Starting /dee2/code/volunteer_pipeline.sh SRR12670113 current disk space = 3057653346304 free memory = 1300795940 SRR12670113 SRAfilesize f38b2af1c465f14065f2ad712b9cba12 SRR12670113.sra SRR12670113.sra file validated SRR12670113 is paired end SRR12670113 is conventional basespace SRR12670113 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670113_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 36.709 37.0 37.0 37.0 37.0 37.0 2 36.46525 37.0 37.0 37.0 37.0 37.0 3 36.5715 37.0 37.0 37.0 37.0 37.0 4 36.6125 37.0 37.0 37.0 37.0 37.0 5 36.6385 37.0 37.0 37.0 37.0 37.0 6 36.639 37.0 37.0 37.0 37.0 37.0 7 36.597 37.0 37.0 37.0 37.0 37.0 8 36.6705 37.0 37.0 37.0 37.0 37.0 9 36.6955 37.0 37.0 37.0 37.0 37.0 10-14 36.656400000000005 37.0 37.0 37.0 37.0 37.0 15-19 36.6178 37.0 37.0 37.0 37.0 37.0 20-24 36.5782 37.0 37.0 37.0 37.0 37.0 25-29 36.571299999999994 37.0 37.0 37.0 37.0 37.0 30-34 36.5388 37.0 37.0 37.0 37.0 37.0 35-39 36.52669999999999 37.0 37.0 37.0 37.0 37.0 40-44 36.5519 37.0 37.0 37.0 37.0 37.0 45-49 36.4728 37.0 37.0 37.0 37.0 37.0 50-54 36.4813 37.0 37.0 37.0 37.0 37.0 55-59 36.449 37.0 37.0 37.0 37.0 37.0 60-64 36.410900000000005 37.0 37.0 37.0 37.0 37.0 65-69 36.39059999999999 37.0 37.0 37.0 37.0 37.0 70-74 36.3428 37.0 37.0 37.0 37.0 37.0 75-79 36.378 37.0 37.0 37.0 37.0 37.0 80-84 36.3576 37.0 37.0 37.0 37.0 37.0 85-89 36.2838 37.0 37.0 37.0 37.0 37.0 90-94 36.330600000000004 37.0 37.0 37.0 37.0 37.0 95-99 36.2576 37.0 37.0 37.0 37.0 37.0 100-104 36.27969999999999 37.0 37.0 37.0 37.0 37.0 105-109 36.2932 37.0 37.0 37.0 37.0 37.0 110-114 36.1451 37.0 37.0 37.0 37.0 37.0 115-119 36.1389 37.0 37.0 37.0 37.0 37.0 120-124 36.062200000000004 37.0 37.0 37.0 37.0 37.0 125-129 35.9315 37.0 37.0 37.0 37.0 37.0 130-134 35.83689999999999 37.0 37.0 37.0 37.0 37.0 135-139 35.6034 37.0 37.0 37.0 37.0 37.0 140-144 35.40160000000001 37.0 37.0 37.0 37.0 37.0 145-149 35.2242 37.0 37.0 37.0 34.6 37.0 150-151 35.085 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 1.0 21 0.0 22 2.0 23 0.0 24 1.0 25 2.0 26 4.0 27 4.0 28 9.0 29 17.0 30 20.0 31 39.0 32 36.0 33 102.0 34 162.0 35 306.0 36 2826.0 37 469.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 40.65 12.975 6.175 40.2 2 19.108439769596792 12.772351615326821 37.215126471324815 30.904082143751566 3 18.35 18.325 26.924999999999997 36.4 4 22.475 24.4 23.799999999999997 29.325000000000003 5 24.075 29.975 25.05 20.9 6 20.325 35.225 22.975 21.475 7 15.925 25.825 40.050000000000004 18.2 8 16.325 25.6 33.324999999999996 24.75 9 18.275 23.575 35.775 22.375 10-14 19.950000000000003 29.165000000000003 27.595 23.29 15-19 20.53 27.655 27.61 24.205 20-24 20.345 28.055000000000003 27.905 23.695 25-29 20.349999999999998 28.134999999999998 27.915 23.599999999999998 30-34 21.11 27.689999999999998 27.88 23.32 35-39 20.45 28.23 27.685 23.635 40-44 20.825 28.305000000000003 27.045 23.825 45-49 20.745 28.349999999999998 27.165 23.74 50-54 20.595 27.894999999999996 27.845 23.665 55-59 21.495 27.589999999999996 27.665 23.25 60-64 20.895 27.175 28.235 23.695 65-69 21.3 28.439999999999998 27.025 23.235 70-74 20.560000000000002 27.83 27.779999999999998 23.830000000000002 75-79 20.495 28.705000000000002 27.205000000000002 23.595 80-84 21.975 28.38 26.474999999999998 23.169999999999998 85-89 21.095 27.91 27.02 23.974999999999998 90-94 21.915000000000003 27.99 26.935 23.16 95-99 21.2 28.615000000000002 26.46 23.724999999999998 100-104 21.595 28.560000000000002 26.755000000000003 23.09 105-109 20.96 28.005000000000003 26.419999999999998 24.615000000000002 110-114 21.97 27.735 26.865 23.43 115-119 21.709999999999997 27.935 27.150000000000002 23.205000000000002 120-124 21.805 27.74 26.740000000000002 23.715 125-129 21.97 27.500000000000004 26.484999999999996 24.044999999999998 130-134 22.025 27.51 26.369999999999997 24.095 135-139 22.79 27.355 25.695 24.16 140-144 22.759999999999998 26.755000000000003 26.505000000000003 23.98 145-149 23.265 26.805 26.14 23.79 150-151 24.224999999999998 24.775 26.787499999999998 24.212500000000002 >>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 0.0 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 0.0 19 0.0 20 0.0 21 0.0 22 0.5 23 1.0 24 1.0 25 0.5 26 1.5 27 4.0 28 4.0 29 5.5 30 9.5 31 13.0 32 22.5 33 34.5 34 49.5 35 67.0 36 76.0 37 99.0 38 127.5 39 152.5 40 196.0 41 218.5 42 212.0 43 221.5 44 268.0 45 294.0 46 264.5 47 244.0 48 224.0 49 216.0 50 200.5 51 154.5 52 129.0 53 98.5 54 79.5 55 70.0 56 58.5 57 53.0 58 36.5 59 26.0 60 26.0 61 20.0 62 8.5 63 3.0 64 2.0 65 1.0 66 0.5 67 1.0 68 2.5 69 2.0 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 0.17500000000000002 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 81.75 #Duplication Level Percentage of deduplicated Percentage of total 1 83.18042813455658 68.0 2 12.7217125382263 20.8 3 3.241590214067278 7.95 4 0.45871559633027525 1.5 5 0.3058103975535168 1.25 6 0.03058103975535168 0.15 7 0.06116207951070336 0.35000000000000003 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 ATCGCCATTTGGCAAAACGTGCTCCCTGTTGGTAGTAAGCAGCTGTGCGG 7 0.17500000000000002 No Hit GGCCTGGCAATCTTGAACCATTCAGTATGGAAAGATCCTTCCACATCAAC 7 0.17500000000000002 No Hit CAAACATCACATCACTACCGTTGATTGCCAGCCTTCTGGTCCTGCTGGTG 6 0.15 No Hit AGATGAGTATGTGTTTCAGCATCAACAAAAGCCTACATGGATAATAAGGC 5 0.125 No Hit TGGGTCACATCTATCCCTGGCCTGAATATATTAGTCTGAGACATTGCAGC 5 0.125 No Hit CCTCTATCAATGGAATCTTGATTGGCTTCACCAAGAGAAGCCTCGCTCAG 5 0.125 No Hit GCTCAATTTCCTCTTGGCTCAGACGACCCTTGTCATTAGTAATGGTGATC 5 0.125 No Hit ATCCTCTTCCACGAACCCCCTAGAAGTAAGAGCCGGTGTTCCCATCCTGA 5 0.125 No Hit CAACAAAAGGGGAGAAACTGGAGGGATTCCCAACAAACAGATGATCAATT 5 0.125 No Hit ACCTCCATAACCTGACTGTTTGCGATCATAACGGCGCTTTCCTTGAGCAG 5 0.125 No Hit CTTCAGTTTTGCTTCAATTTCATGCAGCCTGGAATCTTTCAGCTGTAACT 5 0.125 No Hit CAGCAACTTTATGGTAGCAATTGTCACATAGCATGAAGCAAAGGCGACAT 5 0.125 No Hit AACGCCTTGAAGACATCGGTTCCACGCCTTACACCACCGTCCAAGAACAC 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 0.025 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 0.037500000000000006 0.0 0.0 0.0 0.0 50-51 0.05 0.0 0.0 0.0 0.0 52-53 0.0625 0.0 0.0 0.0 0.0 54-55 0.075 0.0 0.0 0.0 0.0 56-57 0.075 0.0 0.0 0.0 0.0 58-59 0.0875 0.0 0.0 0.0 0.0 60-61 0.15 0.0 0.0 0.0 0.0 62-63 0.2 0.0 0.0 0.0 0.0 64-65 0.2 0.0 0.0 0.0 0.0 66-67 0.275 0.0 0.0 0.0 0.0 68-69 0.4 0.0 0.0 0.0 0.0 70-71 0.5125 0.0 0.0 0.0 0.0 72-73 0.55 0.0 0.0 0.0 0.0 74-75 0.7250000000000001 0.0 0.0 0.0 0.0 76-77 0.8999999999999999 0.0 0.0 0.0 0.0 78-79 1.15 0.0 0.0 0.0 0.0 80-81 1.2999999999999998 0.0 0.0 0.0 0.0 82-83 1.6125 0.0 0.0 0.0 0.0 84-85 1.925 0.0 0.0 0.0 0.0 86-87 2.3875 0.0 0.0 0.0 0.0 88-89 2.7375 0.0 0.0 0.0 0.0 90-91 3.175 0.0 0.0 0.0 0.0 92-93 3.625 0.0 0.0 0.0 0.0 94-95 4.0375 0.0 0.0 0.0 0.0 96-97 4.7125 0.0 0.0 0.0 0.0 98-99 5.25 0.0 0.0 0.0 0.0 100-101 5.737500000000001 0.0 0.0 0.0 0.0 102-103 6.4875 0.0 0.0 0.0 0.0 104-105 7.1125 0.0 0.0 0.0 0.0 106-107 7.6 0.0 0.0 0.0 0.0 108-109 8.5125 0.0 0.0 0.0 0.0 110-111 9.337499999999999 0.0 0.0 0.0 0.0 112-113 10.0125 0.0 0.0 0.0 0.0 114-115 10.8875 0.0 0.0 0.0 0.0 116-117 11.7 0.0 0.0 0.0 0.0 118-119 12.8375 0.0 0.0 0.0 0.0 120-121 13.75 0.0 0.0 0.0 0.0 122-123 14.5625 0.0 0.0 0.0 0.0 124-125 15.5125 0.0 0.0 0.0 0.0 126-127 16.225 0.0 0.0 0.0 0.0 128-129 17.15 0.0 0.0 0.0 0.0 130-131 17.8625 0.0 0.0 0.0 0.0 132-133 18.85 0.0 0.0 0.0 0.0 134-135 19.6625 0.0 0.0 0.0 0.0 136-137 20.45 0.0 0.0 0.0 0.0 138-139 21.5375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR12670113 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670113_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 36.388 37.0 37.0 37.0 37.0 37.0 2 36.0545 37.0 37.0 37.0 37.0 37.0 3 36.137 37.0 37.0 37.0 37.0 37.0 4 36.255 37.0 37.0 37.0 37.0 37.0 5 36.2795 37.0 37.0 37.0 37.0 37.0 6 36.258 37.0 37.0 37.0 37.0 37.0 7 36.353 37.0 37.0 37.0 37.0 37.0 8 36.294 37.0 37.0 37.0 37.0 37.0 9 36.2225 37.0 37.0 37.0 37.0 37.0 10-14 36.318999999999996 37.0 37.0 37.0 37.0 37.0 15-19 36.346 37.0 37.0 37.0 37.0 37.0 20-24 36.30120000000001 37.0 37.0 37.0 37.0 37.0 25-29 36.2895 37.0 37.0 37.0 37.0 37.0 30-34 36.2507 37.0 37.0 37.0 37.0 37.0 35-39 36.1994 37.0 37.0 37.0 37.0 37.0 40-44 36.1891 37.0 37.0 37.0 37.0 37.0 45-49 36.22580000000001 37.0 37.0 37.0 37.0 37.0 50-54 36.1214 37.0 37.0 37.0 37.0 37.0 55-59 36.1356 37.0 37.0 37.0 37.0 37.0 60-64 36.0633 37.0 37.0 37.0 37.0 37.0 65-69 36.0161 37.0 37.0 37.0 37.0 37.0 70-74 36.024300000000004 37.0 37.0 37.0 37.0 37.0 75-79 36.0042 37.0 37.0 37.0 37.0 37.0 80-84 35.9328 37.0 37.0 37.0 37.0 37.0 85-89 35.948 37.0 37.0 37.0 37.0 37.0 90-94 35.9562 37.0 37.0 37.0 37.0 37.0 95-99 35.8714 37.0 37.0 37.0 37.0 37.0 100-104 35.7849 37.0 37.0 37.0 37.0 37.0 105-109 35.682300000000005 37.0 37.0 37.0 37.0 37.0 110-114 35.642599999999995 37.0 37.0 37.0 37.0 37.0 115-119 35.6456 37.0 37.0 37.0 37.0 37.0 120-124 35.508799999999994 37.0 37.0 37.0 37.0 37.0 125-129 35.3316 37.0 37.0 37.0 34.6 37.0 130-134 35.1831 37.0 37.0 37.0 32.2 37.0 135-139 34.987100000000005 37.0 37.0 37.0 25.0 37.0 140-144 34.8217 37.0 37.0 37.0 25.0 37.0 145-149 34.5434 37.0 37.0 37.0 25.0 37.0 150-151 34.408874999999995 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 4.0 14 3.0 15 0.0 16 2.0 17 1.0 18 0.0 19 0.0 20 2.0 21 2.0 22 4.0 23 7.0 24 2.0 25 7.0 26 10.0 27 16.0 28 11.0 29 9.0 30 22.0 31 47.0 32 81.0 33 122.0 34 231.0 35 605.0 36 2554.0 37 258.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 39.15 24.0 9.45 27.400000000000002 2 25.6 27.35 30.475 16.575 3 19.525000000000002 28.675 30.45 21.349999999999998 4 22.225 36.5 23.150000000000002 18.125 5 25.0 38.5 20.0 16.5 6 21.85 39.574999999999996 21.224999999999998 17.349999999999998 7 20.8 22.95 36.199999999999996 20.05 8 21.075 28.525 27.224999999999998 23.175 9 21.4 24.925 29.875 23.799999999999997 10-14 22.715 29.42 26.235000000000003 21.63 15-19 22.7 28.34 27.32 21.64 20-24 23.095 28.815 26.950000000000003 21.14 25-29 23.54 28.544999999999998 27.400000000000002 20.515 30-34 22.845 28.67 27.794999999999998 20.69 35-39 22.405 28.134999999999998 27.605 21.855 40-44 22.655 28.775000000000002 26.855 21.715 45-49 22.43 28.000000000000004 28.12 21.45 50-54 23.02 28.705000000000002 27.11 21.165 55-59 22.33 27.800000000000004 28.26 21.61 60-64 23.36 27.495000000000005 27.925 21.22 65-69 23.07 27.705000000000002 28.244999999999997 20.979999999999997 70-74 23.695 27.345000000000002 27.1 21.86 75-79 22.765 27.445000000000004 27.675 22.115000000000002 80-84 23.18 28.13 27.18 21.51 85-89 23.685000000000002 27.725 27.165 21.425 90-94 24.044999999999998 28.255000000000003 26.810000000000002 20.89 95-99 24.25 27.825 26.815 21.11 100-104 24.455 28.465 26.595000000000002 20.485 105-109 25.674999999999997 27.639999999999997 26.669999999999998 20.015 110-114 25.36 27.85 26.5 20.29 115-119 27.139999999999997 28.02 25.755 19.085 120-124 25.895000000000003 27.765 27.189999999999998 19.15 125-129 27.455000000000002 27.525 26.135 18.884999999999998 130-134 27.87 27.38 26.150000000000002 18.6 135-139 28.910000000000004 26.07 26.584999999999997 18.435000000000002 140-144 30.18 26.424999999999997 24.94 18.455 145-149 30.788078807880787 26.647664766476648 24.897489748974895 17.666766676667667 150-151 32.52906613326666 24.990623827978496 24.778097262157768 17.702212776597072 >>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 1.0 9 1.5 10 0.5 11 1.0 12 1.5 13 1.5 14 1.0 15 0.0 16 0.0 17 0.5 18 0.5 19 1.0 20 1.5 21 0.5 22 0.5 23 0.5 24 0.0 25 1.5 26 2.5 27 1.5 28 2.5 29 6.0 30 11.0 31 17.5 32 23.0 33 30.0 34 52.5 35 68.5 36 79.0 37 115.5 38 137.0 39 166.0 40 200.0 41 197.5 42 233.5 43 264.0 44 251.5 45 260.5 46 275.0 47 269.5 48 242.0 49 207.0 50 173.5 51 145.0 52 124.0 53 94.5 54 66.5 55 60.5 56 62.0 57 44.5 58 24.0 59 23.0 60 22.5 61 12.5 62 8.0 63 6.0 64 1.0 65 0.5 66 0.5 67 0.0 68 0.0 69 0.0 70 0.0 71 0.5 72 0.5 73 0.0 74 0.0 75 0.0 76 0.0 77 0.0 78 0.0 79 0.5 80 0.5 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.5 88 1.0 89 0.5 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 0.0 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 0.0125 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 81.975 #Duplication Level Percentage of deduplicated Percentage of total 1 83.5620616041476 68.5 2 12.564806343397377 20.599999999999998 3 2.866727660872217 7.049999999999999 4 0.5489478499542544 1.7999999999999998 5 0.3354681305275999 1.375 6 0.030497102775236352 0.15 7 0.09149130832570906 0.525 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 ATCTGATCCGTGCAAAGAGTATTGAGAAGGGATGGGACTTGAAATTGGGA 7 0.17500000000000002 No Hit GATGACCAAGTTGATTCCAAGGAACACTGTTATCCCAACCAAGAAATCTC 7 0.17500000000000002 No Hit GATAGAGAGGAGATAAGATATAGACACTTGTTATAGGCTATCTTGCACTG 7 0.17500000000000002 No Hit ACCAATTCAACCAATCACAACATAGCAATCTATGAACTTCAGGAACACCA 6 0.15 No Hit CTTGTAGCCAATCCCATTTAGTTTGGGCCATAGACTTGCTTGCCTTGATT 5 0.125 No Hit GTTGAGAAAGGCTATGAACTTGTTTCTGGTGGAACTGAGAACCATTTAGT 5 0.125 No Hit CAGAAGGAGATACATCAGTTAACTGGGTTGACGCTTCAGCATGAGAATGA 5 0.125 No Hit GTTTGGAACAGCAGCAGCAGGAGGTAGGACAGAGAGCTGTCTCACCCCGT 5 0.125 No Hit AGCAGAGAATGCAATAGCTTCAATGAACGGGGGAACATTGCTTGAACAGG 5 0.125 No Hit AGAACACATTCATACCCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATC 5 0.125 No Hit GACAATCACCAGACTGCCAATTCTGGTGAAGGGTGTGCTCACTGCCGAGG 5 0.125 No Hit CTGCATAGCTTACAAGCTTGTAAGAGATGGCTTCCTCCTCTATGATCTCA 5 0.125 No Hit TGGATCTGCATCCCAAATAAGAGAACTGGCTGATCAGCTAACTGGCCATG 5 0.125 No Hit GTAAATAATCATGTGTATGATATGGCTGATTCTTGGGAAAGAGCAAGTGG 5 0.125 No Hit CTCCTTCAGATACTTACAAAATCTGGAAGAGGGGTGCAAATTTGAGGGCA 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 0.025 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 0.037500000000000006 0.0 0.0 0.0125 0.0 50-51 0.05 0.0 0.0 0.025 0.0 52-53 0.0625 0.0 0.0 0.025 0.0 54-55 0.075 0.0 0.0 0.025 0.0 56-57 0.075 0.0 0.0 0.025 0.0 58-59 0.0875 0.0 0.0 0.025 0.0 60-61 0.15 0.0 0.0 0.025 0.0 62-63 0.2 0.0 0.0 0.025 0.0 64-65 0.2 0.0 0.0 0.025 0.0 66-67 0.2875 0.0 0.0 0.025 0.0 68-69 0.425 0.0 0.0 0.025 0.0 70-71 0.5375000000000001 0.0 0.0 0.025 0.0 72-73 0.575 0.0 0.0 0.025 0.0 74-75 0.75 0.0 0.0 0.025 0.0 76-77 0.925 0.0 0.0 0.025 0.0 78-79 1.175 0.0 0.0 0.025 0.0 80-81 1.3125 0.0 0.0 0.025 0.0 82-83 1.6125 0.0 0.0 0.025 0.0 84-85 1.925 0.0 0.0 0.025 0.0 86-87 2.3875 0.0 0.0 0.025 0.0 88-89 2.7125000000000004 0.0 0.0 0.025 0.0 90-91 3.1624999999999996 0.0 0.0 0.025 0.0 92-93 3.625 0.0 0.0 0.025 0.0 94-95 4.0375 0.0 0.0 0.025 0.0 96-97 4.6875 0.0 0.0 0.025 0.0 98-99 5.25 0.0 0.0 0.025 0.0 100-101 5.7625 0.0 0.0 0.025 0.0 102-103 6.550000000000001 0.0 0.0 0.025 0.0 104-105 7.1875 0.0 0.0 0.025 0.0 106-107 7.675 0.0 0.0 0.025 0.0 108-109 8.5625 0.0 0.0 0.025 0.0 110-111 9.3875 0.0 0.0 0.025 0.0 112-113 10.0625 0.0 0.0 0.025 0.0 114-115 10.9375 0.0 0.0 0.025 0.0 116-117 11.8 0.0 0.0 0.025 0.0 118-119 13.0125 0.0 0.0 0.025 0.0 120-121 13.975 0.0 0.0 0.025 0.0 122-123 14.8125 0.0 0.0 0.025 0.0 124-125 15.7625 0.0 0.0 0.025 0.0 126-127 16.475 0.0 0.0 0.025 0.0 128-129 17.375 0.0 0.0 0.025 0.0 130-131 18.0875 0.0 0.0 0.025 0.0 132-133 19.0625 0.0 0.0 0.025 0.0 134-135 19.875 0.0 0.0 0.025 0.0 136-137 20.65 0.0 0.0 0.025 0.0 138-139 21.737499999999997 0.0 0.0 0.025 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GATGATG 30 0.0014437955 24.166668 105-109 GGGGGGG 320 2.4963352E-5 6.796875 140-144 >>END_MODULE Read 512989 spots for SRR12670113.sra Written 512989 spots for SRR12670113.sra Read 512989 spots for SRR12670113.sra Written 512989 spots for SRR12670113.sra Read 512989 spots for SRR12670113.sra Written 512989 spots for SRR12670113.sra Read 512989 spots for SRR12670113.sra Written 512989 spots for SRR12670113.sra Read 512989 spots for SRR12670113.sra Written 512989 spots for SRR12670113.sra Read 512989 spots for SRR12670113.sra Written 512989 spots for SRR12670113.sra Read 512989 spots for SRR12670113.sra Written 512989 spots for SRR12670113.sra Read 512989 spots for SRR12670113.sra Written 512989 spots for SRR12670113.sra Read 512989 spots for SRR12670113.sra Written 512989 spots for SRR12670113.sra Read 512989 spots for SRR12670113.sra Written 512989 spots for SRR12670113.sra Read 512989 spots for SRR12670113.sra Written 512989 spots for SRR12670113.sra Read 512989 spots for SRR12670113.sra Written 512989 spots for SRR12670113.sra Read 512989 spots for SRR12670113.sra Written 512989 spots for SRR12670113.sra Read 512989 spots for SRR12670113.sra Written 512989 spots for SRR12670113.sra Read 512989 spots for SRR12670113.sra Written 512989 spots for SRR12670113.sra Read 512989 spots for SRR12670113.sra Written 512989 spots for SRR12670113.sra Read 512989 spots for SRR12670113.sra Written 512989 spots for SRR12670113.sra Read 512989 spots for SRR12670113.sra Written 512989 spots for SRR12670113.sra Read 512993 spots for SRR12670113.sra Written 512993 spots for SRR12670113.sra Read 512989 spots for SRR12670113.sra Written 512989 spots for SRR12670113.sra SRR ids: ['SRR12670113.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_4vcipnrc SRR12670113.sra spots: 10259784 blocks: [[1, 512989], [512990, 1025978], [1025979, 1538967], [1538968, 2051956], [2051957, 2564945], [2564946, 3077934], [3077935, 3590923], [3590924, 4103912], [4103913, 4616901], [4616902, 5129890], [5129891, 5642879], [5642880, 6155868], [6155869, 6668857], [6668858, 7181846], [7181847, 7694835], [7694836, 8207824], [8207825, 8720813], [8720814, 9233802], [9233803, 9746791], [9746792, 10259784]] SRR12670113 file size 3465023 SRR12670113 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 SRR12670113 SRR12670113_1.fastq SRR12670113_2.fastq Input file: SRR12670113_1.fastq Paired file: SRR12670113_2.fastq trimmed: SRR12670113-trimmed-pair1.fastq, SRR12670113-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 Mon Feb 10 23:22:59 2025 >> started Mon Feb 10 23:23:15 2025 >> done (16.624s) 10259784 read pairs processed; of these: 52 ( 0.00%) short read pairs filtered out after trimming by size control 4154 ( 0.04%) empty read pairs filtered out after trimming by size control 10255578 (99.96%) read pairs available; of these: 2753244 (26.85%) trimmed read pairs available after processing 7502334 (73.15%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 3 0.00% 19 9 0.00% 20 11 0.00% 21 22 0.00% 22 18 0.00% 23 26 0.00% 24 23 0.00% 25 28 0.00% 26 35 0.00% 27 45 0.00% 28 43 0.00% 29 60 0.00% 30 63 0.00% 31 64 0.00% 32 67 0.00% 33 67 0.00% 34 51 0.00% 35 99 0.00% 36 77 0.00% 37 107 0.00% 38 87 0.00% 39 135 0.00% 40 124 0.00% 41 152 0.00% 42 123 0.00% 43 186 0.00% 44 162 0.00% 45 163 0.00% 46 210 0.00% 47 222 0.00% 48 252 0.00% 49 321 0.00% 50 396 0.00% 51 422 0.00% 52 500 0.00% 53 450 0.00% 54 580 0.01% 55 585 0.01% 56 709 0.01% 57 771 0.01% 58 884 0.01% 59 1002 0.01% 60 1258 0.01% 61 1452 0.01% 62 1666 0.02% 63 1786 0.02% 64 1964 0.02% 65 2160 0.02% 66 2254 0.02% 67 2561 0.02% 68 2886 0.03% 69 3355 0.03% 70 3815 0.04% 71 4389 0.04% 72 4932 0.05% 73 5707 0.06% 74 6193 0.06% 75 6797 0.07% 76 7139 0.07% 77 7609 0.07% 78 8294 0.08% 79 8900 0.09% 80 9831 0.10% 81 11366 0.11% 82 12560 0.12% 83 13526 0.13% 84 14748 0.14% 85 15723 0.15% 86 16284 0.16% 87 16768 0.16% 88 17955 0.18% 89 18600 0.18% 90 19874 0.19% 91 21216 0.21% 92 22643 0.22% 93 24181 0.24% 94 25405 0.25% 95 26800 0.26% 96 27363 0.27% 97 28290 0.28% 98 28742 0.28% 99 28726 0.28% 100 29913 0.29% 101 30648 0.30% 102 32416 0.32% 103 33350 0.33% 104 34862 0.34% 105 35752 0.35% 106 36518 0.36% 107 36686 0.36% 108 36945 0.36% 109 37158 0.36% 110 36799 0.36% 111 38049 0.37% 112 39186 0.38% 113 39731 0.39% 114 40943 0.40% 115 41992 0.41% 116 42977 0.42% 117 43329 0.42% 118 43788 0.43% 119 43312 0.42% 120 43816 0.43% 121 44049 0.43% 122 44528 0.43% 123 45562 0.44% 124 46228 0.45% 125 46522 0.45% 126 47650 0.46% 127 47860 0.47% 128 46774 0.46% 129 47951 0.47% 130 47626 0.46% 131 46843 0.46% 132 47332 0.46% 133 48429 0.47% 134 48581 0.47% 135 49586 0.48% 136 49484 0.48% 137 49817 0.49% 138 49510 0.48% 139 50562 0.49% 140 49524 0.48% 141 49799 0.49% 142 49529 0.48% 143 49579 0.48% 144 50466 0.49% 145 50589 0.49% 146 50932 0.50% 147 51052 0.50% 148 51510 0.50% 149 50915 0.50% 150 51213 0.50% 151 7502334 73.15% 10255578 reads passed initial QC criterion=sequence-density sequence-density=0.46 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=26 prefix-density=0.46 prefix-fanout=2.0 sequence=TTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAGGTGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGG criterion=fanout-score sequence-density=0.03 sequence-density-rank=30 fanout-score=136.29 fanout-score-rank=1 prefix-density=0.28 prefix-fanout=13.3 sequence=TGAAGAAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTG criterion=sequence-density sequence-density=0.78 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=27 prefix-density=0.78 prefix-fanout=2.0 sequence=AACCGCACCCCGGCACA criterion=fanout-score sequence-density=0.01 sequence-density-rank=30 fanout-score=68.53 fanout-score-rank=1 prefix-density=0.16 prefix-fanout=2.6 sequence=AGGAACTCAAACGCATAGCTTCCTACAAATACCCCAGCTAGCCAATACTCTCCACCACTAAACCCAAAGCTCAAAAAAAATCTTAACTGCACCCGCTCATCCAGCAATGGCAGCAGCAACAATGGCCCTCTCGTCCCCTTCGCTAGCCGGAAAGGCGGTGAAGCTCAACCCCTCCTCCTCTGAGATCATGGGCAATGGCCGTGTCTCCATGAGGAAAACCACCAAGCCTGTTCCCTCCGGGAGCCCATGGTACGGACCAGACCGTGTTAAATACTTGGGCCCGTTCTCTGGTGAGCCCCCATCCTACTTGACTGGTGAGTTCCCTGGTGACTACGGCTGGGACACTGCTGG SRR12670113 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 10 23:24:14 Started mapping on | Feb 10 23:24:14 Finished on | Feb 10 23:25:33 Mapping speed, Million of reads per hour | 467.34 Number of input reads | 10255578 Average input read length | 285 UNIQUE READS: Uniquely mapped reads number | 9628929 Uniquely mapped reads % | 93.89% Average mapped length | 283.92 Number of splices: Total | 9421503 Number of splices: Annotated (sjdb) | 9223229 Number of splices: GT/AG | 9222566 Number of splices: GC/AG | 161460 Number of splices: AT/AC | 5406 Number of splices: Non-canonical | 32071 Mismatch rate per base, % | 0.34% Deletion rate per base | 0.02% Deletion average length | 2.85 Insertion rate per base | 0.02% Insertion average length | 2.29 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 229256 % of reads mapped to multiple loci | 2.24% Number of reads mapped to too many loci | 31257 % of reads mapped to too many loci | 0.30% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.46% % of reads unmapped: other | 0.11% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 397393 397393 397393 N_multimapping 229256 229256 229256 N_noFeature 344802 9481242 412549 N_ambiguous 134550 575 54231 UnstrandedReadsAssigned:9149577 PositiveStrandReadsAssigned:147112 NegativeStrandReadsAssigned:9162149 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=136 echo kmer=131 SRR12670113 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: SRR12670113-trimmed-pair1.fastq SRR12670113-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 10,255,578 reads, 9,217,359 reads pseudoaligned [quant] estimated average fragment length: 203.634 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,070 rounds 52401 SRR12670113.ke.tsv 34699 SRR12670113.se.tsv 87100 total ==> SRR12670113.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1815.37 268 15.8477 Potri.005G024800.1.v4.1 1035 832.366 141 18.1844 Potri.004G059700.1.v4.1 961 758.447 0 0 Potri.007G009000.2.v4.1 1416 1213.37 0 0 Potri.003G141000.2.v4.1 2943 2740.37 495.485 19.4096 Potri.016G087400.1.v4.1 270 107.496 321.338 320.896 Potri.015G069301.1.v4.1 564 367.982 0 0 Potri.010G195200.1.v4.1 1773 1570.37 50 3.41794 Potri.012G127500.1.v4.1 977 774.41 38 5.26754 ==> SRR12670113.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 47 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 150 Potri.001G212900.v4.1 52 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 1 Potri.001G452600.v4.1 5 SRR12670113 completed mapping pipeline successfully