0 37.0 130-134 35.6233 37.0 37.0 37.0 37.0 37.0 135-139 35.5309 37.0 37.0 37.0 37.0 37.0 140-144 35.4582 37.0 37.0 37.0 37.0 37.0 145-149 35.3977 37.0 37.0 37.0 37.0 37.0 150-151 35.20475 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 1.0 13 5.0 14 3.0 15 2.0 16 3.0 17 4.0 18 3.0 19 3.0 20 1.0 21 3.0 22 8.0 23 4.0 24 5.0 25 13.0 26 6.0 27 8.0 28 12.0 29 19.0 30 26.0 31 26.0 32 41.0 33 93.0 34 163.0 35 502.0 36 2772.0 37 274.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 45.525 23.799999999999997 8.5 22.175 2 27.425 25.275 30.85 16.45 3 21.95 26.224999999999998 31.95 19.875 4 23.849999999999998 34.425 23.1 18.625 5 26.275 37.574999999999996 20.75 15.4 6 20.875 38.725 22.900000000000002 17.5 7 20.325 21.825 38.775 19.075 8 21.125 25.15 29.625 24.099999999999998 9 22.075 24.8 29.725 23.400000000000002 10-14 23.375 28.915000000000003 26.619999999999997 21.09 15-19 22.755 28.32 27.345000000000002 21.58 20-24 23.395 28.205000000000002 27.08 21.32 25-29 23.830000000000002 27.575 27.925 20.669999999999998 30-34 23.400000000000002 27.875 28.084999999999997 20.64 35-39 22.695 27.865000000000002 27.794999999999998 21.645 40-44 22.66 27.939999999999998 28.199999999999996 21.2 45-49 23.39 28.125 27.62 20.865000000000002 50-54 22.595000000000002 28.544999999999998 27.615000000000002 21.245 55-59 23.215 28.34 26.87 21.575 60-64 22.775000000000002 27.96 28.055000000000003 21.21 65-69 23.77 27.605 27.785 20.84 70-74 23.655 28.785 26.174999999999997 21.385 75-79 23.805 27.939999999999998 27.61 20.645 80-84 23.26 28.34 27.11 21.29 85-89 23.555 27.73 27.834999999999997 20.880000000000003 90-94 23.565 28.18 27.045 21.21 95-99 23.5 28.87 26.875 20.755000000000003 100-104 24.23 28.325 27.205000000000002 20.24 105-109 24.115000000000002 28.199999999999996 27.045 20.64 110-114 24.145 28.449999999999996 26.995 20.41 115-119 24.705 28.29 26.919999999999998 20.085 120-124 25.05 28.51 26.369999999999997 20.07 125-129 24.67 28.95 26.235000000000003 20.145 130-134 25.3 28.075 26.985 19.64 135-139 25.465 28.305000000000003 25.85 20.380000000000003 140-144 25.025 28.415000000000003 26.765 19.794999999999998 145-149 25.802580258025802 28.637863786378638 26.282628262826286 19.276927692769277 150-151 26.0375 29.1875 26.137500000000003 18.637500000000003 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.5 3 0.5 4 0.0 5 0.5 6 0.5 7 0.5 8 2.0 9 2.0 10 1.0 11 1.0 12 1.0 13 0.5 14 1.5 15 1.5 16 1.0 17 1.5 18 1.5 19 1.0 20 1.0 21 1.0 22 0.5 23 1.0 24 1.0 25 3.0 26 7.5 27 9.0 28 4.5 29 9.0 30 18.5 31 18.0 32 24.0 33 33.5 34 38.5 35 54.5 36 75.5 37 99.5 38 145.0 39 187.0 40 205.5 41 208.0 42 235.0 43 264.0 44 257.0 45 241.5 46 247.0 47 259.0 48 227.5 49 200.0 50 180.0 51 146.5 52 116.0 53 97.0 54 87.0 55 67.0 56 55.5 57 45.5 58 29.0 59 19.0 60 16.5 61 10.5 62 7.0 63 8.0 64 3.0 65 0.5 66 0.5 67 1.0 68 1.0 69 0.5 70 0.0 71 0.0 72 0.0 73 1.0 74 1.0 75 0.0 76 0.5 77 1.0 78 0.5 79 0.0 80 0.0 81 0.5 82 0.5 83 1.0 84 1.0 85 0.5 86 1.0 87 0.5 88 0.0 89 0.5 90 0.5 91 0.0 92 0.0 93 0.0 94 0.0 95 0.5 96 0.5 97 0.0 98 0.0 99 0.0 100 2.0 >>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 0.01 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 84.75 #Duplication Level Percentage of deduplicated Percentage of total 1 86.16519174041298 73.02499999999999 2 11.35693215339233 19.25 3 1.6814159292035398 4.275 4 0.4424778761061947 1.5 5 0.14749262536873156 0.625 6 0.08849557522123894 0.44999999999999996 7 0.029498525073746312 0.17500000000000002 8 0.058997050147492625 0.4 9 0.0 0.0 >10 0.029498525073746312 0.3 >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 AGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATC 12 0.3 No Hit AGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAA 8 0.2 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 8 0.2 No Hit CAGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTA 7 0.17500000000000002 No Hit ATTTGATAATGCATCTCAAAGCAGTGCGGCATCGACACCTGTGCATGTAT 6 0.15 No Hit GGCCAAAGCCACTGTACTGCCACCTCAGATGAAAGCTTCTTCAATGACAA 6 0.15 No Hit ATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATCAATCAAT 6 0.15 No Hit GCCAATTCAGCTTGTTCAGAGGCACAGGCAGTTCTATTGTATGTTTTCAA 5 0.125 No Hit TGATCTCTGTAGTTTTATGTCACTACTCTCATCAAGAGGCTGTTCGCAGA 5 0.125 No Hit GGGAAGAATACGAGGAAAATAGGCTAAAGCCTGGCATGGTTCAGCATAAT 5 0.125 No Hit GTTGAGAGTTCAGACACCATTGATAATGTGAAGGCTAAAATCCAGGACAA 5 0.125 No Hit GTCCTAGTGTGGGCATTGATGCTGGAGATCATATCTGGATTTCAAGATAC 5 0.125 No Hit >>END_MODULE >>Adapter Content warn #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 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 0.0125 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.037500000000000006 0.0 0.0 0.0 0.0 68-69 0.0625 0.0 0.0 0.0 0.0 70-71 0.0875 0.0 0.0 0.0 0.0 72-73 0.125 0.0 0.0 0.0 0.0 74-75 0.16249999999999998 0.0 0.0 0.0 0.0 76-77 0.175 0.0 0.0 0.0 0.0 78-79 0.2125 0.0 0.0 0.0 0.0 80-81 0.275 0.0 0.0 0.0 0.0 82-83 0.325 0.0 0.0 0.0 0.0 84-85 0.3875 0.0 0.0 0.0 0.0 86-87 0.475 0.0 0.0 0.0 0.0 88-89 0.5874999999999999 0.0 0.0 0.0 0.0 90-91 0.625 0.0 0.0 0.0 0.0 92-93 0.7625 0.0 0.0 0.0 0.0 94-95 0.9375 0.0 0.0 0.0 0.0 96-97 1.0875 0.0 0.0 0.0 0.0 98-99 1.3 0.0 0.0 0.0 0.0 100-101 1.55 0.0 0.0 0.0 0.0 102-103 1.9125 0.0 0.0 0.0 0.0 104-105 2.1625 0.0 0.0 0.0 0.0 106-107 2.3 0.0 0.0 0.0 0.0 108-109 2.5250000000000004 0.0 0.0 0.0 0.0 110-111 2.825 0.0 0.0 0.0 0.0 112-113 3.15 0.0 0.0 0.0 0.0 114-115 3.475 0.0 0.0 0.0 0.0 116-117 3.75 0.0 0.0 0.0 0.0 118-119 4.0375 0.0 0.0 0.0 0.0 120-121 4.35 0.0 0.0 0.0 0.0 122-123 4.725 0.0 0.0 0.0 0.0 124-125 5.1 0.0 0.0 0.0 0.0 126-127 5.4 0.0 0.0 0.0 0.0 128-129 5.7 0.0 0.0 0.0 0.0 130-131 6.25 0.0 0.0 0.0 0.0 132-133 6.725 0.0 0.0 0.0 0.0 134-135 7.2625 0.0 0.0 0.0 0.0 136-137 7.7625 0.0 0.0 0.0 0.0 138-139 8.2625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 846718 spots for SRR12671347.sra Written 846718 spots for SRR12671347.sra Read 846718 spots for SRR12671347.sra Written 846718 spots for SRR12671347.sra Read 846718 spots for SRR12671347.sra Written 846718 spots for SRR12671347.sra Read 846718 spots for SRR12671347.sra Written 846718 spots for SRR12671347.sra Read 846718 spots for SRR12671347.sra Written 846718 spots for SRR12671347.sra Read 846718 spots for SRR12671347.sra Written 846718 spots for SRR12671347.sra Read 846718 spots for SRR12671347.sra Written 846718 spots for SRR12671347.sra Read 846718 spots for SRR12671347.sra Written 846718 spots for SRR12671347.sra Read 846718 spots for SRR12671347.sra Written 846718 spots for SRR12671347.sra Read 846718 spots for SRR12671347.sra Written 846718 spots for SRR12671347.sra Read 846718 spots for SRR12671347.sra Written 846718 spots for SRR12671347.sra Read 846718 spots for SRR12671347.sra Written 846718 spots for SRR12671347.sra Read 846718 spots for SRR12671347.sra Written 846718 spots for SRR12671347.sra Read 846718 spots for SRR12671347.sra Written 846718 spots for SRR12671347.sra Read 846718 spots for SRR12671347.sra Written 846718 spots for SRR12671347.sra Read 846718 spots for SRR12671347.sra Written 846718 spots for SRR12671347.sra Read 846718 spots for SRR12671347.sra Written 846718 spots for SRR12671347.sra Read 846728 spots for SRR12671347.sra Written 846728 spots for SRR12671347.sra Read 846718 spots for SRR12671347.sra Written 846718 spots for SRR12671347.sra Read 846718 spots for SRR12671347.sra Written 846718 spots for SRR12671347.sra SRR ids: ['SRR12671347.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_w2cvkfco SRR12671347.sra spots: 16934370 blocks: [[1, 846718], [846719, 1693436], [1693437, 2540154], [2540155, 3386872], [3386873, 4233590], [4233591, 5080308], [5080309, 5927026], [5927027, 6773744], [6773745, 7620462], [7620463, 8467180], [8467181, 9313898], [9313899, 10160616], [10160617, 11007334], [11007335, 11854052], [11854053, 12700770], [12700771, 13547488], [13547489, 14394206], [14394207, 15240924], [15240925, 16087642], [16087643, 16934370]] SRR12671347 file size 5733339 SRR12671347 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 SRR12671347 SRR12671347_1.fastq SRR12671347_2.fastq Input file: SRR12671347_1.fastq Paired file: SRR12671347_2.fastq trimmed: SRR12671347-trimmed-pair1.fastq, SRR12671347-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 Feb 11 17:51:54 2025 >> started Tue Feb 11 17:52:13 2025 >> done (19.349s) 16934370 read pairs processed; of these: 64 ( 0.00%) short read pairs filtered out after trimming by size control 9413 ( 0.06%) empty read pairs filtered out after trimming by size control 16924893 (99.94%) read pairs available; of these: 1836502 (10.85%) trimmed read pairs available after processing 15088391 (89.15%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 3 0.00% 19 10 0.00% 20 5 0.00% 21 10 0.00% 22 5 0.00% 23 13 0.00% 24 6 0.00% 25 12 0.00% 26 18 0.00% 27 18 0.00% 28 20 0.00% 29 6 0.00% 30 19 0.00% 31 27 0.00% 32 32 0.00% 33 13 0.00% 34 20 0.00% 35 38 0.00% 36 19 0.00% 37 20 0.00% 38 31 0.00% 39 29 0.00% 40 38 0.00% 41 47 0.00% 42 33 0.00% 43 48 0.00% 44 35 0.00% 45 57 0.00% 46 49 0.00% 47 76 0.00% 48 92 0.00% 49 103 0.00% 50 131 0.00% 51 149 0.00% 52 141 0.00% 53 166 0.00% 54 165 0.00% 55 189 0.00% 56 222 0.00% 57 289 0.00% 58 323 0.00% 59 363 0.00% 60 418 0.00% 61 488 0.00% 62 527 0.00% 63 638 0.00% 64 695 0.00% 65 816 0.00% 66 908 0.01% 67 954 0.01% 68 1205 0.01% 69 1306 0.01% 70 1419 0.01% 71 1730 0.01% 72 2010 0.01% 73 2287 0.01% 74 2606 0.02% 75 2733 0.02% 76 2931 0.02% 77 3192 0.02% 78 3573 0.02% 79 3778 0.02% 80 4033 0.02% 81 4620 0.03% 82 5086 0.03% 83 5650 0.03% 84 6235 0.04% 85 6610 0.04% 86 7071 0.04% 87 7207 0.04% 88 7678 0.05% 89 8174 0.05% 90 8531 0.05% 91 9044 0.05% 92 9426 0.06% 93 10200 0.06% 94 11179 0.07% 95 11783 0.07% 96 12478 0.07% 97 12626 0.07% 98 12916 0.08% 99 13690 0.08% 100 14294 0.08% 101 14198 0.08% 102 15180 0.09% 103 15872 0.09% 104 16749 0.10% 105 17452 0.10% 106 18020 0.11% 107 18774 0.11% 108 19394 0.11% 109 19836 0.12% 110 19779 0.12% 111 20999 0.12% 112 21737 0.13% 113 21976 0.13% 114 23078 0.14% 115 23831 0.14% 116 24476 0.14% 117 26250 0.16% 118 26684 0.16% 119 26929 0.16% 120 28038 0.17% 121 28293 0.17% 122 28867 0.17% 123 29457 0.17% 124 30630 0.18% 125 31199 0.18% 126 32873 0.19% 127 33213 0.20% 128 33803 0.20% 129 35365 0.21% 130 35927 0.21% 131 35865 0.21% 132 36469 0.22% 133 36759 0.22% 134 37960 0.22% 135 39129 0.23% 136 39835 0.24% 137 40791 0.24% 138 41812 0.25% 139 43327 0.26% 140 43534 0.26% 141 44573 0.26% 142 45259 0.27% 143 44976 0.27% 144 46230 0.27% 145 47079 0.28% 146 47551 0.28% 147 48114 0.28% 148 50673 0.30% 149 50175 0.30% 150 51677 0.31% 151 15088391 89.15% 16924893 reads passed initial QC criterion=sequence-density sequence-density=0.51 sequence-density-rank=1 fanout-score=2.38 fanout-score-rank=14 prefix-density=0.55 prefix-fanout=2.2 sequence=TGAGATGCCTCAGTGCATCCAAACATGGGTAG criterion=fanout-score sequence-density=0.02 sequence-density-rank=29 fanout-score=166.49 fanout-score-rank=1 prefix-density=0.26 prefix-fanout=12.2 sequence=TGAAGAAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAGTTGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGGAGTATGAATGTGTTCTCTGTG criterion=sequence-density sequence-density=1.26 sequence-density-rank=1 fanout-score=1.99 fanout-score-rank=34 prefix-density=1.26 prefix-fanout=2.0 sequence=CTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGGAGTGAACAAACAAAAGTGTCCGTGAGTGTCTTTATCTTTGTGTCTTCTTCA criterion=fanout-score sequence-density=0.09 sequence-density-rank=28 fanout-score=12.86 fanout-score-rank=1 prefix-density=0.21 prefix-fanout=5.8 sequence=TGGATGGGAGGCCAAGCGGCACAGCAAGTAAAGGTGCCT SRR12671347 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 17:53:13 Started mapping on | Feb 11 17:53:14 Finished on | Feb 11 17:55:16 Mapping speed, Million of reads per hour | 499.42 Number of input reads | 16924893 Average input read length | 288 UNIQUE READS: Uniquely mapped reads number | 14291766 Uniquely mapped reads % | 84.44% Average mapped length | 288.96 Number of splices: Total | 14114364 Number of splices: Annotated (sjdb) | 13855290 Number of splices: GT/AG | 13828222 Number of splices: GC/AG | 238330 Number of splices: AT/AC | 8684 Number of splices: Non-canonical | 39128 Mismatch rate per base, % | 0.38% Deletion rate per base | 0.03% Deletion average length | 2.77 Insertion rate per base | 0.02% Insertion average length | 2.09 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 339448 % of reads mapped to multiple loci | 2.01% Number of reads mapped to too many loci | 24244 % of reads mapped to too many loci | 0.14% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 13.27% % of reads unmapped: other | 0.14% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 2293679 2293679 2293679 N_multimapping 339448 339448 339448 N_noFeature 455414 14006492 547776 N_ambiguous 336453 2295 141803 UnstrandedReadsAssigned:13499899 PositiveStrandReadsAssigned:282979 NegativeStrandReadsAssigned:13602187 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12671347 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: SRR12671347-trimmed-pair1.fastq SRR12671347-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 16,924,893 reads, 14,931,581 reads pseudoaligned [quant] estimated average fragment length: 244.138 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,206 rounds 52401 SRR12671347.ke.tsv 34699 SRR12671347.se.tsv 87100 total ==> SRR12671347.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1774.86 738 23.4645 Potri.005G024800.1.v4.1 1035 791.862 250 17.816 Potri.004G059700.1.v4.1 961 717.967 1 0.0785985 Potri.007G009000.2.v4.1 1416 1172.86 0 0 Potri.003G141000.2.v4.1 2943 2699.86 833 17.4109 Potri.016G087400.1.v4.1 270 90.7039 697 433.636 Potri.015G069301.1.v4.1 564 331.843 0 0 Potri.010G195200.1.v4.1 1773 1529.86 125 4.6108 Potri.012G127500.1.v4.1 977 733.923 69 5.30539 ==> SRR12671347.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 94 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 279 Potri.001G212900.v4.1 7 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 4 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 0 SRR12671347 completed mapping pipeline successfully