Starting /dee2/code/volunteer_pipeline.sh SRR12671333 current disk space = 3049228201984 free memory = 1459627632 SRR12671333 SRAfilesize 2f2cc0f11745b1aeba508c0349a5fa83 SRR12671333.sra SRR12671333.sra file validated SRR12671333 is paired end SRR12671333 is conventional basespace SRR12671333 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12671333_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 36.5875 37.0 37.0 37.0 37.0 37.0 2 36.4285 37.0 37.0 37.0 37.0 37.0 3 36.528 37.0 37.0 37.0 37.0 37.0 4 36.6675 37.0 37.0 37.0 37.0 37.0 5 36.631 37.0 37.0 37.0 37.0 37.0 6 36.5915 37.0 37.0 37.0 37.0 37.0 7 36.529 37.0 37.0 37.0 37.0 37.0 8 36.591 37.0 37.0 37.0 37.0 37.0 9 36.6545 37.0 37.0 37.0 37.0 37.0 10-14 36.602 37.0 37.0 37.0 37.0 37.0 15-19 36.5918 37.0 37.0 37.0 37.0 37.0 20-24 36.570800000000006 37.0 37.0 37.0 37.0 37.0 25-29 36.539199999999994 37.0 37.0 37.0 37.0 37.0 30-34 36.52080000000001 37.0 37.0 37.0 37.0 37.0 35-39 36.5215 37.0 37.0 37.0 37.0 37.0 40-44 36.445499999999996 37.0 37.0 37.0 37.0 37.0 45-49 36.468399999999995 37.0 37.0 37.0 37.0 37.0 50-54 36.468999999999994 37.0 37.0 37.0 37.0 37.0 55-59 36.3993 37.0 37.0 37.0 37.0 37.0 60-64 36.407500000000006 37.0 37.0 37.0 37.0 37.0 65-69 36.3899 37.0 37.0 37.0 37.0 37.0 70-74 36.3669 37.0 37.0 37.0 37.0 37.0 75-79 36.3817 37.0 37.0 37.0 37.0 37.0 80-84 36.317299999999996 37.0 37.0 37.0 37.0 37.0 85-89 36.2866 37.0 37.0 37.0 37.0 37.0 90-94 36.301500000000004 37.0 37.0 37.0 37.0 37.0 95-99 36.2203 37.0 37.0 37.0 37.0 37.0 100-104 36.2199 37.0 37.0 37.0 37.0 37.0 105-109 36.182 37.0 37.0 37.0 37.0 37.0 110-114 36.169 37.0 37.0 37.0 37.0 37.0 115-119 36.1671 37.0 37.0 37.0 37.0 37.0 120-124 36.1916 37.0 37.0 37.0 37.0 37.0 125-129 36.14489999999999 37.0 37.0 37.0 37.0 37.0 130-134 36.089 37.0 37.0 37.0 37.0 37.0 135-139 36.03 37.0 37.0 37.0 37.0 37.0 140-144 35.9878 37.0 37.0 37.0 37.0 37.0 145-149 35.962599999999995 37.0 37.0 37.0 37.0 37.0 150-151 35.89575 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 18 2.0 19 0.0 20 0.0 21 1.0 22 2.0 23 1.0 24 0.0 25 3.0 26 3.0 27 3.0 28 11.0 29 21.0 30 26.0 31 29.0 32 38.0 33 63.0 34 115.0 35 249.0 36 2921.0 37 512.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 48.075 12.325 4.9 34.699999999999996 2 18.430290872617856 11.760280842527584 39.26780341023069 30.541624874623874 3 17.8 18.6 29.299999999999997 34.300000000000004 4 23.175 25.05 23.799999999999997 27.975 5 24.525 32.75 23.35 19.375 6 19.45 33.900000000000006 24.875 21.775 7 14.299999999999999 26.974999999999998 43.4 15.325 8 16.150000000000002 24.474999999999998 34.8 24.575 9 15.825 24.3 34.675 25.2 10-14 20.02 30.205 27.62 22.155 15-19 19.415 28.854999999999997 27.67 24.060000000000002 20-24 19.759999999999998 28.67 27.71 23.86 25-29 19.79 28.655 27.665 23.89 30-34 19.655 28.465 28.144999999999996 23.735 35-39 19.950000000000003 28.17 27.860000000000003 24.02 40-44 20.25 28.54 27.74 23.47 45-49 20.215 28.575 27.72 23.49 50-54 19.525000000000002 28.625 27.93 23.919999999999998 55-59 19.98 28.89 27.450000000000003 23.68 60-64 19.97 28.285 28.285 23.46 65-69 19.42 29.07 27.689999999999998 23.82 70-74 20.855 27.689999999999998 27.500000000000004 23.955000000000002 75-79 19.475 28.915000000000003 27.625 23.985 80-84 20.445 28.994999999999997 26.950000000000003 23.61 85-89 19.74 28.405 28.360000000000003 23.494999999999997 90-94 20.51 27.99 27.589999999999996 23.91 95-99 20.369999999999997 28.29 27.884999999999998 23.455000000000002 100-104 20.07 28.89 27.705000000000002 23.335 105-109 20.66 28.465 27.284999999999997 23.59 110-114 20.395 28.235 27.47 23.9 115-119 20.599999999999998 28.275 27.495000000000005 23.630000000000003 120-124 20.830000000000002 28.035 27.534999999999997 23.599999999999998 125-129 20.59 28.09 27.67 23.65 130-134 20.775 28.64 27.529999999999998 23.055 135-139 21.404999999999998 28.08 27.265 23.25 140-144 21.52 27.474999999999998 27.045 23.96 145-149 21.095 28.15 27.04 23.715 150-151 20.4375 27.35 27.487499999999997 24.725 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 1.0 1 0.5 2 0.0 3 0.0 4 0.0 5 0.5 6 0.5 7 0.0 8 0.0 9 0.5 10 1.0 11 0.5 12 0.5 13 0.5 14 1.0 15 1.0 16 0.5 17 1.0 18 0.5 19 0.0 20 2.5 21 3.0 22 1.5 23 5.0 24 9.0 25 9.0 26 12.0 27 16.0 28 15.5 29 20.0 30 20.5 31 21.5 32 28.0 33 41.0 34 51.0 35 69.5 36 95.5 37 106.0 38 120.5 39 150.5 40 175.0 41 218.0 42 246.0 43 244.0 44 241.0 45 240.0 46 252.0 47 250.0 48 230.0 49 202.0 50 185.0 51 159.0 52 138.0 53 112.0 54 76.0 55 57.5 56 45.0 57 30.0 58 28.5 59 25.0 60 11.0 61 9.5 62 8.0 63 3.0 64 0.5 65 2.5 66 2.0 67 1.0 68 1.0 69 0.0 70 0.5 71 0.5 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 0.3 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 81.35 #Duplication Level Percentage of deduplicated Percentage of total 1 82.23724646588813 66.9 2 14.136447449293177 23.0 3 2.581438229870928 6.3 4 0.645359557467732 2.1 5 0.33804548248309774 1.375 6 0.030731407498463426 0.15 7 0.030731407498463426 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 GCGCGTTCTAAAATAAACAGTAAGCTGATCTAACACTGCTTGTTCCATAC 7 0.17500000000000002 No Hit CTTGGCTTCTCTGGTGCTGAAAAAGTACCTCTCCTGGTCCAAATCACCTG 6 0.15 No Hit GGGGGTTGAGAGCTCCCCGGGATACGTCTCGCTCGGCCAATTCTCGAGCA 5 0.125 No Hit CCGGAATTCTTTTGATAATGGATTGATCATTGTTACAAGACAGGATTCCA 5 0.125 No Hit CTCCAATTCAAGCAAGGCCTGCTGCTCTCTCGGAGCTCCCTCAAAAGTAC 5 0.125 No Hit GCTAAGGAAAGGAGAACTGCAGGAGCACCGAGCGATCTTAAAGTCAGGTA 5 0.125 No Hit GCCACACCAGAGGCCACAGACATGGCCAATACATAACAATGAAGAAGACA 5 0.125 No Hit GGGTTTTCTAGCATCGCTAGCTTATGCAGATTGGAATGATGTCACTTGCC 5 0.125 No Hit CTTGGCTTCATACACTTTCCTGTGACCCCCGTCAGTTACCTCAAAGGTTA 5 0.125 No Hit CCCGTGTCTTTACCTGGCGCAAAGCTGAATTGGCATTCTGCTGCTGATTC 5 0.125 No Hit CTGGTGAGCTGTGGTGCTCACGGTAGACCCAACCTTTCTCCAACTCGAAT 5 0.125 No Hit GCTTATTTGGGGTTTGGGAAGTAAACAATGGTGTTCACAGAGTGGAAATA 5 0.125 No Hit AGCCGCAGCAGCAAGATACCTTCCCACGCGAGGTTGAAATCTCATTTGGA 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 0.05 0.0 0.0 0.0 0.0 66-67 0.05 0.0 0.0 0.0 0.0 68-69 0.05 0.0 0.0 0.0 0.0 70-71 0.05 0.0 0.0 0.0 0.0 72-73 0.05 0.0 0.0 0.0 0.0 74-75 0.0625 0.0 0.0 0.0 0.0 76-77 0.0875 0.0 0.0 0.0 0.0 78-79 0.1 0.0 0.0 0.0 0.0 80-81 0.1 0.0 0.0 0.0 0.0 82-83 0.15 0.0 0.0 0.0 0.0 84-85 0.21250000000000002 0.0 0.0 0.0 0.0 86-87 0.25 0.0 0.0 0.0 0.0 88-89 0.2875 0.0 0.0 0.0 0.0 90-91 0.3875 0.0 0.0 0.0 0.0 92-93 0.4375 0.0 0.0 0.0 0.0 94-95 0.5 0.0 0.0 0.0 0.0 96-97 0.6125 0.0 0.0 0.0 0.0 98-99 0.7375 0.0 0.0 0.0 0.0 100-101 0.7875000000000001 0.0 0.0 0.0 0.0 102-103 0.8625 0.0 0.0 0.0 0.0 104-105 0.9875 0.0 0.0 0.0 0.0 106-107 1.1749999999999998 0.0 0.0 0.0 0.0 108-109 1.3624999999999998 0.0 0.0 0.0 0.0 110-111 1.5125 0.0 0.0 0.0 0.0 112-113 1.6 0.0 0.0 0.0 0.0 114-115 1.775 0.0 0.0 0.0 0.0 116-117 1.925 0.0 0.0 0.0 0.0 118-119 2.1 0.0 0.0 0.0 0.0 120-121 2.3 0.0 0.0 0.0 0.0 122-123 2.4875 0.0 0.0 0.0 0.0 124-125 2.7125 0.0 0.0 0.0 0.0 126-127 2.8125 0.0 0.0 0.0 0.0 128-129 3.05 0.0 0.0 0.0 0.0 130-131 3.4125 0.0 0.0 0.0 0.0 132-133 3.75 0.0 0.0 0.0 0.0 134-135 3.975 0.0 0.0 0.0 0.0 136-137 4.5625 0.0 0.0 0.0 0.0 138-139 4.9375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR12671333 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12671333_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 36.271 37.0 37.0 37.0 37.0 37.0 2 36.1195 37.0 37.0 37.0 37.0 37.0 3 36.1745 37.0 37.0 37.0 37.0 37.0 4 36.296 37.0 37.0 37.0 37.0 37.0 5 36.3465 37.0 37.0 37.0 37.0 37.0 6 36.282 37.0 37.0 37.0 37.0 37.0 7 36.266 37.0 37.0 37.0 37.0 37.0 8 36.3595 37.0 37.0 37.0 37.0 37.0 9 36.336 37.0 37.0 37.0 37.0 37.0 10-14 36.315999999999995 37.0 37.0 37.0 37.0 37.0 15-19 36.293000000000006 37.0 37.0 37.0 37.0 37.0 20-24 36.2162 37.0 37.0 37.0 37.0 37.0 25-29 36.17999999999999 37.0 37.0 37.0 37.0 37.0 30-34 36.1523 37.0 37.0 37.0 37.0 37.0 35-39 36.0993 37.0 37.0 37.0 37.0 37.0 40-44 36.067 37.0 37.0 37.0 37.0 37.0 45-49 36.11659999999999 37.0 37.0 37.0 37.0 37.0 50-54 36.084 37.0 37.0 37.0 37.0 37.0 55-59 36.0133 37.0 37.0 37.0 37.0 37.0 60-64 35.9978 37.0 37.0 37.0 37.0 37.0 65-69 36.0044 37.0 37.0 37.0 37.0 37.0 70-74 35.903999999999996 37.0 37.0 37.0 37.0 37.0 75-79 36.016999999999996 37.0 37.0 37.0 37.0 37.0 80-84 35.8836 37.0 37.0 37.0 37.0 37.0 85-89 35.9037 37.0 37.0 37.0 37.0 37.0 90-94 35.9296 37.0 37.0 37.0 37.0 37.0 95-99 35.8818 37.0 37.0 37.0 37.0 37.0 100-104 35.8074 37.0 37.0 37.0 37.0 37.0 105-109 35.7485 37.0 37.0 37.0 37.0 37.0 110-114 35.7043 37.0 37.0 37.0 37.0 37.0 115-119 35.8146 37.0 37.0 37.0 37.0 37.0 120-124 35.7956 37.0 37.0 37.0 37.0 37.0 125-129 35.69019999999999 37.0 37.0 37.0 37.0 37.0 130-134 35.6493 37.0 37.0 37.0 37.0 37.0 135-139 35.5267 37.0 37.0 37.0 37.0 37.0 140-144 35.5601 37.0 37.0 37.0 37.0 37.0 145-149 35.4856 37.0 37.0 37.0 37.0 37.0 150-151 35.3405 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 1.0 13 2.0 14 5.0 15 7.0 16 3.0 17 1.0 18 3.0 19 3.0 20 0.0 21 2.0 22 4.0 23 4.0 24 4.0 25 6.0 26 6.0 27 9.0 28 18.0 29 19.0 30 20.0 31 35.0 32 51.0 33 85.0 34 171.0 35 471.0 36 2749.0 37 321.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 43.6 23.925 8.3 24.175 2 25.074999999999996 24.3 35.0 15.625 3 19.775000000000002 26.6 36.8 16.825000000000003 4 23.599999999999998 33.35 23.400000000000002 19.650000000000002 5 27.750000000000004 35.75 20.25 16.25 6 19.900000000000002 40.25 22.175 17.675 7 19.6 22.475 38.324999999999996 19.6 8 18.925 23.674999999999997 31.474999999999998 25.924999999999997 9 23.225 22.2 30.15 24.425 10-14 24.065 28.37 27.08 20.485 15-19 23.785 27.58 27.439999999999998 21.195 20-24 23.075000000000003 28.49 27.595 20.84 25-29 22.71 27.435 28.335 21.52 30-34 22.775000000000002 27.884999999999998 28.235 21.105 35-39 22.765 28.54 27.229999999999997 21.465 40-44 23.71 28.26 27.415 20.615 45-49 23.375 28.095 27.725 20.805 50-54 22.36 28.34 28.18 21.12 55-59 23.46 28.275 27.32 20.945 60-64 22.770000000000003 27.894999999999996 28.155 21.18 65-69 23.54 27.655 27.689999999999998 21.115000000000002 70-74 23.405 27.665 28.000000000000004 20.93 75-79 23.555 27.889999999999997 27.185 21.37 80-84 22.595000000000002 28.15 27.715 21.54 85-89 23.055 28.51 27.365000000000002 21.07 90-94 23.29 27.74 27.845 21.125 95-99 23.175 28.475 27.26 21.09 100-104 23.895 27.750000000000004 27.22 21.135 105-109 23.880000000000003 28.04 27.72 20.36 110-114 23.95 27.52 28.005000000000003 20.525 115-119 24.02 28.26 27.544999999999998 20.175 120-124 24.315 27.85 27.52 20.315 125-129 24.035 27.935 27.48 20.549999999999997 130-134 24.745 27.245 27.529999999999998 20.48 135-139 24.39 28.565 27.24 19.805 140-144 25.040000000000003 27.805000000000003 27.375 19.78 145-149 25.147514751475146 28.132813281328133 26.817681768176815 19.901990199019902 150-151 25.4375 28.9375 26.3 19.325 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.5 5 0.5 6 0.5 7 0.5 8 0.5 9 1.5 10 1.0 11 0.0 12 0.5 13 1.0 14 1.0 15 1.5 16 2.0 17 1.0 18 0.5 19 1.0 20 0.5 21 3.5 22 5.5 23 3.5 24 5.5 25 6.5 26 4.5 27 7.0 28 10.0 29 13.0 30 13.0 31 19.0 32 27.0 33 32.5 34 52.0 35 67.0 36 80.0 37 84.5 38 109.0 39 158.0 40 191.0 41 209.0 42 253.5 43 291.5 44 278.0 45 259.0 46 248.5 47 250.5 48 243.0 49 204.0 50 166.0 51 138.5 52 112.0 53 97.5 54 82.0 55 66.5 56 52.5 57 36.5 58 24.0 59 18.0 60 15.0 61 13.5 62 11.5 63 5.5 64 1.0 65 1.5 66 2.5 67 2.0 68 1.0 69 0.5 70 0.5 71 0.0 72 0.0 73 0.5 74 1.0 75 0.5 76 0.5 77 0.5 78 0.0 79 0.0 80 0.0 81 0.0 82 0.5 83 1.0 84 0.5 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 0.5 96 0.5 97 0.0 98 0.0 99 0.0 100 1.5 >>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 81.85 #Duplication Level Percentage of deduplicated Percentage of total 1 83.01771533292609 67.95 2 13.469761759315821 22.05 3 2.474037874160049 6.075 4 0.5803298717165547 1.9 5 0.3054367745876604 1.25 6 0.12217470983506415 0.6 7 0.030543677458766037 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 CCGAATAGCAGTTGAGGCAGCACTGAACACTGAGGACCCTCAGTATCAGG 7 0.17500000000000002 No Hit GATGGTCGTATGGAGAAATTCTACTGGGCTCCAACCAGAGATGATAGGAT 6 0.15 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 6 0.15 No Hit AGAACACATTCATACCCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATC 6 0.15 No Hit GATTGCCTCCTGGATTTAGGTTCCACCCTACAGACGAGGAGCTTGTAGTC 6 0.15 No Hit GTTCAATGCATGCAGGTGTGGCCACCAACTGGATTGAAGAAGTTCGAGAC 5 0.125 No Hit GGGTGTAATAGCTAAGTAGCCTGTAAGAGATGGCTTCCTCTGTGATTTCA 5 0.125 No Hit AAACAAGAGAGGTGGAGATATAGGAGAGCATAACCATGTTAGTCCCATAT 5 0.125 No Hit GGCAATTCTAGGCCTTATCCAAGCTATATTCCTCATATCTGGAGCAAAAC 5 0.125 No Hit GGAAGCTGACATGTCTGAAGTCATCGACACAGTGAAACAACGGGTTAAAG 5 0.125 No Hit CTCTGATTACTGATGTCCGTTTCAGCCCAAGCATGTCACGACTTGCAACA 5 0.125 No Hit CTCCGACGCCGTCTCCGGCACCGCCGAAGTGGGCTGCGTCGGTGAAATCA 5 0.125 No Hit GTAGGAGTCTCTCTCTCTCTAGAATCTCTGTTTTTATCCTCTCTCTAGAA 5 0.125 No Hit GAAAGAGAGAAATGGCAACAGGTGGTATCAAAGAAGTGGGAGGATCAGCT 5 0.125 No Hit GAAATAGTGAAGGTCCAAAGAGTGACTGCTCCTGTTGGCCAGATGCAGCT 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 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.05 0.0 0.0 0.0 0.0 66-67 0.05 0.0 0.0 0.0 0.0 68-69 0.05 0.0 0.0 0.0 0.0 70-71 0.05 0.0 0.0 0.0 0.0 72-73 0.05 0.0 0.0 0.0 0.0 74-75 0.0625 0.0 0.0 0.0 0.0 76-77 0.0875 0.0 0.0 0.0 0.0 78-79 0.1 0.0 0.0 0.0 0.0 80-81 0.1 0.0 0.0 0.0 0.0 82-83 0.15 0.0 0.0 0.0 0.0 84-85 0.21250000000000002 0.0 0.0 0.0 0.0 86-87 0.25 0.0 0.0 0.0 0.0 88-89 0.2875 0.0 0.0 0.0 0.0 90-91 0.3875 0.0 0.0 0.0 0.0 92-93 0.4625 0.0 0.0 0.0 0.0 94-95 0.525 0.0 0.0 0.0 0.0 96-97 0.6375 0.0 0.0 0.0 0.0 98-99 0.7625 0.0 0.0 0.0 0.0 100-101 0.8125 0.0 0.0 0.0 0.0 102-103 0.8875 0.0 0.0 0.0 0.0 104-105 1.0375 0.0 0.0 0.0 0.0 106-107 1.225 0.0 0.0 0.0 0.0 108-109 1.4125 0.0 0.0 0.0 0.0 110-111 1.5875 0.0 0.0 0.0 0.0 112-113 1.675 0.0 0.0 0.0 0.0 114-115 1.8625 0.0 0.0 0.0 0.0 116-117 2.0250000000000004 0.0 0.0 0.0 0.0 118-119 2.2 0.0 0.0 0.0 0.0 120-121 2.4000000000000004 0.0 0.0 0.0 0.0 122-123 2.5875 0.0 0.0 0.0 0.0 124-125 2.8125 0.0 0.0 0.0 0.0 126-127 2.925 0.0 0.0 0.0 0.0 128-129 3.2 0.0 0.0 0.0 0.0 130-131 3.55 0.0 0.0 0.0 0.0 132-133 3.875 0.0 0.0 0.0 0.0 134-135 4.0875 0.0 0.0 0.0 0.0 136-137 4.6625 0.0 0.0 0.0 0.0 138-139 5.0625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGGGGGG 20 0.00593511 29.0 140-144 >>END_MODULE Read 1004020 spots for SRR12671333.sra Written 1004020 spots for SRR12671333.sra Read 1004020 spots for SRR12671333.sra Written 1004020 spots for SRR12671333.sra Read 1004020 spots for SRR12671333.sra Written 1004020 spots for SRR12671333.sra Read 1004020 spots for SRR12671333.sra Written 1004020 spots for SRR12671333.sra Read 1004020 spots for SRR12671333.sra Written 1004020 spots for SRR12671333.sra Read 1004020 spots for SRR12671333.sra Written 1004020 spots for SRR12671333.sra Read 1004020 spots for SRR12671333.sra Written 1004020 spots for SRR12671333.sra Read 1004020 spots for SRR12671333.sra Written 1004020 spots for SRR12671333.sra Read 1004020 spots for SRR12671333.sra Written 1004020 spots for SRR12671333.sra Read 1004020 spots for SRR12671333.sra Written 1004020 spots for SRR12671333.sra Read 1004020 spots for SRR12671333.sra Written 1004020 spots for SRR12671333.sra Read 1004020 spots for SRR12671333.sra Written 1004020 spots for SRR12671333.sra Read 1004020 spots for SRR12671333.sra Written 1004020 spots for SRR12671333.sra Read 1004020 spots for SRR12671333.sra Written 1004020 spots for SRR12671333.sra Read 1004020 spots for SRR12671333.sra Written 1004020 spots for SRR12671333.sra Read 1004020 spots for SRR12671333.sra Written 1004020 spots for SRR12671333.sra Read 1004020 spots for SRR12671333.sra Written 1004020 spots for SRR12671333.sra Read 1004024 spots for SRR12671333.sra Written 1004024 spots for SRR12671333.sra Read 1004020 spots for SRR12671333.sra Written 1004020 spots for SRR12671333.sra Read 1004020 spots for SRR12671333.sra Written 1004020 spots for SRR12671333.sra SRR ids: ['SRR12671333.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_bx6mutqb SRR12671333.sra spots: 20080404 blocks: [[1, 1004020], [1004021, 2008040], [2008041, 3012060], [3012061, 4016080], [4016081, 5020100], [5020101, 6024120], [6024121, 7028140], [7028141, 8032160], [8032161, 9036180], [9036181, 10040200], [10040201, 11044220], [11044221, 12048240], [12048241, 13052260], [13052261, 14056280], [14056281, 15060300], [15060301, 16064320], [16064321, 17068340], [17068341, 18072360], [18072361, 19076380], [19076381, 20080404]] SRR12671333 file size 6802499 SRR12671333 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 SRR12671333 SRR12671333_1.fastq SRR12671333_2.fastq Input file: SRR12671333_1.fastq Paired file: SRR12671333_2.fastq trimmed: SRR12671333-trimmed-pair1.fastq, SRR12671333-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 16:11:14 2025 >> started Tue Feb 11 16:11:37 2025 >> done (22.575s) 20080404 read pairs processed; of these: 170 ( 0.00%) short read pairs filtered out after trimming by size control 6403 ( 0.03%) empty read pairs filtered out after trimming by size control 20073831 (99.97%) read pairs available; of these: 1455460 ( 7.25%) trimmed read pairs available after processing 18618371 (92.75%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 21 0.00% 19 17 0.00% 20 24 0.00% 21 16 0.00% 22 38 0.00% 23 30 0.00% 24 30 0.00% 25 30 0.00% 26 51 0.00% 27 43 0.00% 28 36 0.00% 29 38 0.00% 30 35 0.00% 31 38 0.00% 32 46 0.00% 33 32 0.00% 34 42 0.00% 35 47 0.00% 36 52 0.00% 37 40 0.00% 38 42 0.00% 39 46 0.00% 40 59 0.00% 41 63 0.00% 42 66 0.00% 43 68 0.00% 44 75 0.00% 45 86 0.00% 46 91 0.00% 47 101 0.00% 48 119 0.00% 49 130 0.00% 50 176 0.00% 51 168 0.00% 52 191 0.00% 53 175 0.00% 54 184 0.00% 55 230 0.00% 56 291 0.00% 57 327 0.00% 58 361 0.00% 59 410 0.00% 60 531 0.00% 61 619 0.00% 62 635 0.00% 63 708 0.00% 64 794 0.00% 65 953 0.00% 66 986 0.00% 67 1051 0.01% 68 1190 0.01% 69 1385 0.01% 70 1627 0.01% 71 1787 0.01% 72 2038 0.01% 73 2222 0.01% 74 2507 0.01% 75 2743 0.01% 76 2934 0.01% 77 3235 0.02% 78 3469 0.02% 79 3707 0.02% 80 3915 0.02% 81 4416 0.02% 82 5002 0.02% 83 5232 0.03% 84 5793 0.03% 85 6257 0.03% 86 6388 0.03% 87 6812 0.03% 88 7245 0.04% 89 7428 0.04% 90 7932 0.04% 91 8139 0.04% 92 8603 0.04% 93 9258 0.05% 94 9917 0.05% 95 10294 0.05% 96 10469 0.05% 97 11253 0.06% 98 11292 0.06% 99 11932 0.06% 100 12096 0.06% 101 12551 0.06% 102 13072 0.07% 103 13393 0.07% 104 13987 0.07% 105 14783 0.07% 106 15226 0.08% 107 15697 0.08% 108 15735 0.08% 109 16432 0.08% 110 16334 0.08% 111 16712 0.08% 112 17370 0.09% 113 17717 0.09% 114 18405 0.09% 115 18959 0.09% 116 19834 0.10% 117 20370 0.10% 118 20669 0.10% 119 20798 0.10% 120 21610 0.11% 121 21904 0.11% 122 22438 0.11% 123 23265 0.12% 124 23575 0.12% 125 24230 0.12% 126 24934 0.12% 127 25217 0.13% 128 26120 0.13% 129 26788 0.13% 130 26799 0.13% 131 27211 0.14% 132 27961 0.14% 133 28322 0.14% 134 28980 0.14% 135 30054 0.15% 136 29613 0.15% 137 30701 0.15% 138 31606 0.16% 139 32454 0.16% 140 32609 0.16% 141 33516 0.17% 142 33974 0.17% 143 33893 0.17% 144 35230 0.18% 145 35759 0.18% 146 36574 0.18% 147 36560 0.18% 148 38445 0.19% 149 38217 0.19% 150 39898 0.20% 151 18618371 92.75% 20073831 reads passed initial QC criterion=sequence-density sequence-density=0.66 sequence-density-rank=1 fanout-score=1.99 fanout-score-rank=25 prefix-density=0.65 prefix-fanout=2.0 sequence=TTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAGGTGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGG criterion=fanout-score sequence-density=0.01 sequence-density-rank=26 fanout-score=411.61 fanout-score-rank=1 prefix-density=0.26 prefix-fanout=15.0 sequence=TGAAGAAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTG criterion=sequence-density sequence-density=0.79 sequence-density-rank=1 fanout-score=2.18 fanout-score-rank=23 prefix-density=0.82 prefix-fanout=2.1 sequence=CCAAGTCTTTTAGTTCATCCATTTAAGCTTAATCAATCAATCATCATGTCTAGCACCTGCGACACCTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAA criterion=fanout-score sequence-density=0.01 sequence-density-rank=31 fanout-score=54.40 fanout-score-rank=1 prefix-density=0.06 prefix-fanout=5.4 sequence=AAACCCAAAGCTCAAAAAAAATCTTAACTGCACCCGCTCATCCAGCAATGGCAGCAGCAACAATGGCCCTCTCCTCCCCTTCGCTAGCCGGAAAGGCGGTGAAGCTCAACCCCTCCTCCTCTGAGATCATGGGCAATGGCCGTGTCTCCATGAGGAAAACCACCAAGCCTGTTCCCTCCGGGAGCCCATGGTACGGACCAGACCGTGTTAAATACTTGGGCCCGTTCTCTGGTGAGCCCCCATCCTACTTGACTGGTGAGTTCCCTGGTGACTACGGCTGGGACACTGCTGG SRR12671333 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 16:12:24 Started mapping on | Feb 11 16:12:24 Finished on | Feb 11 16:14:41 Mapping speed, Million of reads per hour | 527.49 Number of input reads | 20073831 Average input read length | 298 UNIQUE READS: Uniquely mapped reads number | 18582625 Uniquely mapped reads % | 92.57% Average mapped length | 296.42 Number of splices: Total | 18747479 Number of splices: Annotated (sjdb) | 18396583 Number of splices: GT/AG | 18348388 Number of splices: GC/AG | 333352 Number of splices: AT/AC | 11395 Number of splices: Non-canonical | 54344 Mismatch rate per base, % | 0.36% Deletion rate per base | 0.03% Deletion average length | 2.83 Insertion rate per base | 0.02% Insertion average length | 2.16 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 440189 % of reads mapped to multiple loci | 2.19% Number of reads mapped to too many loci | 33650 % of reads mapped to too many loci | 0.17% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.97% % of reads unmapped: other | 0.10% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1051017 1051017 1051017 N_multimapping 440189 440189 440189 N_noFeature 601004 18236132 712111 N_ambiguous 364738 1516 128415 UnstrandedReadsAssigned:17616883 PositiveStrandReadsAssigned:344977 NegativeStrandReadsAssigned:17742099 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12671333 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: SRR12671333-trimmed-pair1.fastq SRR12671333-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 20,073,831 reads, 17,667,893 reads pseudoaligned [quant] estimated average fragment length: 274.75 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,038 rounds 52401 SRR12671333.ke.tsv 34699 SRR12671333.se.tsv 87100 total ==> SRR12671333.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1744.25 731 20.1474 Potri.005G024800.1.v4.1 1035 761.25 228 14.3985 Potri.004G059700.1.v4.1 961 687.384 0 0 Potri.007G009000.2.v4.1 1416 1142.25 0 0 Potri.003G141000.2.v4.1 2943 2669.25 1115 20.0815 Potri.016G087400.1.v4.1 270 77.9571 830.584 512.2 Potri.015G069301.1.v4.1 564 303.951 0 0 Potri.010G195200.1.v4.1 1773 1499.25 138 4.42503 Potri.012G127500.1.v4.1 977 703.303 112 7.65573 ==> SRR12671333.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 191 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 403 Potri.001G212900.v4.1 52 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 3 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 0 SRR12671333 completed mapping pipeline successfully