Starting /dee2/code/volunteer_pipeline.sh SRR12951312 current disk space = 1543065595904 free memory = 1601881936 SRR12951312 SRAfilesize 114a89fe5113fe6d21ef8680f905c4d1 SRR12951312.sra SRR12951312.sra file validated SRR12951312 is paired end SRR12951312 is conventional basespace SRR12951312 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12951312_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 50 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.5 37.0 37.0 37.0 37.0 37.0 2 36.09 37.0 37.0 37.0 37.0 37.0 3 36.417 37.0 37.0 37.0 37.0 37.0 4 36.5375 37.0 37.0 37.0 37.0 37.0 5 36.62 37.0 37.0 37.0 37.0 37.0 6 36.6435 37.0 37.0 37.0 37.0 37.0 7 36.5315 37.0 37.0 37.0 37.0 37.0 8 36.636 37.0 37.0 37.0 37.0 37.0 9 36.6015 37.0 37.0 37.0 37.0 37.0 10-14 36.6044 37.0 37.0 37.0 37.0 37.0 15-19 36.569 37.0 37.0 37.0 37.0 37.0 20-24 36.532000000000004 37.0 37.0 37.0 37.0 37.0 25-29 36.508 37.0 37.0 37.0 37.0 37.0 30-34 36.496700000000004 37.0 37.0 37.0 37.0 37.0 35-39 36.503499999999995 37.0 37.0 37.0 37.0 37.0 40-44 36.4456 37.0 37.0 37.0 37.0 37.0 45-49 36.46660000000001 37.0 37.0 37.0 37.0 37.0 50-54 36.4625 37.0 37.0 37.0 37.0 37.0 55-59 36.375600000000006 37.0 37.0 37.0 37.0 37.0 60-64 36.384499999999996 37.0 37.0 37.0 37.0 37.0 65-69 36.3668 37.0 37.0 37.0 37.0 37.0 70-74 36.3702 37.0 37.0 37.0 37.0 37.0 75-79 36.3387 37.0 37.0 37.0 37.0 37.0 80-84 36.3455 37.0 37.0 37.0 37.0 37.0 85-89 36.2915 37.0 37.0 37.0 37.0 37.0 90-94 36.3113 37.0 37.0 37.0 37.0 37.0 95-99 36.2738 37.0 37.0 37.0 37.0 37.0 100-104 36.2884 37.0 37.0 37.0 37.0 37.0 105-109 36.3183 37.0 37.0 37.0 37.0 37.0 110-114 36.2073 37.0 37.0 37.0 37.0 37.0 115-119 36.2112 37.0 37.0 37.0 37.0 37.0 120-124 36.1512 37.0 37.0 37.0 37.0 37.0 125-129 36.0889 37.0 37.0 37.0 37.0 37.0 130-134 36.078500000000005 37.0 37.0 37.0 37.0 37.0 135-139 36.0305 37.0 37.0 37.0 37.0 37.0 140-144 35.8937 37.0 37.0 37.0 37.0 37.0 145-149 35.89640000000001 37.0 37.0 37.0 37.0 37.0 150-151 35.628 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 22 1.0 23 0.0 24 3.0 25 3.0 26 2.0 27 4.0 28 7.0 29 20.0 30 23.0 31 24.0 32 47.0 33 71.0 34 124.0 35 302.0 36 2857.0 37 512.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 53.175 10.174999999999999 4.8500000000000005 31.8 2 21.694318753142284 10.85972850678733 34.13775766716943 33.30819507290095 3 20.45 17.974999999999998 27.375 34.2 4 28.375 21.55 21.275 28.799999999999997 5 27.275 27.1 23.225 22.400000000000002 6 23.825 30.3 22.025 23.849999999999998 7 18.925 25.924999999999997 37.05 18.099999999999998 8 21.7 22.0 29.65 26.650000000000002 9 21.375 20.8 32.75 25.074999999999996 10-14 24.83 25.31 24.92 24.94 15-19 24.18 24.97 25.319999999999997 25.53 20-24 23.73 25.47 24.47 26.33 25-29 24.13 24.759999999999998 24.865000000000002 26.245 30-34 23.925 24.79 24.785 26.5 35-39 23.98 24.755 25.419999999999998 25.845000000000002 40-44 24.14 24.815 24.875 26.169999999999998 45-49 24.22 24.825 24.195 26.76 50-54 24.525 25.22 24.529999999999998 25.724999999999998 55-59 24.37 24.69 24.93 26.009999999999998 60-64 23.935000000000002 25.355 24.48 26.229999999999997 65-69 23.65 25.665 24.22 26.465 70-74 24.5 25.255 24.22 26.025 75-79 25.14 24.4 23.995 26.465 80-84 24.135 24.27 24.825 26.77 85-89 24.805 24.060000000000002 24.82 26.314999999999998 90-94 24.654999999999998 25.4 23.89 26.055 95-99 24.169999999999998 24.895 24.4 26.534999999999997 100-104 24.97 24.535 24.62 25.874999999999996 105-109 25.005 24.89 24.41 25.695 110-114 24.965 24.81 23.945 26.279999999999998 115-119 25.064999999999998 24.075 23.955000000000002 26.905 120-124 25.28 25.615 23.05 26.055 125-129 25.34 24.490000000000002 23.805 26.365 130-134 24.705 24.485 24.08 26.729999999999997 135-139 24.925 24.759999999999998 23.615 26.700000000000003 140-144 24.745 24.45 24.02 26.784999999999997 145-149 24.91 24.27 23.815 27.005000000000003 150-151 25.4875 23.3 24.087500000000002 27.125 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.5 4 1.0 5 0.5 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 0.5 19 1.0 20 0.5 21 0.0 22 0.0 23 0.0 24 0.5 25 0.5 26 1.5 27 1.5 28 2.0 29 3.5 30 5.5 31 11.0 32 13.5 33 19.0 34 27.5 35 34.0 36 48.5 37 66.0 38 87.0 39 99.0 40 103.5 41 116.5 42 140.5 43 157.5 44 185.0 45 218.0 46 194.0 47 163.5 48 163.0 49 163.5 50 153.5 51 136.0 52 130.0 53 131.0 54 117.5 55 113.5 56 103.0 57 73.5 58 63.5 59 70.0 60 69.0 61 60.5 62 62.5 63 61.0 64 56.5 65 66.0 66 61.5 67 54.5 68 55.0 69 60.0 70 62.5 71 48.0 72 41.0 73 35.0 74 24.5 75 17.5 76 12.0 77 10.0 78 10.5 79 6.5 80 2.0 81 0.0 82 1.5 83 1.5 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 0.5499999999999999 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 82.22500000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 83.09516570386135 68.325 2 13.469139556096078 22.15 3 2.5235633931286103 6.225 4 0.5776831863788386 1.9 5 0.30404378230465184 1.25 6 0.030404378230465188 0.15 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 GGCTGCTTCACAGAATAACCGAAGGGAAATAAGTCAAAACAAATTGCACG 6 0.15 No Hit GTGTAAGTACCTGTACAGCCACCAATGTGCTTTCCACCGATGAAAACATT 5 0.125 No Hit GTCCAGTTTTACAAAATGATAGCTACAAGGTGCATCTCCAACATCAACAA 5 0.125 No Hit GGCCTTCCTTGGGGTTGAGCGTGAAGAAGCCGCCCTCGATGCCGGCGACC 5 0.125 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGCTTAACATCGCGTAT 5 0.125 TruSeq Adapter, Index 2 (97% over 37bp) GACCATGTTAGGCTTCAGAAGGGTACCCTCGAGGAGGACATGGTGCTCAT 5 0.125 No Hit GGGCAATGAAGCATTCATGTGGACGAGCTTTCGTAGTGAGTTCAATTGGC 5 0.125 No Hit CCTTCCACGCCCACGGCCGCGTCCACGACCCCGACCCATAGGCTTTCCTG 5 0.125 No Hit CCTGCCTCCTGCCCCTTCCTTTCTTTGATTGCTGTTGTTCTGCCTGTTCC 5 0.125 No Hit CTTGAATTGCTGGAGCAGCAGGTGGGCCACGATAACCACCACCACCAGCT 5 0.125 No Hit CATTCATGTCAGCAGGTTTAATGACAGTCATCGTAATTCCCCTCTTAGGG 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 0.025 0.0 0.0 0.0 0.0 26-27 0.025 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.05 0.0 0.0 0.0 0.0 66-67 0.1 0.0 0.0 0.0 0.0 68-69 0.125 0.0 0.0 0.0 0.0 70-71 0.15 0.0 0.0 0.0 0.0 72-73 0.225 0.0 0.0 0.0 0.0 74-75 0.3 0.0 0.0 0.0 0.0 76-77 0.375 0.0 0.0 0.0 0.0 78-79 0.42500000000000004 0.0 0.0 0.0 0.0 80-81 0.5875 0.0 0.0 0.0 0.0 82-83 0.75 0.0 0.0 0.0 0.0 84-85 0.925 0.0 0.0 0.0 0.0 86-87 1.1749999999999998 0.0 0.0 0.0 0.0 88-89 1.325 0.0 0.0 0.0 0.0 90-91 1.6375000000000002 0.0 0.0 0.0 0.0 92-93 1.85 0.0 0.0 0.0 0.0 94-95 2.15 0.0 0.0 0.0 0.0 96-97 2.425 0.0 0.0 0.0 0.0 98-99 2.8375 0.0 0.0 0.0 0.0 100-101 3.2125000000000004 0.0 0.0 0.0 0.0 102-103 3.625 0.0 0.0 0.0 0.0 104-105 4.0625 0.0 0.0 0.0 0.0 106-107 4.6375 0.0 0.0 0.0 0.0 108-109 5.0875 0.0 0.0 0.0 0.0 110-111 5.6375 0.0 0.0 0.0 0.0 112-113 6.25 0.0 0.0 0.0 0.0 114-115 6.825 0.0 0.0 0.0 0.0 116-117 7.574999999999999 0.0 0.0 0.0 0.0 118-119 8.175 0.0 0.0 0.0 0.0 120-121 8.9875 0.0 0.0 0.0 0.0 122-123 9.850000000000001 0.0 0.0 0.0 0.0 124-125 10.725 0.0 0.0 0.0 0.0 126-127 11.425 0.0 0.0 0.0 0.0 128-129 12.0 0.0 0.0 0.0 0.0 130-131 12.75 0.0 0.0 0.0 0.0 132-133 13.2375 0.0 0.0 0.0 0.0 134-135 13.8375 0.0 0.0 0.0 0.0 136-137 14.7 0.0 0.0 0.0 0.0 138-139 15.4125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GCACCAT 10 0.006830828 145.0 1 >>END_MODULE SRR12951312 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12951312_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 52 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.213 37.0 37.0 37.0 37.0 37.0 2 35.997 37.0 37.0 37.0 37.0 37.0 3 36.0035 37.0 37.0 37.0 37.0 37.0 4 36.0065 37.0 37.0 37.0 37.0 37.0 5 36.1875 37.0 37.0 37.0 37.0 37.0 6 36.2075 37.0 37.0 37.0 37.0 37.0 7 36.152 37.0 37.0 37.0 37.0 37.0 8 36.192 37.0 37.0 37.0 37.0 37.0 9 36.1975 37.0 37.0 37.0 37.0 37.0 10-14 36.1668 37.0 37.0 37.0 37.0 37.0 15-19 36.113099999999996 37.0 37.0 37.0 37.0 37.0 20-24 36.1149 37.0 37.0 37.0 37.0 37.0 25-29 36.026999999999994 37.0 37.0 37.0 37.0 37.0 30-34 36.00410000000001 37.0 37.0 37.0 37.0 37.0 35-39 35.9728 37.0 37.0 37.0 37.0 37.0 40-44 35.9725 37.0 37.0 37.0 37.0 37.0 45-49 35.992999999999995 37.0 37.0 37.0 37.0 37.0 50-54 35.917100000000005 37.0 37.0 37.0 37.0 37.0 55-59 35.848400000000005 37.0 37.0 37.0 37.0 37.0 60-64 35.8405 37.0 37.0 37.0 37.0 37.0 65-69 35.876999999999995 37.0 37.0 37.0 37.0 37.0 70-74 35.805099999999996 37.0 37.0 37.0 37.0 37.0 75-79 35.7601 37.0 37.0 37.0 37.0 37.0 80-84 35.7719 37.0 37.0 37.0 37.0 37.0 85-89 35.753 37.0 37.0 37.0 37.0 37.0 90-94 35.822 37.0 37.0 37.0 37.0 37.0 95-99 35.6832 37.0 37.0 37.0 37.0 37.0 100-104 35.634 37.0 37.0 37.0 37.0 37.0 105-109 35.615700000000004 37.0 37.0 37.0 37.0 37.0 110-114 35.5532 37.0 37.0 37.0 37.0 37.0 115-119 35.57950000000001 37.0 37.0 37.0 37.0 37.0 120-124 35.377599999999994 37.0 37.0 37.0 37.0 37.0 125-129 35.2673 37.0 37.0 37.0 37.0 37.0 130-134 35.0454 37.0 37.0 37.0 32.2 37.0 135-139 34.9485 37.0 37.0 37.0 25.0 37.0 140-144 34.6886 37.0 37.0 37.0 25.0 37.0 145-149 34.41160000000001 37.0 37.0 37.0 25.0 37.0 150-151 34.039249999999996 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 4.0 13 9.0 14 5.0 15 4.0 16 3.0 17 1.0 18 2.0 19 0.0 20 2.0 21 2.0 22 4.0 23 10.0 24 11.0 25 11.0 26 8.0 27 10.0 28 20.0 29 17.0 30 34.0 31 51.0 32 67.0 33 138.0 34 240.0 35 568.0 36 2491.0 37 288.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 48.175000000000004 20.4 6.4 25.025 2 31.025000000000002 20.45 25.15 23.375 3 23.575 24.325 30.225 21.875 4 25.874999999999996 31.1 21.15 21.875 5 28.225 32.525 18.45 20.8 6 24.625 33.525 18.875 22.975 7 24.675 19.2 32.425 23.7 8 23.724999999999998 23.625 24.675 27.975 9 25.474999999999998 22.2 24.825 27.500000000000004 10-14 26.765 24.77 23.185 25.28 15-19 26.415 24.715 23.61 25.259999999999998 20-24 26.8 24.465 23.43 25.305 25-29 26.240000000000002 24.610000000000003 23.65 25.5 30-34 26.715 23.91 23.705000000000002 25.669999999999998 35-39 26.47 25.145 23.555 24.83 40-44 26.195 24.88 23.125 25.8 45-49 26.729999999999997 24.37 23.695 25.205 50-54 26.6 25.1 23.294999999999998 25.005 55-59 26.950000000000003 24.285 23.715 25.05 60-64 27.595 24.0 23.61 24.795 65-69 26.3 24.310000000000002 24.265 25.124999999999996 70-74 26.36 24.490000000000002 23.54 25.61 75-79 26.985 24.005000000000003 23.919999999999998 25.09 80-84 26.745 24.779999999999998 23.59 24.884999999999998 85-89 27.05 24.34 23.705000000000002 24.905 90-94 26.974999999999998 25.05 23.315 24.66 95-99 27.150000000000002 24.545 23.48 24.825 100-104 27.185 24.54 23.47 24.805 105-109 27.42 24.51 23.715 24.355 110-114 28.294999999999998 24.735 23.235 23.735 115-119 27.825 25.03 23.215 23.93 120-124 28.410000000000004 25.39 22.375 23.825 125-129 29.42 25.055 22.57 22.955000000000002 130-134 29.685 24.295 22.685 23.335 135-139 30.509999999999998 24.12 23.04 22.33 140-144 30.04 24.5 22.98 22.48 145-149 31.81 24.3 21.98 21.91 150-151 31.937500000000004 24.1125 23.1 20.849999999999998 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 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 0.0 15 0.5 16 0.5 17 0.5 18 0.5 19 0.0 20 0.5 21 1.0 22 1.0 23 1.0 24 0.5 25 0.0 26 1.0 27 2.0 28 5.0 29 5.0 30 5.5 31 10.0 32 13.0 33 20.0 34 31.0 35 36.5 36 36.5 37 49.5 38 65.5 39 78.0 40 109.0 41 135.5 42 137.5 43 143.0 44 153.0 45 174.5 46 184.5 47 166.0 48 147.5 49 134.5 50 123.0 51 123.5 52 123.0 53 128.5 54 117.5 55 95.0 56 99.0 57 96.5 58 102.5 59 96.0 60 84.0 61 85.0 62 74.5 63 67.0 64 64.5 65 70.5 66 75.5 67 73.5 68 71.5 69 55.5 70 55.5 71 57.0 72 47.5 73 36.5 74 25.5 75 24.5 76 16.5 77 13.0 78 9.0 79 2.0 80 2.0 81 2.5 82 2.0 83 1.5 84 0.5 85 1.0 86 2.5 87 2.0 88 1.5 89 1.0 90 0.0 91 0.5 92 1.0 93 1.0 94 0.5 95 0.0 96 0.5 97 1.5 98 2.5 99 2.0 100 4.0 >>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 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 82.8 #Duplication Level Percentage of deduplicated Percentage of total 1 83.99758454106279 69.55 2 12.590579710144928 20.849999999999998 3 2.5966183574879227 6.45 4 0.5132850241545894 1.7000000000000002 5 0.2717391304347826 1.125 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.030193236714975844 0.325 >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 13 0.325 No Hit AGCAAAGAGGCCACTGTCAACGAGGAAGAAGAAAAGGAAGAAGATAAGGA 5 0.125 No Hit ATTTGCACAAAAACTTGAGGACGCATGTGTCGGAACTGTGGAGTCAGGGA 5 0.125 No Hit CCTGCCGCTCCGGGGCACCATCACGGCCTCCGGCGACCTGGTCCCGCTCT 5 0.125 No Hit GTGGAACAACCCAACAGATCTGTACTATCCCTCTCTGCTCATCCGCGGCG 5 0.125 No Hit CGTATTCCATGGAGGTCAAGGGTCTCTTCAAGCGGATCGGCGTGCAGCCC 5 0.125 No Hit GCGGCGGAGCCCTACCGCGAACCCCCAGATCCGACGAGGCTGCACCCCAC 5 0.125 No Hit GTTATTATTAGTGTTCTTTTGTTATTAGTTTTGTAAATCAAACAGACTTG 5 0.125 No Hit GATTCCGGCCGCCTCCTCTCCTGCTTCTCCTCCTCGACGCCGCCGCCAAG 5 0.125 No Hit GCCATGATGACCTTGGCAAGCGCTGTGCCAAGTACTACGAGGCTGGTGCC 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 0.025 0.0 0.0 0.0 0.0 26-27 0.025 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.05 0.0 0.0 0.0 0.0 66-67 0.1 0.0 0.0 0.0 0.0 68-69 0.125 0.0 0.0 0.0 0.0 70-71 0.15 0.0 0.0 0.0 0.0 72-73 0.225 0.0 0.0 0.0 0.0 74-75 0.3 0.0 0.0 0.0 0.0 76-77 0.375 0.0 0.0 0.0 0.0 78-79 0.42500000000000004 0.0 0.0 0.0 0.0 80-81 0.5875 0.0 0.0 0.0 0.0 82-83 0.75 0.0 0.0 0.0 0.0 84-85 0.925 0.0 0.0 0.0 0.0 86-87 1.1749999999999998 0.0 0.0 0.0 0.0 88-89 1.325 0.0 0.0 0.0 0.0 90-91 1.6375000000000002 0.0 0.0 0.0 0.0 92-93 1.85 0.0 0.0 0.0 0.0 94-95 2.15 0.0 0.0 0.0 0.0 96-97 2.4375 0.0 0.0 0.0 0.0 98-99 2.8625 0.0 0.0 0.0 0.0 100-101 3.2375 0.0 0.0 0.0 0.0 102-103 3.65 0.0 0.0 0.0 0.0 104-105 4.0875 0.0 0.0 0.0 0.0 106-107 4.6625 0.0 0.0 0.0 0.0 108-109 5.1125 0.0 0.0 0.0 0.0 110-111 5.6625 0.0 0.0 0.0 0.0 112-113 6.2875 0.0 0.0 0.0 0.0 114-115 6.887499999999999 0.0 0.0 0.0 0.0 116-117 7.675000000000001 0.0 0.0 0.0 0.0 118-119 8.275 0.0 0.0 0.0 0.0 120-121 9.0625 0.0 0.0 0.0 0.0 122-123 9.925 0.0 0.0 0.0 0.0 124-125 10.8 0.0 0.0 0.0 0.0 126-127 11.4875 0.0 0.0 0.0 0.0 128-129 12.1 0.0 0.0 0.0 0.0 130-131 12.85 0.0 0.0 0.0 0.0 132-133 13.337499999999999 0.0 0.0 0.0 0.0 134-135 14.0 0.0 0.0 0.0 0.0 136-137 14.925 0.0 0.0 0.0 0.0 138-139 15.6125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AGAGTTG 10 0.006830828 145.0 5 >>END_MODULE Read 1795923 spots for SRR12951312.sra Written 1795923 spots for SRR12951312.sra Read 1795923 spots for SRR12951312.sra Written 1795923 spots for SRR12951312.sra Read 1795923 spots for SRR12951312.sra Written 1795923 spots for SRR12951312.sra Read 1795923 spots for SRR12951312.sra Written 1795923 spots for SRR12951312.sra Read 1795923 spots for SRR12951312.sra Written 1795923 spots for SRR12951312.sra Read 1795923 spots for SRR12951312.sra Written 1795923 spots for SRR12951312.sra Read 1795923 spots for SRR12951312.sra Written 1795923 spots for SRR12951312.sra Read 1795923 spots for SRR12951312.sra Written 1795923 spots for SRR12951312.sra Read 1795923 spots for SRR12951312.sra Written 1795923 spots for SRR12951312.sra Read 1795923 spots for SRR12951312.sra Written 1795923 spots for SRR12951312.sra Read 1795923 spots for SRR12951312.sra Written 1795923 spots for SRR12951312.sra Read 1795942 spots for SRR12951312.sra Written 1795942 spots for SRR12951312.sra Read 1795923 spots for SRR12951312.sra Written 1795923 spots for SRR12951312.sra Read 1795923 spots for SRR12951312.sra Written 1795923 spots for SRR12951312.sra Read 1795923 spots for SRR12951312.sra Written 1795923 spots for SRR12951312.sra Read 1795923 spots for SRR12951312.sra Written 1795923 spots for SRR12951312.sra Read 1795923 spots for SRR12951312.sra Written 1795923 spots for SRR12951312.sra Read 1795923 spots for SRR12951312.sra Written 1795923 spots for SRR12951312.sra Read 1795923 spots for SRR12951312.sra Written 1795923 spots for SRR12951312.sra Read 1795923 spots for SRR12951312.sra Written 1795923 spots for SRR12951312.sra SRR ids: ['SRR12951312.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_2lhy2koa SRR12951312.sra spots: 35918479 blocks: [[1, 1795923], [1795924, 3591846], [3591847, 5387769], [5387770, 7183692], [7183693, 8979615], [8979616, 10775538], [10775539, 12571461], [12571462, 14367384], [14367385, 16163307], [16163308, 17959230], [17959231, 19755153], [19755154, 21551076], [21551077, 23346999], [23347000, 25142922], [25142923, 26938845], [26938846, 28734768], [28734769, 30530691], [30530692, 32326614], [32326615, 34122537], [34122538, 35918479]] SRR12951312 file size 12184970 SRR12951312 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 SRR12951312 SRR12951312_1.fastq SRR12951312_2.fastq Input file: SRR12951312_1.fastq Paired file: SRR12951312_2.fastq trimmed: SRR12951312-trimmed-pair1.fastq, SRR12951312-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 11:29:06 2024 >> started Sat Dec 7 11:29:48 2024 >> done (42.429s) 35918479 read pairs processed; of these: 208 ( 0.00%) short read pairs filtered out after trimming by size control 96655 ( 0.27%) empty read pairs filtered out after trimming by size control 35821616 (99.73%) read pairs available; of these: 6310337 (17.62%) trimmed read pairs available after processing 29511279 (82.38%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 21 0.00% 19 17 0.00% 20 18 0.00% 21 25 0.00% 22 43 0.00% 23 47 0.00% 24 68 0.00% 25 59 0.00% 26 79 0.00% 27 78 0.00% 28 89 0.00% 29 88 0.00% 30 96 0.00% 31 89 0.00% 32 113 0.00% 33 109 0.00% 34 107 0.00% 35 114 0.00% 36 128 0.00% 37 114 0.00% 38 172 0.00% 39 143 0.00% 40 185 0.00% 41 194 0.00% 42 188 0.00% 43 246 0.00% 44 227 0.00% 45 256 0.00% 46 321 0.00% 47 344 0.00% 48 421 0.00% 49 449 0.00% 50 538 0.00% 51 628 0.00% 52 676 0.00% 53 686 0.00% 54 791 0.00% 55 862 0.00% 56 1046 0.00% 57 1146 0.00% 58 1267 0.00% 59 1624 0.00% 60 1870 0.01% 61 2139 0.01% 62 2399 0.01% 63 2658 0.01% 64 2819 0.01% 65 3070 0.01% 66 3449 0.01% 67 3709 0.01% 68 4469 0.01% 69 5417 0.02% 70 6247 0.02% 71 6816 0.02% 72 7853 0.02% 73 8665 0.02% 74 9457 0.03% 75 10501 0.03% 76 11166 0.03% 77 12040 0.03% 78 13637 0.04% 79 15116 0.04% 80 16746 0.05% 81 19278 0.05% 82 21498 0.06% 83 23424 0.07% 84 25897 0.07% 85 27338 0.08% 86 28659 0.08% 87 30680 0.09% 88 32179 0.09% 89 33833 0.09% 90 37064 0.10% 91 39843 0.11% 92 42728 0.12% 93 46616 0.13% 94 48985 0.14% 95 51267 0.14% 96 53279 0.15% 97 54149 0.15% 98 55748 0.16% 99 57592 0.16% 100 59525 0.17% 101 62469 0.17% 102 65821 0.18% 103 70228 0.20% 104 72357 0.20% 105 75983 0.21% 106 76998 0.21% 107 77416 0.22% 108 79663 0.22% 109 80280 0.22% 110 81848 0.23% 111 85103 0.24% 112 88182 0.25% 113 89667 0.25% 114 95266 0.27% 115 97360 0.27% 116 97795 0.27% 117 98667 0.28% 118 98928 0.28% 119 99818 0.28% 120 101862 0.28% 121 103324 0.29% 122 103813 0.29% 123 108192 0.30% 124 111785 0.31% 125 112842 0.32% 126 115558 0.32% 127 115069 0.32% 128 114737 0.32% 129 117355 0.33% 130 116383 0.32% 131 116246 0.32% 132 118864 0.33% 133 120380 0.34% 134 123115 0.34% 135 125562 0.35% 136 126308 0.35% 137 126391 0.35% 138 127345 0.36% 139 127055 0.35% 140 125724 0.35% 141 127259 0.36% 142 127725 0.36% 143 128808 0.36% 144 129445 0.36% 145 131917 0.37% 146 131664 0.37% 147 132947 0.37% 148 132317 0.37% 149 130675 0.36% 150 132084 0.37% 151 29511279 82.38% 35821616 reads passed initial QC criterion=sequence-density sequence-density=0.21 sequence-density-rank=1 fanout-score=2.91 fanout-score-rank=40 prefix-density=0.25 prefix-fanout=2.4 sequence=GAACCGGAACCG criterion=fanout-score sequence-density=0.03 sequence-density-rank=33 fanout-score=418.71 fanout-score-rank=1 prefix-density=0.77 prefix-fanout=16.2 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.91 sequence-density-rank=1 fanout-score=2.04 fanout-score-rank=35 prefix-density=0.92 prefix-fanout=2.0 sequence=CGGTTCCGGTTC criterion=fanout-score sequence-density=0.10 sequence-density-rank=21 fanout-score=230.68 fanout-score-rank=1 prefix-density=1.02 prefix-fanout=23.3 sequence=CGCCGCCGCCGG SRR12951312 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 11:30:36 Started mapping on | Dec 07 11:30:36 Finished on | Dec 07 11:33:38 Mapping speed, Million of reads per hour | 708.56 Number of input reads | 35821616 Average input read length | 291 UNIQUE READS: Uniquely mapped reads number | 33664638 Uniquely mapped reads % | 93.98% Average mapped length | 290.44 Number of splices: Total | 30432655 Number of splices: Annotated (sjdb) | 28128248 Number of splices: GT/AG | 29941712 Number of splices: GC/AG | 403900 Number of splices: AT/AC | 17772 Number of splices: Non-canonical | 69271 Mismatch rate per base, % | 0.25% Deletion rate per base | 0.01% Deletion average length | 2.29 Insertion rate per base | 0.01% Insertion average length | 2.41 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 357969 % of reads mapped to multiple loci | 1.00% Number of reads mapped to too many loci | 59111 % of reads mapped to too many loci | 0.17% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.04% % of reads unmapped: other | 0.81% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1799009 1799009 1799009 N_multimapping 357969 357969 357969 N_noFeature 1644740 32625063 2034565 N_ambiguous 766984 4707 117349 UnstrandedReadsAssigned:31252914 PositiveStrandReadsAssigned:1034868 NegativeStrandReadsAssigned:31512724 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12951312 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: SRR12951312-trimmed-pair1.fastq SRR12951312-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 35,821,616 reads, 32,000,954 reads pseudoaligned [quant] estimated average fragment length: 252.652 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,206 rounds 52973 SRR12951312.ke.tsv 35125 SRR12951312.se.tsv 88098 total ==> SRR12951312.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 684.978 0 0 PNS24247 1044 792.348 174.124 9.83577 PNS24249 1928 1676.35 500.352 13.3591 PNS24246 1044 792.348 174.124 9.83577 PNS24248 1044 792.348 174.124 9.83577 PNS24244 1471 1219.35 297.278 10.9119 PNS24243 293 110.59 2 0.809433 KQK14069 1603 1351.35 92801.5 3073.65 KQK14071 474 249.24 475.227 85.3393 ==> SRR12951312.se.tsv <== BRADI_1g14170v3 94318 BRADI_1g53295v3 285 BRADI_1g59795v3 1205 BRADI_1g07683v3 0 BRADI_1g00485v3 33 BRADI_1g20270v3 532 BRADI_1g74790v3 2719 BRADI_1g09890v3 0 BRADI_1g77505v3 321 BRADI_1g48960v3 0 SRR12951312 completed mapping pipeline successfully