Starting /dee2/code/volunteer_pipeline.sh SRR12671365 current disk space = 3053444800512 free memory = 1474534344 SRR12671365 SRAfilesize b0a9626cb0325d240fcfc4c9a1190d8b SRR12671365.sra SRR12671365.sra file validated SRR12671365 is paired end SRR12671365 is conventional basespace SRR12671365 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12671365_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 36.619 37.0 37.0 37.0 37.0 37.0 2 36.33875 37.0 37.0 37.0 37.0 37.0 3 36.581 37.0 37.0 37.0 37.0 37.0 4 36.6115 37.0 37.0 37.0 37.0 37.0 5 36.5875 37.0 37.0 37.0 37.0 37.0 6 36.601 37.0 37.0 37.0 37.0 37.0 7 36.5365 37.0 37.0 37.0 37.0 37.0 8 36.6485 37.0 37.0 37.0 37.0 37.0 9 36.5935 37.0 37.0 37.0 37.0 37.0 10-14 36.6641 37.0 37.0 37.0 37.0 37.0 15-19 36.6004 37.0 37.0 37.0 37.0 37.0 20-24 36.580600000000004 37.0 37.0 37.0 37.0 37.0 25-29 36.5582 37.0 37.0 37.0 37.0 37.0 30-34 36.5607 37.0 37.0 37.0 37.0 37.0 35-39 36.511 37.0 37.0 37.0 37.0 37.0 40-44 36.475 37.0 37.0 37.0 37.0 37.0 45-49 36.5029 37.0 37.0 37.0 37.0 37.0 50-54 36.488800000000005 37.0 37.0 37.0 37.0 37.0 55-59 36.4385 37.0 37.0 37.0 37.0 37.0 60-64 36.39190000000001 37.0 37.0 37.0 37.0 37.0 65-69 36.3845 37.0 37.0 37.0 37.0 37.0 70-74 36.4142 37.0 37.0 37.0 37.0 37.0 75-79 36.3442 37.0 37.0 37.0 37.0 37.0 80-84 36.3137 37.0 37.0 37.0 37.0 37.0 85-89 36.2989 37.0 37.0 37.0 37.0 37.0 90-94 36.281000000000006 37.0 37.0 37.0 37.0 37.0 95-99 36.265499999999996 37.0 37.0 37.0 37.0 37.0 100-104 36.2902 37.0 37.0 37.0 37.0 37.0 105-109 36.294599999999996 37.0 37.0 37.0 37.0 37.0 110-114 36.201100000000004 37.0 37.0 37.0 37.0 37.0 115-119 36.226299999999995 37.0 37.0 37.0 37.0 37.0 120-124 36.150800000000004 37.0 37.0 37.0 37.0 37.0 125-129 36.1952 37.0 37.0 37.0 37.0 37.0 130-134 36.0784 37.0 37.0 37.0 37.0 37.0 135-139 36.023500000000006 37.0 37.0 37.0 37.0 37.0 140-144 35.9868 37.0 37.0 37.0 37.0 37.0 145-149 35.95290000000001 37.0 37.0 37.0 37.0 37.0 150-151 35.80175 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 1.0 22 1.0 23 1.0 24 0.0 25 1.0 26 5.0 27 7.0 28 10.0 29 15.0 30 17.0 31 28.0 32 48.0 33 69.0 34 97.0 35 252.0 36 2974.0 37 474.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 47.199999999999996 11.85 3.6249999999999996 37.325 2 19.05239408373026 10.579092504387065 40.76209576334921 29.606417648533466 3 17.224999999999998 18.7 29.775000000000002 34.300000000000004 4 24.45 25.8 22.8 26.950000000000003 5 24.125 31.374999999999996 25.374999999999996 19.125 6 18.475 33.425 24.15 23.95 7 14.625 25.374999999999996 43.65 16.35 8 15.775 23.05 37.625 23.549999999999997 9 16.5 22.7 35.0 25.8 10-14 19.845 30.025000000000002 28.005000000000003 22.125 15-19 19.99 27.015 28.33 24.665 20-24 20.755000000000003 27.529999999999998 27.905 23.810000000000002 25-29 20.369999999999997 28.04 28.1 23.49 30-34 19.925 28.185 28.04 23.849999999999998 35-39 20.34 27.87 27.800000000000004 23.990000000000002 40-44 20.31 28.410000000000004 28.27 23.01 45-49 20.305 27.98 28.17 23.544999999999998 50-54 20.78 28.455000000000002 27.185 23.580000000000002 55-59 20.76 27.950000000000003 27.750000000000004 23.54 60-64 19.3 28.96 27.71 24.03 65-69 20.03 27.49 28.720000000000002 23.76 70-74 20.849999999999998 28.7 27.055 23.395 75-79 20.45 28.235 27.97 23.345 80-84 20.3 28.345 27.42 23.935000000000002 85-89 20.544999999999998 28.565 26.85 24.04 90-94 20.080000000000002 28.62 27.575 23.724999999999998 95-99 20.315 27.985 28.084999999999997 23.615 100-104 21.21 27.889999999999997 27.1 23.799999999999997 105-109 20.865000000000002 28.199999999999996 27.794999999999998 23.14 110-114 20.880000000000003 27.93 28.044999999999998 23.145 115-119 21.255 28.965000000000003 26.76 23.02 120-124 21.105 28.12 27.055 23.72 125-129 21.22 28.21 26.540000000000003 24.03 130-134 21.65 28.24 26.52 23.59 135-139 20.955 27.825 27.04 24.18 140-144 21.37 27.92 26.47 24.240000000000002 145-149 20.79 28.060000000000002 25.95 25.2 150-151 20.775 28.037499999999998 26.4125 24.775 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.5 2 0.5 3 0.0 4 0.0 5 0.0 6 0.5 7 0.5 8 0.5 9 0.5 10 0.0 11 0.0 12 0.0 13 0.0 14 0.5 15 0.5 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 1.0 22 2.5 23 2.0 24 0.5 25 0.5 26 3.0 27 8.0 28 11.0 29 13.0 30 17.0 31 21.0 32 29.5 33 43.5 34 61.0 35 74.0 36 81.0 37 99.0 38 113.0 39 153.0 40 192.0 41 212.0 42 244.5 43 249.0 44 253.5 45 265.0 46 279.0 47 275.5 48 231.5 49 188.5 50 171.0 51 154.0 52 127.5 53 98.0 54 73.5 55 62.5 56 51.0 57 34.5 58 21.0 59 18.0 60 16.5 61 17.5 62 12.5 63 3.5 64 2.0 65 3.5 66 2.5 67 0.0 68 0.5 69 0.5 70 0.0 71 0.0 72 0.5 73 1.0 74 0.5 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 0.27499999999999997 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 82.69999999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 83.64570737605804 69.175 2 12.726723095525996 21.05 3 2.962515114873035 7.35 4 0.4534461910519952 1.5 5 0.15114873035066506 0.625 6 0.06045949214026602 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 GGCTCACCAGGAGGTGATACATCTTTTAATGTTCCATTTCTTATGGCTCG 6 0.15 No Hit CTTGGCCAGGGAGTGGAGCAGGCTGGCTCTGGAGCTTGACCTTGATGGTG 6 0.15 No Hit GTTTCTCAACAGCAGTCCCATCTTTGATAGCCTTTACTTGCTCGTACATG 5 0.125 No Hit CCCGTCATCAGTCAATGCAGTAGAATGCCATCCACCAGCAGCAATATCAA 5 0.125 No Hit GGAAAAATGGAAGGAAAGAGGAGAAACCAAGTTTTAAAACATAACACGAC 5 0.125 No Hit GCGGCAATAAAGCTGATGCACTGCACTTGACGCGTGTTGTCGAATCCGAT 5 0.125 No Hit GCATCATCAATCACACAATTTTCTCTTAAGCAAACCCACATTGCATCCAG 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 0.0 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 0.05 0.0 0.0 0.0 0.0 64-65 0.075 0.0 0.0 0.0 0.0 66-67 0.075 0.0 0.0 0.0 0.0 68-69 0.075 0.0 0.0 0.0 0.0 70-71 0.075 0.0 0.0 0.0 0.0 72-73 0.1125 0.0 0.0 0.0 0.0 74-75 0.125 0.0 0.0 0.0 0.0 76-77 0.15 0.0 0.0 0.0 0.0 78-79 0.3125 0.0 0.0 0.0 0.0 80-81 0.35 0.0 0.0 0.0 0.0 82-83 0.425 0.0 0.0 0.0 0.0 84-85 0.575 0.0 0.0 0.0 0.0 86-87 0.7375 0.0 0.0 0.0 0.0 88-89 0.9 0.0 0.0 0.0 0.0 90-91 1.0625 0.0 0.0 0.0 0.0 92-93 1.25 0.0 0.0 0.0 0.0 94-95 1.5 0.0 0.0 0.0 0.0 96-97 1.775 0.0 0.0 0.0 0.0 98-99 2.05 0.0 0.0 0.0 0.0 100-101 2.2875 0.0 0.0 0.0 0.0 102-103 2.5875 0.0 0.0 0.0 0.0 104-105 2.8875 0.0 0.0 0.0 0.0 106-107 3.125 0.0 0.0 0.0 0.0 108-109 3.4625 0.0 0.0 0.0 0.0 110-111 4.0125 0.0 0.0 0.0 0.0 112-113 4.5875 0.0 0.0 0.0 0.0 114-115 5.175000000000001 0.0 0.0 0.0 0.0 116-117 5.575 0.0 0.0 0.0 0.0 118-119 6.1875 0.0 0.0 0.0 0.0 120-121 6.9375 0.0 0.0 0.0 0.0 122-123 7.550000000000001 0.0 0.0 0.0 0.0 124-125 8.2875 0.0 0.0 0.0 0.0 126-127 8.85 0.0 0.0 0.0 0.0 128-129 9.7625 0.0 0.0 0.0 0.0 130-131 10.3125 0.0 0.0 0.0 0.0 132-133 10.975 0.0 0.0 0.0 0.0 134-135 11.55 0.0 0.0 0.0 0.0 136-137 12.125 0.0 0.0 0.0 0.0 138-139 12.9 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GAGTGAA 10 0.006830828 145.0 4 ACTCATA 10 0.006830828 145.0 145 CCATTTC 10 0.006830828 145.0 3 GAATCCG 10 0.006830828 145.0 5 AGGCATC 10 0.006830828 145.0 145 TCATAAA 10 0.006830828 145.0 8 >>END_MODULE SRR12671365 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12671365_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 36.33 37.0 37.0 37.0 37.0 37.0 2 36.0895 37.0 37.0 37.0 37.0 37.0 3 36.3015 37.0 37.0 37.0 37.0 37.0 4 36.312 37.0 37.0 37.0 37.0 37.0 5 36.354 37.0 37.0 37.0 37.0 37.0 6 36.285 37.0 37.0 37.0 37.0 37.0 7 36.3005 37.0 37.0 37.0 37.0 37.0 8 36.3015 37.0 37.0 37.0 37.0 37.0 9 36.359 37.0 37.0 37.0 37.0 37.0 10-14 36.326800000000006 37.0 37.0 37.0 37.0 37.0 15-19 36.3739 37.0 37.0 37.0 37.0 37.0 20-24 36.3144 37.0 37.0 37.0 37.0 37.0 25-29 36.256099999999996 37.0 37.0 37.0 37.0 37.0 30-34 36.2346 37.0 37.0 37.0 37.0 37.0 35-39 36.2457 37.0 37.0 37.0 37.0 37.0 40-44 36.2044 37.0 37.0 37.0 37.0 37.0 45-49 36.1554 37.0 37.0 37.0 37.0 37.0 50-54 36.1451 37.0 37.0 37.0 37.0 37.0 55-59 36.130100000000006 37.0 37.0 37.0 37.0 37.0 60-64 36.0961 37.0 37.0 37.0 37.0 37.0 65-69 36.1057 37.0 37.0 37.0 37.0 37.0 70-74 36.088899999999995 37.0 37.0 37.0 37.0 37.0 75-79 36.002300000000005 37.0 37.0 37.0 37.0 37.0 80-84 35.9752 37.0 37.0 37.0 37.0 37.0 85-89 36.0453 37.0 37.0 37.0 37.0 37.0 90-94 36.0058 37.0 37.0 37.0 37.0 37.0 95-99 35.9562 37.0 37.0 37.0 37.0 37.0 100-104 35.8879 37.0 37.0 37.0 37.0 37.0 105-109 35.8605 37.0 37.0 37.0 37.0 37.0 110-114 35.7965 37.0 37.0 37.0 37.0 37.0 115-119 35.8628 37.0 37.0 37.0 37.0 37.0 120-124 35.757999999999996 37.0 37.0 37.0 37.0 37.0 125-129 35.715199999999996 37.0 37.0 37.0 37.0 37.0 130-134 35.6168 37.0 37.0 37.0 37.0 37.0 135-139 35.4279 37.0 37.0 37.0 37.0 37.0 140-144 35.437200000000004 37.0 37.0 37.0 37.0 37.0 145-149 35.2575 37.0 37.0 37.0 34.6 37.0 150-151 35.18625 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 1.0 13 1.0 14 3.0 15 1.0 16 0.0 17 3.0 18 1.0 19 4.0 20 2.0 21 2.0 22 3.0 23 6.0 24 8.0 25 9.0 26 6.0 27 12.0 28 10.0 29 14.0 30 25.0 31 33.0 32 48.0 33 93.0 34 173.0 35 469.0 36 2702.0 37 371.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 44.025 23.925 5.7 26.35 2 26.174999999999997 23.974999999999998 35.05 14.799999999999999 3 20.025000000000002 25.900000000000002 35.25 18.825 4 24.45 34.25 21.0 20.3 5 25.025 40.35 19.55 15.075 6 18.3 41.375 22.525000000000002 17.8 7 20.4 21.025 39.025 19.55 8 19.375 26.0 30.3 24.325 9 21.925 22.925 31.525 23.625 10-14 23.66 29.110000000000003 26.790000000000003 20.44 15-19 22.965 28.37 27.38 21.285 20-24 23.305 28.565 27.224999999999998 20.905 25-29 22.759999999999998 27.875 28.13 21.235 30-34 23.105 27.644999999999996 27.91 21.34 35-39 22.795 27.98 27.810000000000002 21.415 40-44 22.445 28.444999999999997 27.41 21.7 45-49 22.795 28.09 27.834999999999997 21.279999999999998 50-54 22.665 28.244999999999997 27.650000000000002 21.44 55-59 22.78 27.29 28.355000000000004 21.575 60-64 23.335 27.16 28.144999999999996 21.36 65-69 23.169999999999998 27.845 27.415 21.57 70-74 23.45 27.845 27.884999999999998 20.82 75-79 22.88 28.48 27.055 21.584999999999997 80-84 23.630000000000003 27.575 27.215 21.58 85-89 23.494999999999997 27.975 27.765 20.765 90-94 22.99 28.360000000000003 26.865 21.785 95-99 22.825 27.625 28.060000000000002 21.490000000000002 100-104 23.95 27.900000000000002 26.790000000000003 21.36 105-109 24.065 27.925 27.589999999999996 20.419999999999998 110-114 24.115000000000002 28.165000000000003 27.465 20.255000000000003 115-119 24.16 28.78 26.450000000000003 20.61 120-124 24.48 28.32 27.045 20.155 125-129 25.124999999999996 28.144999999999996 26.51 20.22 130-134 26.179999999999996 27.775 26.555 19.49 135-139 26.005 27.689999999999998 26.825 19.48 140-144 26.945000000000004 28.189999999999998 26.07 18.795 145-149 27.62104841936775 27.696078431372552 25.80032012805122 18.882553021208484 150-151 27.187499999999996 27.8125 25.7375 19.2625 >>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 0.5 6 0.5 7 0.0 8 0.5 9 0.5 10 0.0 11 1.0 12 1.5 13 0.5 14 0.0 15 0.5 16 0.5 17 0.0 18 1.0 19 1.5 20 1.5 21 1.0 22 1.0 23 2.5 24 4.0 25 5.5 26 6.5 27 8.0 28 7.0 29 8.0 30 14.0 31 18.5 32 30.0 33 39.5 34 50.5 35 71.0 36 83.5 37 108.0 38 129.5 39 147.5 40 194.5 41 221.0 42 248.0 43 254.5 44 242.5 45 262.0 46 278.5 47 255.5 48 214.0 49 206.5 50 186.0 51 145.5 52 109.5 53 93.5 54 84.5 55 62.5 56 44.5 57 31.5 58 24.0 59 19.0 60 16.0 61 11.5 62 6.5 63 4.5 64 3.0 65 7.0 66 6.5 67 2.0 68 2.5 69 2.0 70 2.0 71 1.5 72 0.0 73 0.5 74 0.5 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 1.0 84 1.0 85 0.0 86 0.5 87 0.5 88 0.5 89 1.0 90 0.5 91 0.0 92 0.5 93 0.5 94 0.0 95 0.0 96 0.0 97 0.5 98 0.5 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 0.04 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 83.075 #Duplication Level Percentage of deduplicated Percentage of total 1 84.2913030394222 70.025 2 12.308155281372255 20.45 3 2.6181161600962986 6.525 4 0.45139933794763765 1.5 5 0.24074631357207343 1.0 6 0.06018657839301836 0.3 7 0.0 0.0 8 0.03009328919650918 0.2 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 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 8 0.2 No Hit CTCTAATCACCCAGAATTCTTAAATCTCACCAGCTCCCTACCCCCTCTTA 6 0.15 No Hit CGTAGCTGCTGATAACGACGGAGAAGATGGTGTCTCTTTGGGGACCTTGA 6 0.15 No Hit GAGTGAGGCTCATTGCAGTTGGAGCATTTCATAATTTAGCTCTTCAAGAA 5 0.125 No Hit GGGAGTTTCAAGTTGGACCTTCAGTCGGTATCTCCGCCGGAGATGAATTA 5 0.125 No Hit GTTTAGACGATTATCACTCACTTGATAGGACTGGAAGGAAAGAGAAGGGT 5 0.125 No Hit AATAAATAAGAGGGGGAAAAAAAAATGTTAGCTGGTCAGCACTCTCCAAT 5 0.125 No Hit AGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAA 5 0.125 No Hit ATTCTATCTCAGTTGAACCTAGAGACTGGAATTCCCATTTACGAAGCAGA 5 0.125 No Hit GTTCAAAGGCTGGCAAAATATCGTTTTTTGAAGAAACAATCAGATCTTTT 5 0.125 No Hit AGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATC 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 0.0 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 0.05 0.0 0.0 0.0 0.0 64-65 0.075 0.0 0.0 0.0 0.0 66-67 0.075 0.0 0.0 0.0 0.0 68-69 0.075 0.0 0.0 0.0 0.0 70-71 0.075 0.0 0.0 0.0 0.0 72-73 0.1125 0.0 0.0 0.0 0.0 74-75 0.125 0.0 0.0 0.0 0.0 76-77 0.15 0.0 0.0 0.0 0.0 78-79 0.3125 0.0 0.0 0.0 0.0 80-81 0.35 0.0 0.0 0.0 0.0 82-83 0.425 0.0 0.0 0.0 0.0 84-85 0.55 0.0 0.0 0.0 0.0 86-87 0.7125 0.0 0.0 0.0 0.0 88-89 0.875 0.0 0.0 0.0 0.0 90-91 1.0375 0.0 0.0 0.0 0.0 92-93 1.25 0.0 0.0 0.0 0.0 94-95 1.5 0.0 0.0 0.0 0.0 96-97 1.775 0.0 0.0 0.0 0.0 98-99 2.05 0.0 0.0 0.0 0.0 100-101 2.2875 0.0 0.0 0.0 0.0 102-103 2.5875 0.0 0.0 0.0 0.0 104-105 2.8875 0.0 0.0 0.0 0.0 106-107 3.1500000000000004 0.0 0.0 0.0 0.0 108-109 3.4875 0.0 0.0 0.0 0.0 110-111 4.0375 0.0 0.0 0.0 0.0 112-113 4.6 0.0 0.0 0.0 0.0 114-115 5.1625 0.0 0.0 0.0 0.0 116-117 5.6 0.0 0.0 0.0 0.0 118-119 6.2125 0.0 0.0 0.0 0.0 120-121 7.0 0.0 0.0 0.0 0.0 122-123 7.675000000000001 0.0 0.0 0.0 0.0 124-125 8.4125 0.0 0.0 0.0 0.0 126-127 8.95 0.0 0.0 0.0 0.0 128-129 9.8125 0.0 0.0 0.0 0.0 130-131 10.3625 0.0 0.0 0.0 0.0 132-133 11.025 0.0 0.0 0.0 0.0 134-135 11.575 0.0 0.0 0.0 0.0 136-137 12.15 0.0 0.0 0.0 0.0 138-139 12.925 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AATAGCT 10 0.006830828 145.0 7 CTCATGG 10 0.006830828 145.0 145 >>END_MODULE Read 1080623 spots for SRR12671365.sra Written 1080623 spots for SRR12671365.sra Read 1080623 spots for SRR12671365.sra Written 1080623 spots for SRR12671365.sra Read 1080623 spots for SRR12671365.sra Written 1080623 spots for SRR12671365.sra Read 1080623 spots for SRR12671365.sra Written 1080623 spots for SRR12671365.sra Read 1080623 spots for SRR12671365.sra Written 1080623 spots for SRR12671365.sra Read 1080623 spots for SRR12671365.sra Written 1080623 spots for SRR12671365.sra Read 1080623 spots for SRR12671365.sra Written 1080623 spots for SRR12671365.sra Read 1080623 spots for SRR12671365.sra Written 1080623 spots for SRR12671365.sra Read 1080623 spots for SRR12671365.sra Written 1080623 spots for SRR12671365.sra Read 1080623 spots for SRR12671365.sra Written 1080623 spots for SRR12671365.sra Read 1080623 spots for SRR12671365.sra Written 1080623 spots for SRR12671365.sra Read 1080623 spots for SRR12671365.sra Written 1080623 spots for SRR12671365.sra Read 1080623 spots for SRR12671365.sra Written 1080623 spots for SRR12671365.sra Read 1080623 spots for SRR12671365.sra Written 1080623 spots for SRR12671365.sra Read 1080623 spots for SRR12671365.sra Written 1080623 spots for SRR12671365.sra Read 1080623 spots for SRR12671365.sra Written 1080623 spots for SRR12671365.sra Read 1080623 spots for SRR12671365.sra Written 1080623 spots for SRR12671365.sra Read 1080623 spots for SRR12671365.sra Written 1080623 spots for SRR12671365.sra Read 1080633 spots for SRR12671365.sra Written 1080633 spots for SRR12671365.sra Read 1080623 spots for SRR12671365.sra Written 1080623 spots for SRR12671365.sra SRR ids: ['SRR12671365.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_budjbxxn SRR12671365.sra spots: 21612470 blocks: [[1, 1080623], [1080624, 2161246], [2161247, 3241869], [3241870, 4322492], [4322493, 5403115], [5403116, 6483738], [6483739, 7564361], [7564362, 8644984], [8644985, 9725607], [9725608, 10806230], [10806231, 11886853], [11886854, 12967476], [12967477, 14048099], [14048100, 15128722], [15128723, 16209345], [16209346, 17289968], [17289969, 18370591], [18370592, 19451214], [19451215, 20531837], [20531838, 21612470]] SRR12671365 file size 7323162 SRR12671365 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 SRR12671365 SRR12671365_1.fastq SRR12671365_2.fastq Input file: SRR12671365_1.fastq Paired file: SRR12671365_2.fastq trimmed: SRR12671365-trimmed-pair1.fastq, SRR12671365-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 19:18:25 2025 >> started Tue Feb 11 19:18:53 2025 >> done (28.677s) 21612470 read pairs processed; of these: 304 ( 0.00%) short read pairs filtered out after trimming by size control 3995 ( 0.02%) empty read pairs filtered out after trimming by size control 21608171 (99.98%) read pairs available; of these: 3257957 (15.08%) trimmed read pairs available after processing 18350214 (84.92%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 24 0.00% 19 31 0.00% 20 22 0.00% 21 20 0.00% 22 24 0.00% 23 36 0.00% 24 29 0.00% 25 29 0.00% 26 45 0.00% 27 49 0.00% 28 37 0.00% 29 61 0.00% 30 49 0.00% 31 43 0.00% 32 58 0.00% 33 57 0.00% 34 75 0.00% 35 44 0.00% 36 63 0.00% 37 68 0.00% 38 70 0.00% 39 59 0.00% 40 68 0.00% 41 83 0.00% 42 75 0.00% 43 89 0.00% 44 82 0.00% 45 88 0.00% 46 125 0.00% 47 115 0.00% 48 161 0.00% 49 156 0.00% 50 194 0.00% 51 242 0.00% 52 270 0.00% 53 276 0.00% 54 328 0.00% 55 314 0.00% 56 369 0.00% 57 409 0.00% 58 507 0.00% 59 668 0.00% 60 745 0.00% 61 839 0.00% 62 1002 0.00% 63 1041 0.00% 64 1163 0.01% 65 1337 0.01% 66 1497 0.01% 67 1687 0.01% 68 1969 0.01% 69 2237 0.01% 70 2639 0.01% 71 3103 0.01% 72 3372 0.02% 73 3833 0.02% 74 4373 0.02% 75 4932 0.02% 76 5409 0.03% 77 5838 0.03% 78 6353 0.03% 79 6998 0.03% 80 7660 0.04% 81 8772 0.04% 82 9553 0.04% 83 10441 0.05% 84 11779 0.05% 85 12732 0.06% 86 13336 0.06% 87 14603 0.07% 88 15671 0.07% 89 16062 0.07% 90 17156 0.08% 91 18584 0.09% 92 19486 0.09% 93 20907 0.10% 94 22244 0.10% 95 23895 0.11% 96 24887 0.12% 97 26360 0.12% 98 26543 0.12% 99 28038 0.13% 100 29131 0.13% 101 29790 0.14% 102 31109 0.14% 103 32820 0.15% 104 33854 0.16% 105 35360 0.16% 106 36745 0.17% 107 37435 0.17% 108 38788 0.18% 109 39964 0.18% 110 40804 0.19% 111 41752 0.19% 112 42733 0.20% 113 43170 0.20% 114 45458 0.21% 115 46464 0.22% 116 48013 0.22% 117 49259 0.23% 118 50869 0.24% 119 50824 0.24% 120 52326 0.24% 121 52847 0.24% 122 53661 0.25% 123 55166 0.26% 124 56598 0.26% 125 56668 0.26% 126 59498 0.28% 127 60375 0.28% 128 60898 0.28% 129 62333 0.29% 130 62592 0.29% 131 62752 0.29% 132 63840 0.30% 133 64854 0.30% 134 65067 0.30% 135 66646 0.31% 136 67208 0.31% 137 67788 0.31% 138 68976 0.32% 139 70859 0.33% 140 70510 0.33% 141 70822 0.33% 142 71864 0.33% 143 71357 0.33% 144 72710 0.34% 145 73286 0.34% 146 73851 0.34% 147 74682 0.35% 148 76064 0.35% 149 75684 0.35% 150 77145 0.36% 151 18350214 84.92% 21608171 reads passed initial QC criterion=sequence-density sequence-density=0.40 sequence-density-rank=1 fanout-score=2.17 fanout-score-rank=32 prefix-density=0.42 prefix-fanout=2.0 sequence=TTCCACATAGTCCAGTAGCGTCCATCATAGTACCCTGGTGAGCTGTGGTGCTCACGGTAGACCCAACCTTTCTCCAACTCGAATTCCAAGCAAGGAACCCACTTCGAGCGAAGAAGGTAATCAATTTCCTTGGCCAATTCCTCCTCTGTGAGATCTGGAAGGTAAGAAAGAGTCTCGAACTTCTTCAATCCAGTTGGTGGCCACACCTGCATGCATTGAACTCGTCCACCATTGCTTGCAATGGAAGTAATGTCATTAGCCTTTCTGGTACTGACTGGGAAAGCTGCGGCAGACTTGAGACCATTGAATGGTGCCACCATGTTGGCTTGTGCCGGGGTGCGGTTGACGGTGGCAACGGCTGCCGATGAGATCATAGAGGAGGAAGCCAT criterion=fanout-score sequence-density=0.01 sequence-density-rank=37 fanout-score=389.39 fanout-score-rank=1 prefix-density=0.27 prefix-fanout=15.5 sequence=TGAAGAAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAGTTGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGGAGTATGAATGTGTTCTCTG criterion=sequence-density sequence-density=0.66 sequence-density-rank=1 fanout-score=1.99 fanout-score-rank=34 prefix-density=0.66 prefix-fanout=2.0 sequence=CTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGGAGTGAACAAACAAAAGTGTCCGTGAGTGTCTTTATCTTTGTGTCTTCTTCA criterion=fanout-score sequence-density=0.15 sequence-density-rank=13 fanout-score=34.69 fanout-score-rank=1 prefix-density=0.41 prefix-fanout=12.5 sequence=AAAGAAAAGAAAA SRR12671365 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 19:19:36 Started mapping on | Feb 11 19:19:36 Finished on | Feb 11 19:21:43 Mapping speed, Million of reads per hour | 612.52 Number of input reads | 21608171 Average input read length | 293 UNIQUE READS: Uniquely mapped reads number | 20008684 Uniquely mapped reads % | 92.60% Average mapped length | 291.95 Number of splices: Total | 19574306 Number of splices: Annotated (sjdb) | 19136291 Number of splices: GT/AG | 19170014 Number of splices: GC/AG | 331961 Number of splices: AT/AC | 13431 Number of splices: Non-canonical | 58900 Mismatch rate per base, % | 0.36% Deletion rate per base | 0.03% Deletion average length | 2.90 Insertion rate per base | 0.02% Insertion average length | 2.26 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 511721 % of reads mapped to multiple loci | 2.37% Number of reads mapped to too many loci | 183876 % of reads mapped to too many loci | 0.85% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.98% % of reads unmapped: other | 0.20% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1087766 1087766 1087766 N_multimapping 511721 511721 511721 N_noFeature 821841 19724170 943142 N_ambiguous 279652 1199 115796 UnstrandedReadsAssigned:18907191 PositiveStrandReadsAssigned:283315 NegativeStrandReadsAssigned:18949746 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12671365 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: SRR12671365-trimmed-pair1.fastq SRR12671365-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 21,608,171 reads, 19,056,507 reads pseudoaligned [quant] estimated average fragment length: 247.12 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,023 rounds 52401 SRR12671365.ke.tsv 34699 SRR12671365.se.tsv 87100 total ==> SRR12671365.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1771.88 668 20.3551 Potri.005G024800.1.v4.1 1035 788.88 213 14.5781 Potri.004G059700.1.v4.1 961 715.129 6 0.453001 Potri.007G009000.2.v4.1 1416 1169.88 0 0 Potri.003G141000.2.v4.1 2943 2696.88 1060.87 21.239 Potri.016G087400.1.v4.1 270 94.6593 721 411.248 Potri.015G069301.1.v4.1 564 333.669 0 0 Potri.010G195200.1.v4.1 1773 1526.88 22 0.777946 Potri.012G127500.1.v4.1 977 731.011 94 6.94282 ==> SRR12671365.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 147 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 212 Potri.001G212900.v4.1 2 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 11 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 9 SRR12671365 completed mapping pipeline successfully