Starting /dee2/code/volunteer_pipeline.sh SRR12670147 current disk space = 3056955293696 free memory = 1479986936 SRR12670147 SRAfilesize ff60a714498b88df3c16bdeead29d976 SRR12670147.sra SRR12670147.sra file validated SRR12670147 is paired end SRR12670147 is conventional basespace SRR12670147 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670147_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 36.593 37.0 37.0 37.0 37.0 37.0 2 36.45 37.0 37.0 37.0 37.0 37.0 3 36.6325 37.0 37.0 37.0 37.0 37.0 4 36.6 37.0 37.0 37.0 37.0 37.0 5 36.6525 37.0 37.0 37.0 37.0 37.0 6 36.6295 37.0 37.0 37.0 37.0 37.0 7 36.602 37.0 37.0 37.0 37.0 37.0 8 36.6335 37.0 37.0 37.0 37.0 37.0 9 36.5725 37.0 37.0 37.0 37.0 37.0 10-14 36.629200000000004 37.0 37.0 37.0 37.0 37.0 15-19 36.5818 37.0 37.0 37.0 37.0 37.0 20-24 36.5346 37.0 37.0 37.0 37.0 37.0 25-29 36.4719 37.0 37.0 37.0 37.0 37.0 30-34 36.477 37.0 37.0 37.0 37.0 37.0 35-39 36.468 37.0 37.0 37.0 37.0 37.0 40-44 36.4506 37.0 37.0 37.0 37.0 37.0 45-49 36.4275 37.0 37.0 37.0 37.0 37.0 50-54 36.4128 37.0 37.0 37.0 37.0 37.0 55-59 36.394 37.0 37.0 37.0 37.0 37.0 60-64 36.3163 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 36.26129999999999 37.0 37.0 37.0 37.0 37.0 75-79 36.281600000000005 37.0 37.0 37.0 37.0 37.0 80-84 36.2125 37.0 37.0 37.0 37.0 37.0 85-89 36.2157 37.0 37.0 37.0 37.0 37.0 90-94 36.2167 37.0 37.0 37.0 37.0 37.0 95-99 36.1909 37.0 37.0 37.0 37.0 37.0 100-104 36.1712 37.0 37.0 37.0 37.0 37.0 105-109 36.1962 37.0 37.0 37.0 37.0 37.0 110-114 36.0511 37.0 37.0 37.0 37.0 37.0 115-119 36.062400000000004 37.0 37.0 37.0 37.0 37.0 120-124 35.898900000000005 37.0 37.0 37.0 37.0 37.0 125-129 35.739999999999995 37.0 37.0 37.0 37.0 37.0 130-134 35.5436 37.0 37.0 37.0 37.0 37.0 135-139 35.3134 37.0 37.0 37.0 37.0 37.0 140-144 35.0444 37.0 37.0 37.0 25.0 37.0 145-149 34.772299999999994 37.0 37.0 37.0 25.0 37.0 150-151 34.518249999999995 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 22 1.0 23 0.0 24 3.0 25 0.0 26 2.0 27 3.0 28 11.0 29 22.0 30 24.0 31 36.0 32 65.0 33 108.0 34 181.0 35 439.0 36 2804.0 37 301.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 39.775 11.075 6.2 42.95 2 18.56856856856857 11.861861861861863 37.36236236236236 32.207207207207205 3 16.675 16.950000000000003 26.275 40.1 4 22.7 24.425 23.150000000000002 29.725 5 22.75 31.0 25.374999999999996 20.875 6 21.375 33.4 24.175 21.05 7 16.55 25.074999999999996 40.625 17.75 8 19.6 26.3 31.7 22.400000000000002 9 18.3 23.45 34.55 23.7 10-14 20.45 28.970000000000002 27.825 22.755 15-19 20.505000000000003 27.375 27.839999999999996 24.279999999999998 20-24 20.625 27.644999999999996 28.095 23.635 25-29 20.4 28.415000000000003 27.595 23.59 30-34 20.244999999999997 27.93 27.79 24.035 35-39 20.65 28.025 28.439999999999998 22.884999999999998 40-44 20.560000000000002 28.065 27.625 23.75 45-49 20.65 27.605 28.110000000000003 23.635 50-54 21.37 27.939999999999998 27.165 23.525 55-59 20.335 27.785 28.49 23.39 60-64 20.544999999999998 27.544999999999998 28.32 23.59 65-69 20.905 27.68 27.77 23.645 70-74 20.424999999999997 28.16 27.584999999999997 23.830000000000002 75-79 20.77 28.025 28.1 23.105 80-84 20.855 28.015 27.485 23.645 85-89 21.08 28.294999999999998 27.3 23.325000000000003 90-94 21.22 28.225 27.04 23.515 95-99 21.255 28.265 26.61 23.87 100-104 21.55 29.075 26.235000000000003 23.14 105-109 21.529999999999998 28.02 26.645000000000003 23.805 110-114 21.955 28.744999999999997 26.07 23.23 115-119 21.575 27.944999999999997 25.885 24.595 120-124 20.465 28.34 25.96 25.235000000000003 125-129 20.89 27.775 25.765 25.569999999999997 130-134 21.365000000000002 27.810000000000002 26.365 24.46 135-139 21.7 27.165 26.02 25.115 140-144 22.405 26.14 26.145000000000003 25.31 145-149 22.29 26.215 26.445 25.05 150-151 24.025 24.875 26.424999999999997 24.675 >>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 0.5 17 0.5 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.5 25 0.5 26 2.0 27 5.0 28 4.5 29 6.5 30 11.5 31 15.0 32 23.0 33 37.0 34 48.5 35 67.0 36 87.0 37 93.0 38 119.0 39 151.5 40 183.0 41 209.0 42 242.0 43 250.5 44 261.0 45 280.0 46 260.0 47 252.0 48 232.5 49 208.5 50 180.5 51 154.0 52 143.0 53 107.5 54 75.5 55 74.0 56 60.0 57 47.0 58 37.0 59 23.0 60 16.0 61 13.0 62 8.0 63 2.0 64 2.5 65 3.0 66 2.5 67 0.5 68 0.0 69 0.0 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 0.1 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 80.925 #Duplication Level Percentage of deduplicated Percentage of total 1 82.39110287303059 66.675 2 13.253012048192772 21.45 3 3.1819586036453504 7.725 4 0.8032128514056224 2.6 5 0.3089280197713933 1.25 6 0.06178560395427865 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 CTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAAC 6 0.15 No Hit CGTCTGCGCTGCTGTTGATGCATGTAATTTGTGAGACGACGGGCACACAT 6 0.15 No Hit GCATAATTTGATGAAGATAGCTCTCTTGATTTGATAATAGCTTTATTTGG 5 0.125 No Hit GCCAAGGCGTTCAAACTGGAATCTATCCCCCATGGCAGCATCTCTAAGTG 5 0.125 No Hit CACTAGGGCAGAGAGAACGATAATATTTGGCAAACTTATCACACTCTGAA 5 0.125 No Hit CTTGATTTGAATGGCCGCTCGCCCAAAACTCGAATCAAGTCTTCTTGGTG 5 0.125 No Hit CTCTCCTAGAGCGTTGTAGTTCTTTCCATGCTTTACAAGCCACTCCTCGT 5 0.125 No Hit ACCTGGCCCTGCATCTGTTGCCCTGGAAAACCTTGGGGAGGCAGCATTGG 5 0.125 No Hit CCTGGTTCTGCTGGTTTCCAAATCTCAACAAGAGATGACAGAACATTAAC 5 0.125 No Hit AGGGTCAACGCTGTACCAGTGGCTCTTAGCCCTTCTGATCTCTCTAACAC 5 0.125 No Hit CCTGTCGTTGAGCTGCTATTATACAAAGCAATAAAAGTCTTTTCTTTTTT 5 0.125 No Hit GGAAAGGGGACTGGACTGTGTGAGTATGCTGGAAAGGGGTCACAATGAGA 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 0.025 0.0 0.0 0.0 0.0 44-45 0.0625 0.0 0.0 0.0 0.0 46-47 0.075 0.0 0.0 0.0 0.0 48-49 0.1 0.0 0.0 0.0 0.0 50-51 0.125 0.0 0.0 0.0 0.0 52-53 0.15 0.0 0.0 0.0 0.0 54-55 0.175 0.0 0.0 0.0 0.0 56-57 0.1875 0.0 0.0 0.0 0.0 58-59 0.25 0.0 0.0 0.0 0.0 60-61 0.3 0.0 0.0 0.0 0.0 62-63 0.45 0.0 0.0 0.0 0.0 64-65 0.6000000000000001 0.0 0.0 0.0 0.0 66-67 0.675 0.0 0.0 0.0 0.0 68-69 0.725 0.0 0.0 0.0 0.0 70-71 0.8374999999999999 0.0 0.0 0.0 0.0 72-73 1.0375 0.0 0.0 0.0 0.0 74-75 1.2125 0.0 0.0 0.0 0.0 76-77 1.5 0.0 0.0 0.0 0.0 78-79 1.7625 0.0 0.0 0.0 0.0 80-81 2.1500000000000004 0.0 0.0 0.0 0.0 82-83 2.6625 0.0 0.0 0.0 0.0 84-85 3.0875000000000004 0.0 0.0 0.0 0.0 86-87 3.7125000000000004 0.0 0.0 0.0 0.0 88-89 4.525 0.0 0.0 0.0 0.0 90-91 5.4375 0.0 0.0 0.0 0.0 92-93 6.375 0.0 0.0 0.0 0.0 94-95 7.2625 0.0 0.0 0.0 0.0 96-97 7.987500000000001 0.0 0.0 0.0 0.0 98-99 9.075 0.0 0.0 0.0 0.0 100-101 10.1625 0.0 0.0 0.0 0.0 102-103 11.524999999999999 0.0 0.0 0.0 0.0 104-105 12.525 0.0 0.0 0.0 0.0 106-107 13.5 0.0 0.0 0.0 0.0 108-109 14.7375 0.0 0.0 0.0 0.0 110-111 15.9875 0.0 0.0 0.0 0.0 112-113 17.15 0.0 0.0 0.0 0.0 114-115 18.2125 0.0 0.0 0.0 0.0 116-117 19.3125 0.0 0.0 0.0 0.0 118-119 20.25 0.0 0.0 0.0 0.0 120-121 21.2875 0.0 0.0 0.0 0.0 122-123 22.5 0.0 0.0 0.0 0.0 124-125 23.8375 0.0 0.0 0.0 0.0 126-127 24.9625 0.0 0.0 0.0 0.0 128-129 25.9375 0.0 0.0 0.0 0.0 130-131 26.8125 0.0 0.0 0.0 0.0 132-133 27.549999999999997 0.0 0.0 0.0 0.0 134-135 28.6875 0.0 0.0 0.0 0.0 136-137 29.5375 0.0 0.0 0.0 0.0 138-139 30.5125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ATCTCGT 40 2.9585467E-4 21.75 140-144 GATCTCG 40 0.0076550315 18.125 140-144 CCGAGAT 50 0.0013298223 17.4 135-139 ACTTACC 55 0.0025160722 15.818182 130-134 >>END_MODULE SRR12670147 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670147_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 36.402 37.0 37.0 37.0 37.0 37.0 2 36.203 37.0 37.0 37.0 37.0 37.0 3 36.16 37.0 37.0 37.0 37.0 37.0 4 36.3525 37.0 37.0 37.0 37.0 37.0 5 36.372 37.0 37.0 37.0 37.0 37.0 6 36.2575 37.0 37.0 37.0 37.0 37.0 7 36.1845 37.0 37.0 37.0 37.0 37.0 8 36.378 37.0 37.0 37.0 37.0 37.0 9 36.3315 37.0 37.0 37.0 37.0 37.0 10-14 36.3772 37.0 37.0 37.0 37.0 37.0 15-19 36.333 37.0 37.0 37.0 37.0 37.0 20-24 36.2679 37.0 37.0 37.0 37.0 37.0 25-29 36.2635 37.0 37.0 37.0 37.0 37.0 30-34 36.2427 37.0 37.0 37.0 37.0 37.0 35-39 36.1806 37.0 37.0 37.0 37.0 37.0 40-44 36.161 37.0 37.0 37.0 37.0 37.0 45-49 36.2097 37.0 37.0 37.0 37.0 37.0 50-54 36.096199999999996 37.0 37.0 37.0 37.0 37.0 55-59 36.1424 37.0 37.0 37.0 37.0 37.0 60-64 36.025099999999995 37.0 37.0 37.0 37.0 37.0 65-69 36.081500000000005 37.0 37.0 37.0 37.0 37.0 70-74 36.015 37.0 37.0 37.0 37.0 37.0 75-79 36.0033 37.0 37.0 37.0 37.0 37.0 80-84 35.942600000000006 37.0 37.0 37.0 37.0 37.0 85-89 35.971000000000004 37.0 37.0 37.0 37.0 37.0 90-94 35.8993 37.0 37.0 37.0 37.0 37.0 95-99 35.8654 37.0 37.0 37.0 37.0 37.0 100-104 35.792699999999996 37.0 37.0 37.0 37.0 37.0 105-109 35.6752 37.0 37.0 37.0 37.0 37.0 110-114 35.5981 37.0 37.0 37.0 37.0 37.0 115-119 35.5655 37.0 37.0 37.0 37.0 37.0 120-124 35.392399999999995 37.0 37.0 37.0 37.0 37.0 125-129 35.18079999999999 37.0 37.0 37.0 32.2 37.0 130-134 34.8887 37.0 37.0 37.0 25.0 37.0 135-139 34.57379999999999 37.0 37.0 37.0 25.0 37.0 140-144 34.2422 37.0 37.0 37.0 25.0 37.0 145-149 33.7389 37.0 37.0 37.0 22.2 37.0 150-151 33.244749999999996 37.0 37.0 37.0 11.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 6.0 14 0.0 15 2.0 16 2.0 17 1.0 18 2.0 19 0.0 20 0.0 21 0.0 22 2.0 23 4.0 24 3.0 25 5.0 26 13.0 27 11.0 28 17.0 29 16.0 30 36.0 31 56.0 32 98.0 33 156.0 34 272.0 35 600.0 36 2470.0 37 228.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 38.324999999999996 22.725 9.700000000000001 29.25 2 26.25 26.525 31.225 16.0 3 19.7 27.425 31.65 21.224999999999998 4 22.1 33.925 25.0 18.975 5 26.5 35.025 20.7 17.775 6 21.725 38.85 22.5 16.925 7 19.3 23.225 37.824999999999996 19.650000000000002 8 21.325 26.05 28.449999999999996 24.175 9 22.650000000000002 27.0 29.025000000000002 21.325 10-14 23.055 29.65 26.245 21.05 15-19 23.810000000000002 28.060000000000002 27.82 20.31 20-24 23.255 28.33 27.465 20.95 25-29 22.845 28.735 27.83 20.59 30-34 23.135 28.13 27.63 21.105 35-39 22.225 28.925 27.68 21.17 40-44 22.835 28.205000000000002 27.750000000000004 21.21 45-49 22.84 27.705000000000002 28.134999999999998 21.32 50-54 22.195 28.88 27.750000000000004 21.175 55-59 22.855 28.43 27.345000000000002 21.37 60-64 23.845 28.044999999999998 27.310000000000002 20.8 65-69 23.830000000000002 27.284999999999997 27.73 21.154999999999998 70-74 24.22 27.915 26.455000000000002 21.41 75-79 24.09 28.345 27.05 20.515 80-84 23.745 27.965 27.35 20.94 85-89 24.47 28.799999999999997 26.1 20.630000000000003 90-94 24.54 27.650000000000002 26.755000000000003 21.055 95-99 25.324999999999996 28.32 26.135 20.22 100-104 25.674999999999997 28.26 25.5 20.565 105-109 26.41 27.474999999999998 26.14 19.975 110-114 26.87 27.944999999999997 26.005 19.18 115-119 27.47 28.854999999999997 24.635 19.040000000000003 120-124 27.500000000000004 28.494999999999997 25.2 18.805 125-129 27.97 28.005000000000003 24.965 19.06 130-134 29.599999999999998 26.5 26.06 17.84 135-139 29.959999999999997 26.840000000000003 25.014999999999997 18.185000000000002 140-144 30.875000000000004 25.929999999999996 25.935000000000002 17.26 145-149 32.684999999999995 25.755 24.45 17.11 150-151 34.525 24.887500000000003 23.9125 16.675 >>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 0.5 11 1.0 12 0.5 13 0.0 14 0.0 15 0.0 16 0.5 17 1.0 18 1.5 19 2.0 20 1.0 21 0.0 22 0.5 23 1.0 24 1.5 25 1.0 26 1.0 27 3.5 28 5.5 29 7.5 30 8.5 31 15.5 32 27.5 33 33.5 34 38.5 35 58.0 36 81.0 37 111.0 38 134.0 39 162.0 40 204.0 41 226.5 42 246.0 43 262.0 44 276.5 45 284.5 46 271.5 47 248.0 48 222.0 49 202.5 50 170.0 51 134.0 52 115.0 53 103.5 54 81.5 55 58.0 56 45.0 57 34.5 58 29.5 59 21.0 60 16.5 61 16.0 62 9.5 63 5.0 64 4.0 65 1.0 66 1.0 67 1.0 68 0.5 69 0.5 70 0.5 71 1.0 72 1.0 73 0.0 74 0.0 75 0.0 76 0.0 77 0.5 78 0.5 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 0.5 89 0.5 90 0.5 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 1.0 97 1.5 98 0.5 99 0.5 100 0.5 >>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 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 80.975 #Duplication Level Percentage of deduplicated Percentage of total 1 82.7107131830812 66.975 2 12.7817227539364 20.7 3 3.272615004631059 7.95 4 0.8335906143871564 2.7 5 0.33961099104661935 1.375 6 0.06174745291756715 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 CAACAATTTCAACAACAGAACTTACCTTTGAGATCTCCAGTAAAATCAGT 6 0.15 No Hit AACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATCAA 6 0.15 No Hit CATAAGATATCCTGCTGGCCAAAAGGCATACAAATTGTATAACCTTTCAA 5 0.125 No Hit AAGCACACAAATTAAGGCTTAAAGATATAGAGAGAAAGAAACAACATGTC 5 0.125 No Hit CAGCTTTTATATCCCCTATTCTCTTCGTGAAGATGTCTTGCTGTGGAGGA 5 0.125 No Hit CAACCATTAATCTTGATGAGGAAACCCTTGGTAGCATTAGCACAGTTGCC 5 0.125 No Hit AACAAACCTCAATCTGTTGCTGCAGCCAATGGCACACTGCCTTCTCAACC 5 0.125 No Hit GGTGACGAAAATGACATACGCCCAAGTTGCAGTGTATGGTTTTAGTGACA 5 0.125 No Hit GCTGTAGATGAGGATTATCTATTTGTTATTTTAGGCAACCCAAGTTTAAC 5 0.125 No Hit CAGAGAACACATTCATACCCCAAGTCTTTTAGTTCATCCATTTAAGCTTA 5 0.125 No Hit CCGCAGTCCAAAGTGGTGATATCCGGTGCATATGCTGTACCATCACTTAG 5 0.125 No Hit GTGTTAAATAGATTGACATATGCCTCTACACTGTCACATTTAAGAAGATT 5 0.125 No Hit TACAAGTTTGACATGAAAACCCTTGTTCTAAAGGTTCCTTCAAGCCAGAG 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 0.025 0.0 0.0 0.0 0.0 44-45 0.0625 0.0 0.0 0.0 0.0 46-47 0.075 0.0 0.0 0.0 0.0 48-49 0.1 0.0 0.0 0.0 0.0 50-51 0.125 0.0 0.0 0.0 0.0 52-53 0.15 0.0 0.0 0.0 0.0 54-55 0.175 0.0 0.0 0.0 0.0 56-57 0.1875 0.0 0.0 0.0 0.0 58-59 0.25 0.0 0.0 0.0 0.0 60-61 0.3 0.0 0.0 0.0 0.0 62-63 0.45 0.0 0.0 0.0 0.0 64-65 0.6000000000000001 0.0 0.0 0.0 0.0 66-67 0.6625000000000001 0.0 0.0 0.0 0.0 68-69 0.7124999999999999 0.0 0.0 0.0 0.0 70-71 0.8374999999999999 0.0 0.0 0.0 0.0 72-73 1.0375 0.0 0.0 0.0 0.0 74-75 1.2125 0.0 0.0 0.0 0.0 76-77 1.5 0.0 0.0 0.0 0.0 78-79 1.7625 0.0 0.0 0.0 0.0 80-81 2.1500000000000004 0.0 0.0 0.0 0.0 82-83 2.6625 0.0 0.0 0.0 0.0 84-85 3.0875000000000004 0.0 0.0 0.0 0.0 86-87 3.7125000000000004 0.0 0.0 0.0 0.0 88-89 4.525 0.0 0.0 0.0 0.0 90-91 5.4375 0.0 0.0 0.0 0.0 92-93 6.3625 0.0 0.0 0.0 0.0 94-95 7.25 0.0 0.0 0.0 0.0 96-97 8.0 0.0 0.0 0.0 0.0 98-99 9.0625 0.0 0.0 0.0 0.0 100-101 10.1125 0.0 0.0 0.0 0.0 102-103 11.475000000000001 0.0 0.0 0.0 0.0 104-105 12.475 0.0 0.0 0.0 0.0 106-107 13.475 0.0 0.0 0.0 0.0 108-109 14.725000000000001 0.0 0.0 0.0 0.0 110-111 15.9375 0.0 0.0 0.0 0.0 112-113 17.1 0.0 0.0 0.0 0.0 114-115 18.1625 0.0 0.0 0.0 0.0 116-117 19.2375 0.0 0.0 0.0 0.0 118-119 20.2 0.0 0.0 0.0 0.0 120-121 21.3 0.0 0.0 0.0 0.0 122-123 22.55 0.0 0.0 0.0 0.0 124-125 23.8875 0.0 0.0 0.0 0.0 126-127 24.9875 0.0 0.0 0.0 0.0 128-129 25.9625 0.0 0.0 0.0 0.0 130-131 26.8625 0.0 0.0 0.0 0.0 132-133 27.5625 0.0 0.0 0.0 0.0 134-135 28.725 0.0 0.0 0.0 0.0 136-137 29.6375 0.0 0.0 0.0 0.0 138-139 30.6375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AGAGGTA 10 0.006830828 145.0 4 GCTGTAG 10 0.006830828 145.0 1 TAGAGTA 10 0.006830828 145.0 7 CTGTAGA 10 0.006830828 145.0 2 CGAGGTG 50 0.0013298223 17.4 135-139 TTTACCG 60 0.004491891 14.500001 130-134 GTTTACC 65 0.0076375785 13.384615 130-134 GGAAAGA 90 0.0048656333 11.277777 120-124 >>END_MODULE Read 619721 spots for SRR12670147.sra Written 619721 spots for SRR12670147.sra Read 619715 spots for SRR12670147.sra Written 619715 spots for SRR12670147.sra Read 619715 spots for SRR12670147.sra Written 619715 spots for SRR12670147.sra Read 619715 spots for SRR12670147.sra Written 619715 spots for SRR12670147.sra Read 619715 spots for SRR12670147.sra Written 619715 spots for SRR12670147.sra Read 619715 spots for SRR12670147.sra Written 619715 spots for SRR12670147.sra Read 619715 spots for SRR12670147.sra Written 619715 spots for SRR12670147.sra Read 619715 spots for SRR12670147.sra Written 619715 spots for SRR12670147.sra Read 619715 spots for SRR12670147.sra Written 619715 spots for SRR12670147.sra Read 619715 spots for SRR12670147.sra Written 619715 spots for SRR12670147.sra Read 619715 spots for SRR12670147.sra Written 619715 spots for SRR12670147.sra Read 619715 spots for SRR12670147.sra Written 619715 spots for SRR12670147.sra Read 619715 spots for SRR12670147.sra Written 619715 spots for SRR12670147.sra Read 619715 spots for SRR12670147.sra Written 619715 spots for SRR12670147.sra Read 619715 spots for SRR12670147.sra Written 619715 spots for SRR12670147.sra Read 619715 spots for SRR12670147.sra Written 619715 spots for SRR12670147.sra Read 619715 spots for SRR12670147.sra Written 619715 spots for SRR12670147.sra Read 619715 spots for SRR12670147.sra Written 619715 spots for SRR12670147.sra Read 619715 spots for SRR12670147.sra Written 619715 spots for SRR12670147.sra Read 619715 spots for SRR12670147.sra Written 619715 spots for SRR12670147.sra SRR ids: ['SRR12670147.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_xmptiwlc SRR12670147.sra spots: 12394306 blocks: [[1, 619715], [619716, 1239430], [1239431, 1859145], [1859146, 2478860], [2478861, 3098575], [3098576, 3718290], [3718291, 4338005], [4338006, 4957720], [4957721, 5577435], [5577436, 6197150], [6197151, 6816865], [6816866, 7436580], [7436581, 8056295], [8056296, 8676010], [8676011, 9295725], [9295726, 9915440], [9915441, 10535155], [10535156, 11154870], [11154871, 11774585], [11774586, 12394306]] SRR12670147 file size 4190427 SRR12670147 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 SRR12670147 SRR12670147_1.fastq SRR12670147_2.fastq Input file: SRR12670147_1.fastq Paired file: SRR12670147_2.fastq trimmed: SRR12670147-trimmed-pair1.fastq, SRR12670147-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 02:53:32 2025 >> started Tue Feb 11 03:05:43 2025 >> done (731.094s) 12394306 read pairs processed; of these: 44 ( 0.00%) short read pairs filtered out after trimming by size control 10798 ( 0.09%) empty read pairs filtered out after trimming by size control 12383464 (99.91%) read pairs available; of these: 4149945 (33.51%) trimmed read pairs available after processing 8233519 (66.49%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 2 0.00% 19 2 0.00% 20 11 0.00% 21 5 0.00% 22 8 0.00% 23 12 0.00% 24 16 0.00% 25 10 0.00% 26 27 0.00% 27 34 0.00% 28 45 0.00% 29 62 0.00% 30 59 0.00% 31 85 0.00% 32 78 0.00% 33 88 0.00% 34 105 0.00% 35 129 0.00% 36 162 0.00% 37 177 0.00% 38 224 0.00% 39 264 0.00% 40 330 0.00% 41 367 0.00% 42 427 0.00% 43 432 0.00% 44 446 0.00% 45 443 0.00% 46 562 0.00% 47 671 0.01% 48 826 0.01% 49 961 0.01% 50 1220 0.01% 51 1373 0.01% 52 1436 0.01% 53 1611 0.01% 54 1629 0.01% 55 1776 0.01% 56 1978 0.02% 57 2290 0.02% 58 2692 0.02% 59 3213 0.03% 60 3945 0.03% 61 4306 0.03% 62 4887 0.04% 63 5497 0.04% 64 5779 0.05% 65 6245 0.05% 66 6605 0.05% 67 7323 0.06% 68 8123 0.07% 69 9464 0.08% 70 10861 0.09% 71 12178 0.10% 72 14177 0.11% 73 15633 0.13% 74 16595 0.13% 75 17959 0.15% 76 18576 0.15% 77 19702 0.16% 78 20743 0.17% 79 22868 0.18% 80 24632 0.20% 81 27491 0.22% 82 29970 0.24% 83 32243 0.26% 84 35019 0.28% 85 36340 0.29% 86 37763 0.30% 87 38665 0.31% 88 39896 0.32% 89 40351 0.33% 90 42925 0.35% 91 44957 0.36% 92 46489 0.38% 93 50153 0.40% 94 52388 0.42% 95 54058 0.44% 96 54342 0.44% 97 54971 0.44% 98 55448 0.45% 99 54847 0.44% 100 56227 0.45% 101 55926 0.45% 102 58102 0.47% 103 59492 0.48% 104 60537 0.49% 105 61952 0.50% 106 62663 0.51% 107 61835 0.50% 108 60998 0.49% 109 61336 0.50% 110 59751 0.48% 111 59687 0.48% 112 60938 0.49% 113 61190 0.49% 114 62762 0.51% 115 63719 0.51% 116 63205 0.51% 117 63755 0.51% 118 62848 0.51% 119 61885 0.50% 120 61663 0.50% 121 60713 0.49% 122 60967 0.49% 123 61547 0.50% 124 61292 0.49% 125 61570 0.50% 126 62622 0.51% 127 62519 0.50% 128 61082 0.49% 129 60383 0.49% 130 59624 0.48% 131 58431 0.47% 132 58660 0.47% 133 58912 0.48% 134 58423 0.47% 135 58725 0.47% 136 58812 0.47% 137 58628 0.47% 138 58501 0.47% 139 58576 0.47% 140 57322 0.46% 141 57070 0.46% 142 56350 0.46% 143 55600 0.45% 144 56821 0.46% 145 56184 0.45% 146 56320 0.45% 147 56002 0.45% 148 56355 0.46% 149 55050 0.44% 150 55711 0.45% 151 8233519 66.49% 12383464 reads passed initial QC criterion=sequence-density sequence-density=0.46 sequence-density-rank=1 fanout-score=1.99 fanout-score-rank=21 prefix-density=0.43 prefix-fanout=2.0 sequence=GTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAGGTGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGG criterion=fanout-score sequence-density=0.02 sequence-density-rank=23 fanout-score=21.02 fanout-score-rank=1 prefix-density=0.13 prefix-fanout=3.1 sequence=ACCACACCAGAGGCCACAGACATGGCCAATACATAACAATGAAGAAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTC criterion=sequence-density sequence-density=0.81 sequence-density-rank=1 fanout-score=2.20 fanout-score-rank=24 prefix-density=0.83 prefix-fanout=2.2 sequence=CCAAGTCTTTTAGTTCATCCATTTAAGCTTAATCAATCAATCATCATGTCTAGCACCTGCGACACCTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGAC criterion=fanout-score sequence-density=0.14 sequence-density-rank=17 fanout-score=30.90 fanout-score-rank=1 prefix-density=0.38 prefix-fanout=11.6 sequence=AAAGAAAAGAAAA SRR12670147 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 03:47:56 Started mapping on | Feb 11 03:48:01 Finished on | Feb 11 05:23:19 Mapping speed, Million of reads per hour | 7.80 Number of input reads | 12383464 Average input read length | 277 UNIQUE READS: Uniquely mapped reads number | 11645197 Uniquely mapped reads % | 94.04% Average mapped length | 276.07 Number of splices: Total | 10809244 Number of splices: Annotated (sjdb) | 10556185 Number of splices: GT/AG | 10586949 Number of splices: GC/AG | 174959 Number of splices: AT/AC | 7191 Number of splices: Non-canonical | 40145 Mismatch rate per base, % | 0.36% Deletion rate per base | 0.03% Deletion average length | 2.77 Insertion rate per base | 0.02% Insertion average length | 2.37 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 270697 % of reads mapped to multiple loci | 2.19% Number of reads mapped to too many loci | 91783 % of reads mapped to too many loci | 0.74% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.85% % of reads unmapped: other | 0.19% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 467570 467570 467570 N_multimapping 270697 270697 270697 N_noFeature 475317 11439451 572691 N_ambiguous 168650 772 59813 UnstrandedReadsAssigned:11001230 PositiveStrandReadsAssigned:204974 NegativeStrandReadsAssigned:11012693 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=122 echo kmer=117 SRR12670147 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: SRR12670147-trimmed-pair1.fastq SRR12670147-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 12,383,464 reads, 11,061,286 reads pseudoaligned [quant] estimated average fragment length: 197.294 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,094 rounds 52401 SRR12670147.ke.tsv 34699 SRR12670147.se.tsv 87100 total ==> SRR12670147.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1821.71 313 15.6525 Potri.005G024800.1.v4.1 1035 838.706 115 12.4913 Potri.004G059700.1.v4.1 961 764.773 0 0 Potri.007G009000.2.v4.1 1416 1219.71 0 0 Potri.003G141000.2.v4.1 2943 2746.71 567.904 18.8357 Potri.016G087400.1.v4.1 270 119.101 415 317.432 Potri.015G069301.1.v4.1 564 376.039 0 0 Potri.010G195200.1.v4.1 1773 1576.71 17 0.982237 Potri.012G127500.1.v4.1 977 780.748 81 9.45132 ==> SRR12670147.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 129 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 176 Potri.001G212900.v4.1 5 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 9 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 7 SRR12670147 completed mapping pipeline successfully