Starting /dee2/code/volunteer_pipeline.sh SRR12670178 current disk space = 3055708598272 free memory = 1263602768 SRR12670178 SRAfilesize 2afb3bfbd4fe87fdd3169a4b32dab3df SRR12670178.sra SRR12670178.sra file validated SRR12670178 is paired end SRR12670178 is conventional basespace SRR12670178 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670178_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 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.6125 37.0 37.0 37.0 37.0 37.0 2 36.49775 37.0 37.0 37.0 37.0 37.0 3 36.6315 37.0 37.0 37.0 37.0 37.0 4 36.719 37.0 37.0 37.0 37.0 37.0 5 36.721 37.0 37.0 37.0 37.0 37.0 6 36.6775 37.0 37.0 37.0 37.0 37.0 7 36.5735 37.0 37.0 37.0 37.0 37.0 8 36.6785 37.0 37.0 37.0 37.0 37.0 9 36.6035 37.0 37.0 37.0 37.0 37.0 10-14 36.6471 37.0 37.0 37.0 37.0 37.0 15-19 36.591699999999996 37.0 37.0 37.0 37.0 37.0 20-24 36.5496 37.0 37.0 37.0 37.0 37.0 25-29 36.4868 37.0 37.0 37.0 37.0 37.0 30-34 36.533300000000004 37.0 37.0 37.0 37.0 37.0 35-39 36.5313 37.0 37.0 37.0 37.0 37.0 40-44 36.469500000000004 37.0 37.0 37.0 37.0 37.0 45-49 36.4402 37.0 37.0 37.0 37.0 37.0 50-54 36.46470000000001 37.0 37.0 37.0 37.0 37.0 55-59 36.427800000000005 37.0 37.0 37.0 37.0 37.0 60-64 36.418800000000005 37.0 37.0 37.0 37.0 37.0 65-69 36.3437 37.0 37.0 37.0 37.0 37.0 70-74 36.3465 37.0 37.0 37.0 37.0 37.0 75-79 36.348299999999995 37.0 37.0 37.0 37.0 37.0 80-84 36.2992 37.0 37.0 37.0 37.0 37.0 85-89 36.3236 37.0 37.0 37.0 37.0 37.0 90-94 36.3449 37.0 37.0 37.0 37.0 37.0 95-99 36.295500000000004 37.0 37.0 37.0 37.0 37.0 100-104 36.294799999999995 37.0 37.0 37.0 37.0 37.0 105-109 36.2639 37.0 37.0 37.0 37.0 37.0 110-114 36.1666 37.0 37.0 37.0 37.0 37.0 115-119 36.192 37.0 37.0 37.0 37.0 37.0 120-124 36.1197 37.0 37.0 37.0 37.0 37.0 125-129 35.9894 37.0 37.0 37.0 37.0 37.0 130-134 36.010000000000005 37.0 37.0 37.0 37.0 37.0 135-139 35.8888 37.0 37.0 37.0 37.0 37.0 140-144 35.693200000000004 37.0 37.0 37.0 37.0 37.0 145-149 35.6768 37.0 37.0 37.0 37.0 37.0 150-151 35.41025 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 1.0 22 0.0 23 1.0 24 4.0 25 3.0 26 8.0 27 4.0 28 15.0 29 18.0 30 22.0 31 22.0 32 32.0 33 69.0 34 102.0 35 300.0 36 2967.0 37 432.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 36.975 11.1 6.875000000000001 45.050000000000004 2 19.99498872463042 12.427962916562265 36.03106990729141 31.54597845151591 3 17.95 16.325 27.400000000000002 38.324999999999996 4 21.55 23.549999999999997 25.074999999999996 29.825000000000003 5 25.15 30.0 23.5 21.349999999999998 6 20.875 31.0 26.450000000000003 21.675 7 16.375 27.150000000000002 39.300000000000004 17.175 8 20.1 25.624999999999996 31.075000000000003 23.200000000000003 9 17.875 24.5 35.199999999999996 22.425 10-14 20.119999999999997 28.355000000000004 28.410000000000004 23.115 15-19 19.555 26.85 28.915000000000003 24.68 20-24 20.895 28.01 28.285 22.81 25-29 20.45 28.299999999999997 27.405 23.845 30-34 20.365 28.560000000000002 26.985 24.09 35-39 20.375 27.73 27.99 23.905 40-44 21.099999999999998 27.815 28.205000000000002 22.88 45-49 20.560000000000002 28.005000000000003 27.889999999999997 23.544999999999998 50-54 21.305 28.03 27.235 23.43 55-59 21.095 27.435 28.035 23.435 60-64 20.615 27.235 28.215 23.935000000000002 65-69 20.64 27.48 28.125 23.755000000000003 70-74 20.979999999999997 28.199999999999996 27.145000000000003 23.674999999999997 75-79 20.995 27.529999999999998 28.075 23.400000000000002 80-84 21.060000000000002 28.815 27.215 22.91 85-89 21.385 28.775000000000002 27.27 22.57 90-94 21.715 27.800000000000004 27.544999999999998 22.939999999999998 95-99 21.834999999999997 28.82 26.284999999999997 23.06 100-104 21.455 28.99 26.02 23.535 105-109 22.09 28.54 26.415 22.955000000000002 110-114 21.32 28.249999999999996 26.52 23.91 115-119 21.85 29.395 25.430000000000003 23.325000000000003 120-124 21.634999999999998 28.285 25.75 24.33 125-129 21.92 27.639999999999997 26.235000000000003 24.205 130-134 22.185 27.345000000000002 26.029999999999998 24.44 135-139 22.2 28.065 26.055 23.68 140-144 22.11 26.915 26.26 24.715 145-149 22.75 26.584999999999997 26.255 24.41 150-151 22.5 25.7375 26.2125 25.55 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.5 4 0.5 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.5 13 0.5 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 1.0 21 1.0 22 0.5 23 0.5 24 0.0 25 4.0 26 5.0 27 5.5 28 9.0 29 9.5 30 12.0 31 15.0 32 19.0 33 19.5 34 29.5 35 60.5 36 84.0 37 109.0 38 129.5 39 135.5 40 171.5 41 222.5 42 252.5 43 241.0 44 237.0 45 274.0 46 276.0 47 256.0 48 250.0 49 231.5 50 196.0 51 165.0 52 133.0 53 109.0 54 86.5 55 59.0 56 44.5 57 30.5 58 28.5 59 32.0 60 23.0 61 9.5 62 4.0 63 2.5 64 1.0 65 3.0 66 5.0 67 3.0 68 1.0 69 0.5 70 0.0 71 0.0 72 0.0 73 0.0 74 0.0 75 0.0 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.22499999999999998 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 78.45 #Duplication Level Percentage of deduplicated Percentage of total 1 80.05098789037604 62.8 2 14.531548757170173 22.8 3 3.9196940726577436 9.225 4 0.9560229445506693 3.0 5 0.47801147227533464 1.875 6 0.06373486297004462 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 CTCCCTTAAGGACGTTGTTGTGGATATCAGCTTTTTCTTTCTCAATCTCT 6 0.15 No Hit GTGTAAGAGTTGTGATCCGTTTCGGGGTCGTTGGAAGGGTGGATTTTGGC 6 0.15 No Hit GAACCCTTTCGATTTCCCTGTTTGCTTATCAAAACCTAACGGACCCTCCT 5 0.125 No Hit CCTTGTCATCCAAAGCATCTCTAAGGGCAGATGTTGCTTTTTCCCATATA 5 0.125 No Hit CTGGAAGGAAAACATTATTTCAGTGTTTCTGGAAGCGAATGACAGAAAAA 5 0.125 No Hit CCTGCATGCATTGAACTCTTCCGCCATTGCTTGCAATGGAAGTAATGTCA 5 0.125 No Hit GAATCGTTGAGTTTACTCAGGGAATCATCAAACTGACTCACACAATCTTT 5 0.125 No Hit GCACACCACAGGAGAAGACGAAGAAGAAGCAGAGAAAGACACTGACTTTG 5 0.125 No Hit CTCCTGTGGCCATGGTCATAACATTGCGAGCTATCTTTCGGCAGTAAGCA 5 0.125 No Hit GAGTAAATATGGTTGTTCGTGGTGGTGGTGAGTGTTGTTCAAAGGAGAGC 5 0.125 No Hit CCCATCTATAGGCACTCCTGGGGCCATGTTAATGAGGATTTATTTAAGCT 5 0.125 No Hit GTAAAAAATCCTCTTTCTGATGCCAAACAGGCAAATTCTTCCTCTTCTCT 5 0.125 No Hit CTGGCATTTCCAGCTAATATCTCAAGTTTATATATTTGATGCTTTTCCTT 5 0.125 No Hit CTGCACTTGACGAGTGTTGTCGAATCCAATGATACGGATAAAGGAGTTAG 5 0.125 No Hit CCCCTCTGCAGTGAATGAGTTCGGACTCCTTGTATCTCTCCAGATTCTCA 5 0.125 No Hit GGATGCTCACTGCCAAGAGGCACATTTCCCACCATTACAGTACGTGTTTT 5 0.125 No Hit GTCCGTTTAGGACAGCTCCAGCGGTAGCAGCCATCTCTCTGGTTCAAGAA 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 0.0 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 0.0125 0.0 0.0 0.0 0.0 56-57 0.05 0.0 0.0 0.0 0.0 58-59 0.0875 0.0 0.0 0.0 0.0 60-61 0.1 0.0 0.0 0.0 0.0 62-63 0.1 0.0 0.0 0.0 0.0 64-65 0.15 0.0 0.0 0.0 0.0 66-67 0.275 0.0 0.0 0.0 0.0 68-69 0.2875 0.0 0.0 0.0 0.0 70-71 0.4125 0.0 0.0 0.0 0.0 72-73 0.5375 0.0 0.0 0.0 0.0 74-75 0.7250000000000001 0.0 0.0 0.0 0.0 76-77 0.95 0.0 0.0 0.0 0.0 78-79 1.1 0.0 0.0 0.0 0.0 80-81 1.4 0.0 0.0 0.0 0.0 82-83 1.6875 0.0 0.0 0.0 0.0 84-85 2.075 0.0 0.0 0.0 0.0 86-87 2.5375 0.0 0.0 0.0 0.0 88-89 3.125 0.0 0.0 0.0 0.0 90-91 3.725 0.0 0.0 0.0 0.0 92-93 4.175000000000001 0.0 0.0 0.0 0.0 94-95 5.0625 0.0 0.0 0.0 0.0 96-97 5.85 0.0 0.0 0.0 0.0 98-99 6.9375 0.0 0.0 0.0 0.0 100-101 7.737500000000001 0.0 0.0 0.0 0.0 102-103 8.6 0.0 0.0 0.0 0.0 104-105 9.2625 0.0 0.0 0.0 0.0 106-107 10.075 0.0 0.0 0.0 0.0 108-109 11.275 0.0 0.0 0.0 0.0 110-111 12.287500000000001 0.0 0.0 0.0 0.0 112-113 13.3625 0.0 0.0 0.0 0.0 114-115 14.1625 0.0 0.0 0.0 0.0 116-117 15.337499999999999 0.0 0.0 0.0 0.0 118-119 16.3125 0.0 0.0 0.0 0.0 120-121 17.1125 0.0 0.0 0.0 0.0 122-123 18.2875 0.0 0.0 0.0 0.0 124-125 19.2875 0.0 0.0 0.0 0.0 126-127 20.425 0.0 0.0 0.0 0.0 128-129 21.55 0.0 0.0 0.0 0.0 130-131 22.475 0.0 0.0 0.0 0.0 132-133 23.6 0.0 0.0 0.0 0.0 134-135 24.725 0.0 0.0 0.0 0.0 136-137 25.8375 0.0 0.0 0.0 0.0 138-139 26.7125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CCAATTT 10 0.006830828 145.0 2 TTCATGC 10 0.006830828 145.0 7 CCCAATT 10 0.006830828 145.0 1 TCATGCA 10 0.006830828 145.0 8 CATGCAG 10 0.006830828 145.0 9 >>END_MODULE SRR12670178 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670178_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 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.384 37.0 37.0 37.0 37.0 37.0 2 36.402 37.0 37.0 37.0 37.0 37.0 3 36.2675 37.0 37.0 37.0 37.0 37.0 4 36.2985 37.0 37.0 37.0 37.0 37.0 5 36.3465 37.0 37.0 37.0 37.0 37.0 6 36.4245 37.0 37.0 37.0 37.0 37.0 7 36.43 37.0 37.0 37.0 37.0 37.0 8 36.473 37.0 37.0 37.0 37.0 37.0 9 36.467 37.0 37.0 37.0 37.0 37.0 10-14 36.4091 37.0 37.0 37.0 37.0 37.0 15-19 36.4735 37.0 37.0 37.0 37.0 37.0 20-24 36.3797 37.0 37.0 37.0 37.0 37.0 25-29 36.330400000000004 37.0 37.0 37.0 37.0 37.0 30-34 36.3113 37.0 37.0 37.0 37.0 37.0 35-39 36.264199999999995 37.0 37.0 37.0 37.0 37.0 40-44 36.259699999999995 37.0 37.0 37.0 37.0 37.0 45-49 36.251400000000004 37.0 37.0 37.0 37.0 37.0 50-54 36.201499999999996 37.0 37.0 37.0 37.0 37.0 55-59 36.1981 37.0 37.0 37.0 37.0 37.0 60-64 36.1345 37.0 37.0 37.0 37.0 37.0 65-69 36.1441 37.0 37.0 37.0 37.0 37.0 70-74 36.1097 37.0 37.0 37.0 37.0 37.0 75-79 36.0646 37.0 37.0 37.0 37.0 37.0 80-84 36.0446 37.0 37.0 37.0 37.0 37.0 85-89 36.0668 37.0 37.0 37.0 37.0 37.0 90-94 36.0786 37.0 37.0 37.0 37.0 37.0 95-99 36.08409999999999 37.0 37.0 37.0 37.0 37.0 100-104 35.9045 37.0 37.0 37.0 37.0 37.0 105-109 35.86280000000001 37.0 37.0 37.0 37.0 37.0 110-114 35.789300000000004 37.0 37.0 37.0 37.0 37.0 115-119 35.704899999999995 37.0 37.0 37.0 37.0 37.0 120-124 35.478699999999996 37.0 37.0 37.0 37.0 37.0 125-129 35.254000000000005 37.0 37.0 37.0 37.0 37.0 130-134 34.8425 37.0 37.0 37.0 27.4 37.0 135-139 34.5261 37.0 37.0 37.0 25.0 37.0 140-144 34.2034 37.0 37.0 37.0 25.0 37.0 145-149 33.8 37.0 37.0 37.0 25.0 37.0 150-151 33.56375 37.0 37.0 37.0 18.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 1.0 14 3.0 15 0.0 16 1.0 17 1.0 18 0.0 19 3.0 20 4.0 21 2.0 22 4.0 23 3.0 24 5.0 25 7.0 26 6.0 27 8.0 28 9.0 29 16.0 30 33.0 31 50.0 32 78.0 33 176.0 34 235.0 35 579.0 36 2474.0 37 302.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 37.125 20.625 11.975 30.275000000000002 2 26.900000000000002 25.525 31.15 16.425 3 19.650000000000002 28.499999999999996 32.025 19.825 4 23.525 33.825 23.5 19.15 5 25.224999999999998 35.449999999999996 21.95 17.375 6 21.025 37.724999999999994 22.900000000000002 18.35 7 20.150000000000002 23.65 38.875 17.325 8 21.099999999999998 24.474999999999998 27.975 26.450000000000003 9 20.575 24.425 30.475 24.525 10-14 22.865 29.054999999999996 26.795 21.285 15-19 23.085 28.194999999999997 27.474999999999998 21.245 20-24 22.66 27.805000000000003 27.855 21.68 25-29 22.89 28.189999999999998 27.74 21.18 30-34 22.09 28.62 28.065 21.224999999999998 35-39 22.435 28.28 27.560000000000002 21.725 40-44 23.115 28.355000000000004 27.025 21.505 45-49 22.495 27.834999999999997 28.395 21.275 50-54 23.0 27.800000000000004 27.515 21.685 55-59 23.119999999999997 27.54 28.205000000000002 21.135 60-64 23.1 27.83 27.24 21.83 65-69 23.275000000000002 27.800000000000004 27.655 21.27 70-74 23.369999999999997 27.794999999999998 27.37 21.465 75-79 23.365 28.375 27.055 21.205 80-84 23.61 28.15 27.084999999999997 21.154999999999998 85-89 24.38 28.275 26.284999999999997 21.060000000000002 90-94 24.205 28.215 26.47 21.11 95-99 24.495 29.020000000000003 26.255 20.23 100-104 24.740000000000002 28.535 26.085 20.64 105-109 25.629999999999995 27.889999999999997 25.665 20.815 110-114 25.755 27.91 26.58 19.755 115-119 27.1 28.225 25.759999999999998 18.915000000000003 120-124 27.195000000000004 28.410000000000004 25.14 19.255 125-129 27.98 27.589999999999996 25.974999999999998 18.455 130-134 28.875 27.245 25.545 18.335 135-139 30.345 26.724999999999998 25.46 17.47 140-144 30.825000000000003 26.86 25.0 17.315 145-149 31.97 25.369999999999997 25.085 17.575 150-151 34.175 25.05 24.625 16.150000000000002 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.0 2 0.5 3 0.5 4 0.0 5 0.5 6 1.0 7 0.5 8 0.0 9 0.0 10 0.0 11 0.5 12 0.5 13 1.0 14 1.0 15 1.0 16 1.5 17 1.0 18 0.5 19 0.0 20 0.0 21 0.5 22 0.5 23 1.0 24 1.5 25 1.0 26 2.0 27 2.5 28 3.0 29 7.5 30 9.0 31 9.0 32 15.5 33 31.5 34 44.0 35 59.5 36 89.5 37 100.0 38 126.5 39 177.0 40 198.5 41 207.5 42 238.0 43 243.5 44 268.5 45 292.0 46 267.0 47 270.0 48 254.5 49 213.5 50 172.0 51 146.0 52 126.5 53 96.0 54 87.0 55 71.0 56 40.0 57 29.0 58 24.0 59 19.5 60 14.0 61 7.0 62 3.5 63 5.0 64 5.5 65 1.5 66 0.5 67 0.0 68 0.5 69 0.5 70 0.0 71 0.0 72 0.0 73 0.0 74 0.0 75 0.0 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.5 88 0.5 89 0.0 90 0.5 91 0.5 92 0.5 93 1.0 94 1.5 95 1.0 96 0.0 97 0.0 98 0.5 99 0.5 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 77.9 #Duplication Level Percentage of deduplicated Percentage of total 1 79.78177150192555 62.150000000000006 2 14.505776636713735 22.6 3 4.07573812580231 9.525 4 0.9627727856225932 3.0 5 0.5776636713735559 2.25 6 0.06418485237483953 0.3 7 0.03209242618741977 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 CAGAGAACACATTCATACCCCAAGTCTTTTAGTTCATCCATTTAAGCTTA 7 0.17500000000000002 No Hit GTAGCCTAACGTCTTATGGACTAGGGATTTCATGCACCTACAATGTCATG 6 0.15 No Hit CATTCTCTCCCTCTCCCCACTCCAACTGCAAAAAGAAACACATTCATGGC 6 0.15 No Hit TAAATCGGTGGAACGGGAAGCCTTACTCTCAGAGATACTACGAGATATTA 5 0.125 No Hit CACAATGGAGCGCTTTGCTCTGCTCGCTCTACTCCTTCTTACACTCATAA 5 0.125 No Hit TGTTTTATGATTGTGAAGGTAGGTGGAAATGGCTACTGGGGCAGTACCGG 5 0.125 No Hit GCAAAAATGGCAGCCACTACCATGATGACTGCTACTGCTCTCCCACAATT 5 0.125 No Hit CATATTTTGTTATACAAAAGAAAGCTCAACTCTTATCGTGATTTCCCAAT 5 0.125 No Hit GGTTCCTGCTGCAGAATTCACCAAGGAGAATGGTGTTATGTGGGTATCAT 5 0.125 No Hit GTAGCAGCTGCTTGTGCTTATCTGCAGAATAATACCCCTCTGATCGCTTC 5 0.125 No Hit AGAAGTGCCAGTTCAATATGGTGGACTAAGCAAGGATGGCGAATTCACAG 5 0.125 No Hit AGAGAACACATTCATACCCCAAGTCTTTTAGTTCATCCATTTAAGCTTAA 5 0.125 No Hit GACGTGACTCTGTATCCATCCTCCTGCTTCACAAGCATATCCTCTCTTAA 5 0.125 No Hit GATCAACTCTCTGAGGATCTAAATGTCAAAATGCCAGAGGGCCATCAGTA 5 0.125 No Hit GCTAACTGGATGCCAGGCCAGCCTCGTCCACCTTACCTCGATGGCTCAGC 5 0.125 No Hit AGTGGCCATATTTTATCTCTCTATCCATCTAGACTCCACTGCATGAGATG 5 0.125 No Hit GTAGAATTCTCGCGGGACAAACAGTACAGGGACCTCAAGGGATTCGCTAC 5 0.125 No Hit AAAAAATCTTAACTGCACCCGCTCATCCAGCAATGGCAGCAGCAACAATG 5 0.125 No Hit CAGACTTCTTGTTCTCTCCCTCCCTTACCCAAAAAATGGCGTCCTCCTCG 5 0.125 No Hit GTGCGTTATTGGCTTTGAAAGAGCCCAGTAAGAAAATTGATGGGCGCGTG 5 0.125 No Hit GAAACAACCTCGCTCAGGAGGCGCCGCTACTTCCATCTAAGCTTGCATAG 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 0.0 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 0.0125 0.0 0.0 0.0 0.0 56-57 0.05 0.0 0.0 0.0 0.0 58-59 0.0875 0.0 0.0 0.0 0.0 60-61 0.1 0.0 0.0 0.0 0.0 62-63 0.1 0.0 0.0 0.0 0.0 64-65 0.15 0.0 0.0 0.0 0.0 66-67 0.275 0.0 0.0 0.0 0.0 68-69 0.2875 0.0 0.0 0.0 0.0 70-71 0.4125 0.0 0.0 0.0 0.0 72-73 0.5125 0.0 0.0 0.0 0.0 74-75 0.7 0.0 0.0 0.0 0.0 76-77 0.925 0.0 0.0 0.0 0.0 78-79 1.075 0.0 0.0 0.0 0.0 80-81 1.375 0.0 0.0 0.0 0.0 82-83 1.6625 0.0 0.0 0.0 0.0 84-85 2.05 0.0 0.0 0.0 0.0 86-87 2.5125 0.0 0.0 0.0 0.0 88-89 3.0999999999999996 0.0 0.0 0.0 0.0 90-91 3.7249999999999996 0.0 0.0 0.0 0.0 92-93 4.175000000000001 0.0 0.0 0.0 0.0 94-95 5.0875 0.0 0.0 0.0 0.0 96-97 5.875 0.0 0.0 0.0 0.0 98-99 6.9625 0.0 0.0 0.0 0.0 100-101 7.762499999999999 0.0 0.0 0.0 0.0 102-103 8.662500000000001 0.0 0.0 0.0 0.0 104-105 9.3875 0.0 0.0 0.0 0.0 106-107 10.2 0.0 0.0 0.0 0.0 108-109 11.4125 0.0 0.0 0.0 0.0 110-111 12.425 0.0 0.0 0.0 0.0 112-113 13.5 0.0 0.0 0.0 0.0 114-115 14.3125 0.0 0.0 0.0 0.0 116-117 15.4875 0.0 0.0 0.0 0.0 118-119 16.4625 0.0 0.0 0.0 0.0 120-121 17.3125 0.0 0.0 0.0 0.0 122-123 18.4875 0.0 0.0 0.0 0.0 124-125 19.5375 0.0 0.0 0.0 0.0 126-127 20.65 0.0 0.0 0.0 0.0 128-129 21.75 0.0 0.0 0.0 0.0 130-131 22.7 0.0 0.0 0.0 0.0 132-133 23.85 0.0 0.0 0.0 0.0 134-135 24.975 0.0 0.0 0.0 0.0 136-137 26.0875 0.0 0.0 0.0 0.0 138-139 26.9625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GAGGAGC 10 0.006830828 145.0 3 GAGCATT 10 0.006830828 145.0 6 GGAGCAT 10 0.006830828 145.0 5 AGGAGCA 10 0.006830828 145.0 4 AGAGGAG 25 8.7132835E-4 87.0 2 >>END_MODULE Read 818178 spots for SRR12670178.sra Written 818178 spots for SRR12670178.sra Read 818178 spots for SRR12670178.sra Written 818178 spots for SRR12670178.sra Read 818178 spots for SRR12670178.sra Written 818178 spots for SRR12670178.sra Read 818178 spots for SRR12670178.sra Written 818178 spots for SRR12670178.sra Read 818178 spots for SRR12670178.sra Written 818178 spots for SRR12670178.sra Read 818178 spots for SRR12670178.sra Written 818178 spots for SRR12670178.sra Read 818178 spots for SRR12670178.sra Written 818178 spots for SRR12670178.sra Read 818178 spots for SRR12670178.sra Written 818178 spots for SRR12670178.sra Read 818178 spots for SRR12670178.sra Written 818178 spots for SRR12670178.sra Read 818178 spots for SRR12670178.sra Written 818178 spots for SRR12670178.sra Read 818178 spots for SRR12670178.sra Written 818178 spots for SRR12670178.sra Read 818178 spots for SRR12670178.sra Written 818178 spots for SRR12670178.sra Read 818178 spots for SRR12670178.sra Written 818178 spots for SRR12670178.sra Read 818178 spots for SRR12670178.sra Written 818178 spots for SRR12670178.sra Read 818178 spots for SRR12670178.sra Written 818178 spots for SRR12670178.sra Read 818178 spots for SRR12670178.sra Written 818178 spots for SRR12670178.sra Read 818178 spots for SRR12670178.sra Written 818178 spots for SRR12670178.sra Read 818178 spots for SRR12670178.sra Written 818178 spots for SRR12670178.sra Read 818178 spots for SRR12670178.sra Written 818178 spots for SRR12670178.sra Read 818190 spots for SRR12670178.sra Written 818190 spots for SRR12670178.sra SRR ids: ['SRR12670178.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_n2g_7wjb SRR12670178.sra spots: 16363572 blocks: [[1, 818178], [818179, 1636356], [1636357, 2454534], [2454535, 3272712], [3272713, 4090890], [4090891, 4909068], [4909069, 5727246], [5727247, 6545424], [6545425, 7363602], [7363603, 8181780], [8181781, 8999958], [8999959, 9818136], [9818137, 10636314], [10636315, 11454492], [11454493, 12272670], [12272671, 13090848], [13090849, 13909026], [13909027, 14727204], [14727205, 15545382], [15545383, 16363572]] SRR12670178 file size 5539357 SRR12670178 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 SRR12670178 SRR12670178_1.fastq SRR12670178_2.fastq Input file: SRR12670178_1.fastq Paired file: SRR12670178_2.fastq trimmed: SRR12670178-trimmed-pair1.fastq, SRR12670178-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 08:32:28 2025 >> started Tue Feb 11 08:32:55 2025 >> done (26.955s) 16363572 read pairs processed; of these: 95 ( 0.00%) short read pairs filtered out after trimming by size control 11555 ( 0.07%) empty read pairs filtered out after trimming by size control 16351922 (99.93%) read pairs available; of these: 4956844 (30.31%) trimmed read pairs available after processing 11395078 (69.69%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 2 0.00% 19 4 0.00% 20 6 0.00% 21 4 0.00% 22 16 0.00% 23 5 0.00% 24 21 0.00% 25 17 0.00% 26 29 0.00% 27 27 0.00% 28 54 0.00% 29 43 0.00% 30 40 0.00% 31 59 0.00% 32 64 0.00% 33 54 0.00% 34 96 0.00% 35 105 0.00% 36 106 0.00% 37 126 0.00% 38 149 0.00% 39 183 0.00% 40 199 0.00% 41 298 0.00% 42 281 0.00% 43 320 0.00% 44 264 0.00% 45 266 0.00% 46 299 0.00% 47 441 0.00% 48 554 0.00% 49 638 0.00% 50 839 0.01% 51 959 0.01% 52 1111 0.01% 53 1032 0.01% 54 1190 0.01% 55 1289 0.01% 56 1418 0.01% 57 1737 0.01% 58 2014 0.01% 59 2324 0.01% 60 2821 0.02% 61 3209 0.02% 62 3749 0.02% 63 4082 0.02% 64 4473 0.03% 65 4851 0.03% 66 5516 0.03% 67 6027 0.04% 68 6844 0.04% 69 7999 0.05% 70 9001 0.06% 71 10216 0.06% 72 11833 0.07% 73 13343 0.08% 74 14382 0.09% 75 15714 0.10% 76 16905 0.10% 77 17912 0.11% 78 19251 0.12% 79 21103 0.13% 80 22961 0.14% 81 25708 0.16% 82 28553 0.17% 83 30842 0.19% 84 33834 0.21% 85 35869 0.22% 86 37134 0.23% 87 38455 0.24% 88 40679 0.25% 89 41799 0.26% 90 43984 0.27% 91 46725 0.29% 92 48996 0.30% 93 52615 0.32% 94 55339 0.34% 95 57722 0.35% 96 58541 0.36% 97 60279 0.37% 98 60501 0.37% 99 61066 0.37% 100 63213 0.39% 101 63433 0.39% 102 65182 0.40% 103 68381 0.42% 104 69325 0.42% 105 70989 0.43% 106 71862 0.44% 107 72773 0.45% 108 71952 0.44% 109 73041 0.45% 110 71515 0.44% 111 72491 0.44% 112 74366 0.45% 113 74614 0.46% 114 75708 0.46% 115 77833 0.48% 116 77877 0.48% 117 78469 0.48% 118 78560 0.48% 119 77055 0.47% 120 77531 0.47% 121 78095 0.48% 122 77677 0.48% 123 78348 0.48% 124 79120 0.48% 125 78720 0.48% 126 80234 0.49% 127 80860 0.49% 128 79286 0.48% 129 78748 0.48% 130 78594 0.48% 131 77232 0.47% 132 78085 0.48% 133 77722 0.48% 134 76999 0.47% 135 78088 0.48% 136 78431 0.48% 137 78563 0.48% 138 78284 0.48% 139 78886 0.48% 140 76824 0.47% 141 76643 0.47% 142 77129 0.47% 143 75524 0.46% 144 76556 0.47% 145 76540 0.47% 146 76872 0.47% 147 75778 0.46% 148 76478 0.47% 149 75325 0.46% 150 75517 0.46% 151 11395078 69.69% 16351922 reads passed initial QC criterion=sequence-density sequence-density=0.59 sequence-density-rank=1 fanout-score=1.97 fanout-score-rank=23 prefix-density=0.59 prefix-fanout=2.0 sequence=CGGTAGACCCAACCTTTCTCCAACTCGAATTCCAAGCAAGGAACCCACTT criterion=fanout-score sequence-density=0.02 sequence-density-rank=24 fanout-score=100.42 fanout-score-rank=1 prefix-density=0.28 prefix-fanout=7.8 sequence=TTCATCTCCAAAAACCCAATAAAAAAGGAAGAGGTAAAGCATTTTGCCAAGGTCTAAGTACAATTTAAACAAACCACCCCTAAGGCCCTAACAGATA criterion=sequence-density sequence-density=0.79 sequence-density-rank=1 fanout-score=2.04 fanout-score-rank=22 prefix-density=0.79 prefix-fanout=2.0 sequence=TGTAAGAGATGGCTTCCTC criterion=fanout-score sequence-density=0.02 sequence-density-rank=25 fanout-score=16.75 fanout-score-rank=1 prefix-density=0.05 prefix-fanout=4.9 sequence=ACTGAGCTTGAGTGCATTCTTCTAAGTAAAAGAAATCCCTTAATTTCATCACACTTTCCTTCTTTTCCAACAGAAAATGTCTTGCTGTGGAGGAAACTGTGG SRR12670178 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 08:33:36 Started mapping on | Feb 11 08:33:37 Finished on | Feb 11 08:35:11 Mapping speed, Million of reads per hour | 626.24 Number of input reads | 16351922 Average input read length | 281 UNIQUE READS: Uniquely mapped reads number | 15565849 Uniquely mapped reads % | 95.19% Average mapped length | 280.15 Number of splices: Total | 14829382 Number of splices: Annotated (sjdb) | 14520878 Number of splices: GT/AG | 14530564 Number of splices: GC/AG | 244747 Number of splices: AT/AC | 8836 Number of splices: Non-canonical | 45235 Mismatch rate per base, % | 0.35% Deletion rate per base | 0.03% Deletion average length | 2.86 Insertion rate per base | 0.02% Insertion average length | 2.37 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 376560 % of reads mapped to multiple loci | 2.30% Number of reads mapped to too many loci | 38866 % of reads mapped to too many loci | 0.24% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.17% % of reads unmapped: other | 0.10% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 409513 409513 409513 N_multimapping 376560 376560 376560 N_noFeature 459414 15329843 562004 N_ambiguous 220471 794 86634 UnstrandedReadsAssigned:14885964 PositiveStrandReadsAssigned:235212 NegativeStrandReadsAssigned:14917211 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=128 echo kmer=123 SRR12670178 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: SRR12670178-trimmed-pair1.fastq SRR12670178-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 16,351,922 reads, 14,943,374 reads pseudoaligned [quant] estimated average fragment length: 200.309 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,002 rounds 52401 SRR12670178.ke.tsv 34699 SRR12670178.se.tsv 87100 total ==> SRR12670178.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1818.69 531 19.5487 Potri.005G024800.1.v4.1 1035 835.691 165 13.2197 Potri.004G059700.1.v4.1 961 761.79 14 1.23048 Potri.007G009000.2.v4.1 1416 1216.69 0 0 Potri.003G141000.2.v4.1 2943 2743.69 593.346 14.4796 Potri.016G087400.1.v4.1 270 114.733 831.441 485.206 Potri.015G069301.1.v4.1 564 372.712 0 0 Potri.010G195200.1.v4.1 1773 1573.69 21 0.893477 Potri.012G127500.1.v4.1 977 777.721 188 16.1852 ==> SRR12670178.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 542 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 211 Potri.001G212900.v4.1 1 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 13 Potri.001G416900.v4.1 1 Potri.001G452600.v4.1 14 SRR12670178 completed mapping pipeline successfully