Starting /dee2/code/volunteer_pipeline.sh SRR12670118 current disk space = 3057549025280 free memory = 1195263132 SRR12670118 SRAfilesize f17b430c87114128d012d51581aa54f9 SRR12670118.sra SRR12670118.sra file validated SRR12670118 is paired end SRR12670118 is conventional basespace SRR12670118 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670118_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 36.6905 37.0 37.0 37.0 37.0 37.0 2 36.5405 37.0 37.0 37.0 37.0 37.0 3 36.6455 37.0 37.0 37.0 37.0 37.0 4 36.6845 37.0 37.0 37.0 37.0 37.0 5 36.6915 37.0 37.0 37.0 37.0 37.0 6 36.6995 37.0 37.0 37.0 37.0 37.0 7 36.5875 37.0 37.0 37.0 37.0 37.0 8 36.708 37.0 37.0 37.0 37.0 37.0 9 36.578 37.0 37.0 37.0 37.0 37.0 10-14 36.6291 37.0 37.0 37.0 37.0 37.0 15-19 36.59440000000001 37.0 37.0 37.0 37.0 37.0 20-24 36.5284 37.0 37.0 37.0 37.0 37.0 25-29 36.523 37.0 37.0 37.0 37.0 37.0 30-34 36.5258 37.0 37.0 37.0 37.0 37.0 35-39 36.5049 37.0 37.0 37.0 37.0 37.0 40-44 36.486000000000004 37.0 37.0 37.0 37.0 37.0 45-49 36.4395 37.0 37.0 37.0 37.0 37.0 50-54 36.446600000000004 37.0 37.0 37.0 37.0 37.0 55-59 36.42999999999999 37.0 37.0 37.0 37.0 37.0 60-64 36.420100000000005 37.0 37.0 37.0 37.0 37.0 65-69 36.403999999999996 37.0 37.0 37.0 37.0 37.0 70-74 36.3381 37.0 37.0 37.0 37.0 37.0 75-79 36.348400000000005 37.0 37.0 37.0 37.0 37.0 80-84 36.3189 37.0 37.0 37.0 37.0 37.0 85-89 36.3073 37.0 37.0 37.0 37.0 37.0 90-94 36.3211 37.0 37.0 37.0 37.0 37.0 95-99 36.2608 37.0 37.0 37.0 37.0 37.0 100-104 36.2688 37.0 37.0 37.0 37.0 37.0 105-109 36.257 37.0 37.0 37.0 37.0 37.0 110-114 36.1613 37.0 37.0 37.0 37.0 37.0 115-119 36.1842 37.0 37.0 37.0 37.0 37.0 120-124 36.0928 37.0 37.0 37.0 37.0 37.0 125-129 35.9927 37.0 37.0 37.0 37.0 37.0 130-134 35.9633 37.0 37.0 37.0 37.0 37.0 135-139 35.8429 37.0 37.0 37.0 37.0 37.0 140-144 35.630900000000004 37.0 37.0 37.0 37.0 37.0 145-149 35.583800000000004 37.0 37.0 37.0 37.0 37.0 150-151 35.30075 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 22 1.0 23 0.0 24 2.0 25 4.0 26 2.0 27 8.0 28 6.0 29 15.0 30 21.0 31 45.0 32 33.0 33 68.0 34 113.0 35 349.0 36 2950.0 37 383.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 39.050000000000004 10.65 6.9750000000000005 43.325 2 19.188376753507015 13.10120240480962 37.02404809619239 30.68637274549098 3 17.5 16.225 28.125 38.15 4 21.95 24.425 23.599999999999998 30.025000000000002 5 23.625 30.85 24.25 21.275 6 21.5 34.150000000000006 23.799999999999997 20.549999999999997 7 14.825 25.324999999999996 43.95 15.9 8 17.525 25.525 32.125 24.825 9 16.775000000000002 23.125 36.15 23.95 10-14 20.04 29.535 27.650000000000002 22.775000000000002 15-19 20.565 28.194999999999997 27.950000000000003 23.29 20-24 20.225 27.944999999999997 27.779999999999998 24.05 25-29 20.145 28.265 27.38 24.21 30-34 20.005 28.64 28.13 23.225 35-39 20.285 28.16 27.950000000000003 23.605 40-44 20.560000000000002 28.139999999999997 27.655 23.645 45-49 20.31 27.875 27.955000000000002 23.86 50-54 19.935 28.89 27.134999999999998 24.04 55-59 20.89 28.349999999999998 27.560000000000002 23.200000000000003 60-64 20.775 28.345 27.82 23.06 65-69 20.785 28.455000000000002 27.46 23.3 70-74 20.68 28.155 27.455000000000002 23.71 75-79 20.54 28.005000000000003 28.310000000000002 23.145 80-84 20.695 28.71 26.700000000000003 23.895 85-89 20.119999999999997 29.265 26.56 24.055 90-94 21.355 28.16 27.229999999999997 23.255 95-99 20.49 28.215 27.775 23.52 100-104 21.26 28.634999999999998 26.5 23.605 105-109 21.0 28.57 26.88 23.549999999999997 110-114 21.33 28.665000000000003 27.05 22.955000000000002 115-119 21.23 28.565 25.674999999999997 24.529999999999998 120-124 21.8 28.18 26.090000000000003 23.93 125-129 20.794999999999998 28.000000000000004 26.455000000000002 24.75 130-134 20.845 27.57 26.685 24.9 135-139 21.36 26.924999999999997 26.474999999999998 25.240000000000002 140-144 21.43 26.715 26.905 24.95 145-149 21.335 26.86 26.525 25.28 150-151 20.625 27.125 26.700000000000003 25.55 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.5 5 0.5 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.5 15 0.5 16 0.0 17 0.5 18 0.5 19 0.0 20 0.0 21 1.0 22 1.5 23 0.5 24 1.5 25 2.0 26 2.0 27 5.0 28 9.0 29 17.0 30 18.5 31 24.5 32 31.5 33 30.5 34 37.0 35 59.5 36 83.5 37 104.0 38 138.0 39 161.0 40 168.0 41 185.5 42 216.0 43 251.0 44 274.0 45 276.0 46 276.5 47 268.5 48 272.5 49 242.5 50 173.0 51 141.5 52 112.5 53 90.5 54 83.0 55 59.0 56 41.0 57 40.5 58 32.0 59 22.0 60 19.5 61 13.0 62 5.0 63 2.0 64 1.5 65 0.5 66 0.5 67 1.0 68 1.0 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 0.2 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 77.875 #Duplication Level Percentage of deduplicated Percentage of total 1 79.26163723916532 61.724999999999994 2 15.441412520064205 24.05 3 3.8202247191011236 8.924999999999999 4 0.8346709470304976 2.6 5 0.4815409309791332 1.875 6 0.09630818619582665 0.44999999999999996 7 0.03210272873194221 0.17500000000000002 8 0.03210272873194221 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 GTCCGCAAGTCGTCTGCGAAAAAAAATGGTTAAATAAAAAGGAAATCAGA 8 0.2 No Hit CACGAATTTCAGACTTGTTTTGGAGATCTTGAACAAGATTACTTGCAGGC 7 0.17500000000000002 No Hit GTCATCAACATCTTCCTTCTCATCAACCTGGCTATGAGTTGGCGAGATTC 6 0.15 No Hit CTGCAATAACGGGGTGTTGTGCAATGGAATAAAAGCTTGAGTGCAAGGAA 6 0.15 No Hit CGCTAGGAATTTTCAAATCATCTGACTCTGTCGAATGTAACAAACCTTCC 6 0.15 No Hit GTTGGATTTGTCGGACTGATAATCAAATTTCCTTCATCAGCTAAGATAAG 5 0.125 No Hit CAGGATTCTCATTGCCTGTTATCCAATATAAACATGTAATACCTGCATTG 5 0.125 No Hit GGGAGAGTCTTTGCGACCATGCCAGCATCGCAGGAAGTTCCTGCCAATGC 5 0.125 No Hit CGACCATCACGGATAAGAGGAGCATACAATGTTGAAAAATCGTTACCAGT 5 0.125 No Hit CGGCTGTCGAGTTGTACGGCCGTTCAGCCACGAGTCACGGGGTCTAACGC 5 0.125 No Hit TACCGGGAAGACACTGCACATGATACAGCTTCATTAAACGCATCAATACA 5 0.125 No Hit CTGTGATTACTGACAGGACACGTTTCCTAGTTAGCTCATCTGGTGAAGTA 5 0.125 No Hit GGCTTGGAGGCGATAAAACTGATGCACTGCACTTGACGAGTGTTGTCGAA 5 0.125 No Hit CATCTTTACTCCTTTCTCTTTGTTTCTCTTTAACAATAACACTACCACTA 5 0.125 No Hit GTCCTGCAAGCACTTGGACTGTCTCACAAGCTTGCGGATCTTGGCAATAT 5 0.125 No Hit CTCCAGCCTTTCCAAGAATTTCTGGTGCAATGGCACCAACCGCCCCCAAC 5 0.125 No Hit CTCCCAACATCCCCGAATTTGATCTCAAAAGTGAAGGAGAAACAGACTGG 5 0.125 No Hit CAGGAGTGACGGACAGCAGGTAATTCAGCATGTTGAAAGGCAGTAAAGGA 5 0.125 No Hit CCCATGAGTGCCATCTCGAAAACAAACAGCGTGTATGGATCTGCCCAGTA 5 0.125 No Hit CGTTAAGATTTTCATTCCTGGGTAGATCCTCGAGAAAGGAACTCAGGAAA 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 0.0125 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.037500000000000006 0.0 0.0 0.0 0.0 52-53 0.05 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 0.1125 0.0 0.0 0.0 0.0 60-61 0.1375 0.0 0.0 0.0 0.0 62-63 0.2 0.0 0.0 0.0 0.0 64-65 0.275 0.0 0.0 0.0 0.0 66-67 0.32499999999999996 0.0 0.0 0.0 0.0 68-69 0.38749999999999996 0.0 0.0 0.0 0.0 70-71 0.4625 0.0 0.0 0.0 0.0 72-73 0.6000000000000001 0.0 0.0 0.0 0.0 74-75 0.8625 0.0 0.0 0.0 0.0 76-77 1.0125 0.0 0.0 0.0 0.0 78-79 1.2 0.0 0.0 0.0 0.0 80-81 1.5 0.0 0.0 0.0 0.0 82-83 1.825 0.0 0.0 0.0 0.0 84-85 2.225 0.0 0.0 0.0 0.0 86-87 2.6 0.0 0.0 0.0 0.0 88-89 3.1125 0.0 0.0 0.0 0.0 90-91 3.7125000000000004 0.0 0.0 0.0 0.0 92-93 4.3875 0.0 0.0 0.0 0.0 94-95 5.025 0.0 0.0 0.0 0.0 96-97 5.7625 0.0 0.0 0.0 0.0 98-99 6.225 0.0 0.0 0.0 0.0 100-101 7.074999999999999 0.0 0.0 0.0 0.0 102-103 8.0 0.0 0.0 0.0 0.0 104-105 8.9875 0.0 0.0 0.0 0.0 106-107 10.075 0.0 0.0 0.0 0.0 108-109 10.7375 0.0 0.0 0.0 0.0 110-111 11.5625 0.0 0.0 0.0 0.0 112-113 12.45 0.0 0.0 0.0 0.0 114-115 13.337499999999999 0.0 0.0 0.0 0.0 116-117 14.25 0.0 0.0 0.0 0.0 118-119 15.075 0.0 0.0 0.0 0.0 120-121 16.075 0.0 0.0 0.0 0.0 122-123 16.95 0.0 0.0 0.0 0.0 124-125 17.775 0.0 0.0 0.0 0.0 126-127 18.612499999999997 0.0 0.0 0.0 0.0 128-129 19.975 0.0 0.0 0.0 0.0 130-131 21.1 0.0 0.0 0.0 0.0 132-133 22.1 0.0 0.0 0.0 0.0 134-135 23.049999999999997 0.0 0.0 0.0 0.0 136-137 24.2625 0.0 0.0 0.0 0.0 138-139 25.175 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TGATACA 10 0.006830828 145.0 4 >>END_MODULE SRR12670118 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670118_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 36.2865 37.0 37.0 37.0 37.0 37.0 2 36.114 37.0 37.0 37.0 37.0 37.0 3 36.14 37.0 37.0 37.0 37.0 37.0 4 36.324 37.0 37.0 37.0 37.0 37.0 5 36.3165 37.0 37.0 37.0 37.0 37.0 6 36.2685 37.0 37.0 37.0 37.0 37.0 7 36.2565 37.0 37.0 37.0 37.0 37.0 8 36.2725 37.0 37.0 37.0 37.0 37.0 9 36.163 37.0 37.0 37.0 37.0 37.0 10-14 36.261900000000004 37.0 37.0 37.0 37.0 37.0 15-19 36.2787 37.0 37.0 37.0 37.0 37.0 20-24 36.259100000000004 37.0 37.0 37.0 37.0 37.0 25-29 36.2374 37.0 37.0 37.0 37.0 37.0 30-34 36.198800000000006 37.0 37.0 37.0 37.0 37.0 35-39 36.17100000000001 37.0 37.0 37.0 37.0 37.0 40-44 36.2013 37.0 37.0 37.0 37.0 37.0 45-49 36.1948 37.0 37.0 37.0 37.0 37.0 50-54 36.1428 37.0 37.0 37.0 37.0 37.0 55-59 36.0963 37.0 37.0 37.0 37.0 37.0 60-64 36.0862 37.0 37.0 37.0 37.0 37.0 65-69 36.0583 37.0 37.0 37.0 37.0 37.0 70-74 35.977500000000006 37.0 37.0 37.0 37.0 37.0 75-79 35.9791 37.0 37.0 37.0 37.0 37.0 80-84 35.965500000000006 37.0 37.0 37.0 37.0 37.0 85-89 35.9526 37.0 37.0 37.0 37.0 37.0 90-94 35.9346 37.0 37.0 37.0 37.0 37.0 95-99 35.90089999999999 37.0 37.0 37.0 37.0 37.0 100-104 35.7983 37.0 37.0 37.0 37.0 37.0 105-109 35.759 37.0 37.0 37.0 37.0 37.0 110-114 35.7231 37.0 37.0 37.0 37.0 37.0 115-119 35.71040000000001 37.0 37.0 37.0 37.0 37.0 120-124 35.537 37.0 37.0 37.0 37.0 37.0 125-129 35.3846 37.0 37.0 37.0 37.0 37.0 130-134 35.1814 37.0 37.0 37.0 32.2 37.0 135-139 34.9185 37.0 37.0 37.0 25.0 37.0 140-144 34.655699999999996 37.0 37.0 37.0 25.0 37.0 145-149 34.2365 37.0 37.0 37.0 25.0 37.0 150-151 33.8895 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 1.0 13 4.0 14 3.0 15 3.0 16 0.0 17 0.0 18 1.0 19 0.0 20 2.0 21 3.0 22 9.0 23 4.0 24 5.0 25 9.0 26 1.0 27 10.0 28 18.0 29 23.0 30 32.0 31 57.0 32 67.0 33 118.0 34 226.0 35 575.0 36 2534.0 37 295.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 36.65 24.725 10.125 28.499999999999996 2 26.75 27.0 31.25 15.0 3 19.15 27.775 34.175 18.9 4 23.150000000000002 33.375 25.25 18.224999999999998 5 25.7 37.175000000000004 21.4 15.725 6 21.075 38.324999999999996 23.549999999999997 17.05 7 20.349999999999998 21.65 39.050000000000004 18.95 8 21.975 24.775 28.525 24.725 9 20.150000000000002 26.075 30.625000000000004 23.150000000000002 10-14 23.02 29.43 26.465 21.085 15-19 23.32 27.87 27.935 20.875 20-24 23.53 28.015 27.589999999999996 20.865000000000002 25-29 23.775 28.27 28.28 19.675 30-34 22.5 28.835 28.15 20.515 35-39 23.52 28.439999999999998 27.305 20.735 40-44 23.599999999999998 28.035 27.644999999999996 20.72 45-49 23.205000000000002 27.66 27.884999999999998 21.25 50-54 22.78 28.665000000000003 27.73 20.825 55-59 23.04 28.294999999999998 27.74 20.925 60-64 23.03 27.800000000000004 28.060000000000002 21.11 65-69 22.91 27.905 28.355000000000004 20.830000000000002 70-74 23.835 28.345 27.27 20.549999999999997 75-79 23.580000000000002 27.96 28.075 20.385 80-84 24.115000000000002 28.565 27.584999999999997 19.735 85-89 24.154999999999998 27.16 27.589999999999996 21.095 90-94 24.64 27.935 26.97 20.455000000000002 95-99 25.005 28.255000000000003 26.55 20.19 100-104 25.16 28.51 26.35 19.98 105-109 25.1 27.365000000000002 27.279999999999998 20.255000000000003 110-114 26.155 28.494999999999997 25.88 19.470000000000002 115-119 27.33 27.065 25.855 19.75 120-124 27.055 26.855 26.650000000000002 19.439999999999998 125-129 27.605 27.525 25.86 19.009999999999998 130-134 28.189999999999998 26.889999999999997 25.919999999999998 19.0 135-139 28.705000000000002 26.645000000000003 26.07 18.58 140-144 29.14 25.905 26.355 18.6 145-149 30.04 26.005 26.035000000000004 17.919999999999998 150-151 31.337500000000002 26.5625 24.8125 17.2875 >>END_MODULE >>Per sequence GC content warn #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 0.5 9 0.5 10 0.0 11 1.0 12 2.0 13 1.0 14 1.5 15 2.0 16 1.5 17 2.0 18 1.0 19 0.5 20 0.5 21 1.0 22 1.0 23 0.5 24 2.5 25 4.5 26 5.5 27 6.5 28 5.5 29 10.0 30 14.5 31 15.0 32 22.5 33 44.5 34 60.0 35 63.5 36 87.0 37 117.0 38 133.0 39 167.0 40 205.5 41 227.5 42 261.5 43 285.0 44 274.0 45 241.0 46 238.0 47 235.0 48 207.5 49 203.0 50 185.5 51 144.5 52 114.0 53 91.0 54 70.5 55 56.0 56 45.5 57 37.0 58 27.0 59 18.5 60 15.0 61 10.0 62 4.0 63 3.5 64 3.5 65 2.0 66 1.0 67 1.0 68 1.0 69 2.0 70 1.5 71 0.0 72 0.5 73 0.5 74 0.5 75 0.5 76 0.0 77 0.0 78 1.0 79 1.0 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 0.5 91 0.5 92 0.5 93 0.5 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.5 100 3.5 >>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 77.875 #Duplication Level Percentage of deduplicated Percentage of total 1 79.74317817014446 62.1 2 14.735152487961475 22.95 3 3.8523274478330656 9.0 4 1.0914927768860354 3.4000000000000004 5 0.3531300160513644 1.375 6 0.09630818619582665 0.44999999999999996 7 0.09630818619582665 0.525 8 0.03210272873194221 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 AGATAGAAGAAATGAAAGCAACGGAGAAGGTAACCGATGAGGATACAATA 8 0.2 No Hit AGGGAGCACTGCATAGCTTATAAGCTTGTAAGAGATGGCTTCCTCCTCTA 7 0.17500000000000002 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 7 0.17500000000000002 No Hit CTAATAATTGCCAGATTTCTCCACAAAATTTCCTGAACAGAAACCAACTA 7 0.17500000000000002 No Hit GAAATCTGTTGTGTGTGTGTGTGTGTGTATTGCAGGGTTGTAGAGTATCA 6 0.15 No Hit GCTGCATGTGGTTTTATGTCTGATGTAGATATGAGGGACAAGCTCACGTC 6 0.15 No Hit GTTAGCAAGAGATCATGAATTTGTAATCTGGGTTCTCATTGTTCATCACT 6 0.15 No Hit TCTGGCTGAAAGATTTCAGTCTACCAGGACAGCAGGACCAAAATTTGCTT 5 0.125 No Hit GTCGAAATGGTGTGCAGATGCATCAGAAAGTCATGAGTTTTCTAACAAAC 5 0.125 No Hit AGCAGCTTCTACTCCCCCTGTTAAGCAAGGAAACAGGCAGCTGTGGTTCG 5 0.125 No Hit GATTCATCCCCATCACACCATCCGTAGACTTGTATTTTTTGGTCGGGAAT 5 0.125 No Hit GTGTAACCTATGCCAAGAACGCTAGTGAGGGATCCTTCTTTGATGTGGTG 5 0.125 No Hit CAACAAATGTGCAACTTCCCGGCATGTACAACAAGGAGGAGAATCCACGT 5 0.125 No Hit CTCAAAACCATTCTTCTTAGACTCTCTATACATTCCAAATAACCTAATTT 5 0.125 No Hit ACTTGGCTTCAGCATCGGCTGAGATAGCGAGAGGTGAAACTGCGAATTCT 5 0.125 No Hit TCGGACTTTCAGACCCTGAAGGCACAGGAGGTTTCATTGAGCCAAAATGG 5 0.125 No Hit GAAAATGAAAAACATCCACCTCCCTCTCCACCAAGATGATTCCTCCACCG 5 0.125 No Hit GCGGGTTATAGCTTTTCAGTCTCGACGGGCTAGCACACATCTGGTTGACT 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 0.0125 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.037500000000000006 0.0 0.0 0.0 0.0 52-53 0.05 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 0.1125 0.0 0.0 0.0 0.0 60-61 0.1375 0.0 0.0 0.0 0.0 62-63 0.2 0.0 0.0 0.0 0.0 64-65 0.275 0.0 0.0 0.0 0.0 66-67 0.32499999999999996 0.0 0.0 0.0 0.0 68-69 0.38749999999999996 0.0 0.0 0.0 0.0 70-71 0.4625 0.0 0.0 0.0 0.0 72-73 0.6000000000000001 0.0 0.0 0.0 0.0 74-75 0.8625 0.0 0.0 0.0 0.0 76-77 1.025 0.0 0.0 0.0 0.0 78-79 1.225 0.0 0.0 0.0 0.0 80-81 1.525 0.0 0.0 0.0 0.0 82-83 1.85 0.0 0.0 0.0 0.0 84-85 2.25 0.0 0.0 0.0 0.0 86-87 2.625 0.0 0.0 0.0 0.0 88-89 3.1375 0.0 0.0 0.0 0.0 90-91 3.75 0.0 0.0 0.0 0.0 92-93 4.45 0.0 0.0 0.0 0.0 94-95 5.125 0.0 0.0 0.0 0.0 96-97 5.8875 0.0 0.0 0.0 0.0 98-99 6.35 0.0 0.0 0.0 0.0 100-101 7.237500000000001 0.0 0.0 0.0 0.0 102-103 8.15 0.0 0.0 0.0 0.0 104-105 9.1375 0.0 0.0 0.0 0.0 106-107 10.287500000000001 0.0 0.0 0.0 0.0 108-109 11.0125 0.0 0.0 0.0 0.0 110-111 11.875 0.0 0.0 0.0 0.0 112-113 12.825 0.0 0.0 0.0 0.0 114-115 13.712499999999999 0.0 0.0 0.0 0.0 116-117 14.625 0.0 0.0 0.0 0.0 118-119 15.525 0.0 0.0 0.0 0.0 120-121 16.5375 0.0 0.0 0.0 0.0 122-123 17.425 0.0 0.0 0.0 0.0 124-125 18.25 0.0 0.0 0.0 0.0 126-127 19.0625 0.0 0.0 0.0 0.0 128-129 20.450000000000003 0.0 0.0 0.0 0.0 130-131 21.575000000000003 0.0 0.0 0.0 0.0 132-133 22.575000000000003 0.0 0.0 0.0 0.0 134-135 23.525 0.0 0.0 0.0 0.0 136-137 24.725 0.0 0.0 0.0 0.0 138-139 25.625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AAATTTC 10 0.006830828 145.0 8 ATTTCAT 10 0.006830828 145.0 1 GGGGGGG 260 1.2156337E-5 11.153846 145 >>END_MODULE Read 609423 spots for SRR12670118.sra Written 609423 spots for SRR12670118.sra Read 609423 spots for SRR12670118.sra Written 609423 spots for SRR12670118.sra Read 609423 spots for SRR12670118.sra Written 609423 spots for SRR12670118.sra Read 609423 spots for SRR12670118.sra Written 609423 spots for SRR12670118.sra Read 609423 spots for SRR12670118.sra Written 609423 spots for SRR12670118.sra Read 609423 spots for SRR12670118.sra Written 609423 spots for SRR12670118.sra Read 609423 spots for SRR12670118.sra Written 609423 spots for SRR12670118.sra Read 609424 spots for SRR12670118.sra Written 609424 spots for SRR12670118.sra Read 609423 spots for SRR12670118.sra Written 609423 spots for SRR12670118.sra Read 609423 spots for SRR12670118.sra Written 609423 spots for SRR12670118.sra Read 609423 spots for SRR12670118.sra Written 609423 spots for SRR12670118.sra Read 609423 spots for SRR12670118.sra Written 609423 spots for SRR12670118.sra Read 609423 spots for SRR12670118.sra Written 609423 spots for SRR12670118.sra Read 609423 spots for SRR12670118.sra Written 609423 spots for SRR12670118.sra Read 609423 spots for SRR12670118.sra Written 609423 spots for SRR12670118.sra Read 609423 spots for SRR12670118.sra Written 609423 spots for SRR12670118.sra Read 609423 spots for SRR12670118.sra Written 609423 spots for SRR12670118.sra Read 609423 spots for SRR12670118.sra Written 609423 spots for SRR12670118.sra Read 609423 spots for SRR12670118.sra Written 609423 spots for SRR12670118.sra Read 609423 spots for SRR12670118.sra Written 609423 spots for SRR12670118.sra SRR ids: ['SRR12670118.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_xyu4__kv SRR12670118.sra spots: 12188461 blocks: [[1, 609423], [609424, 1218846], [1218847, 1828269], [1828270, 2437692], [2437693, 3047115], [3047116, 3656538], [3656539, 4265961], [4265962, 4875384], [4875385, 5484807], [5484808, 6094230], [6094231, 6703653], [6703654, 7313076], [7313077, 7922499], [7922500, 8531922], [8531923, 9141345], [9141346, 9750768], [9750769, 10360191], [10360192, 10969614], [10969615, 11579037], [11579038, 12188461]] SRR12670118 file size 4120471 SRR12670118 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 SRR12670118 SRR12670118_1.fastq SRR12670118_2.fastq Input file: SRR12670118_1.fastq Paired file: SRR12670118_2.fastq trimmed: SRR12670118-trimmed-pair1.fastq, SRR12670118-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 23:37:28 2025 >> started Mon Feb 10 23:37:48 2025 >> done (19.945s) 12188461 read pairs processed; of these: 48 ( 0.00%) short read pairs filtered out after trimming by size control 2734 ( 0.02%) empty read pairs filtered out after trimming by size control 12185679 (99.98%) read pairs available; of these: 3617370 (29.69%) trimmed read pairs available after processing 8568309 (70.31%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 2 0.00% 19 7 0.00% 20 2 0.00% 21 11 0.00% 22 9 0.00% 23 13 0.00% 24 16 0.00% 25 23 0.00% 26 26 0.00% 27 27 0.00% 28 38 0.00% 29 37 0.00% 30 44 0.00% 31 72 0.00% 32 66 0.00% 33 83 0.00% 34 75 0.00% 35 81 0.00% 36 83 0.00% 37 119 0.00% 38 121 0.00% 39 193 0.00% 40 218 0.00% 41 226 0.00% 42 232 0.00% 43 251 0.00% 44 226 0.00% 45 308 0.00% 46 303 0.00% 47 351 0.00% 48 459 0.00% 49 531 0.00% 50 677 0.01% 51 776 0.01% 52 797 0.01% 53 836 0.01% 54 959 0.01% 55 1036 0.01% 56 1116 0.01% 57 1195 0.01% 58 1529 0.01% 59 1751 0.01% 60 2035 0.02% 61 2396 0.02% 62 2631 0.02% 63 2859 0.02% 64 3054 0.03% 65 3338 0.03% 66 3767 0.03% 67 3963 0.03% 68 4606 0.04% 69 4992 0.04% 70 5969 0.05% 71 6814 0.06% 72 7900 0.06% 73 8535 0.07% 74 9437 0.08% 75 10093 0.08% 76 10910 0.09% 77 11694 0.10% 78 12811 0.11% 79 13839 0.11% 80 15187 0.12% 81 17205 0.14% 82 19104 0.16% 83 20585 0.17% 84 22700 0.19% 85 24220 0.20% 86 25291 0.21% 87 26103 0.21% 88 27326 0.22% 89 28582 0.23% 90 30986 0.25% 91 32963 0.27% 92 34796 0.29% 93 37621 0.31% 94 39926 0.33% 95 41499 0.34% 96 42782 0.35% 97 43570 0.36% 98 43835 0.36% 99 44467 0.36% 100 46227 0.38% 101 46926 0.39% 102 49416 0.41% 103 50733 0.42% 104 51970 0.43% 105 53536 0.44% 106 54055 0.44% 107 53724 0.44% 108 53614 0.44% 109 54015 0.44% 110 53377 0.44% 111 54154 0.44% 112 55900 0.46% 113 56867 0.47% 114 57820 0.47% 115 58573 0.48% 116 59119 0.49% 117 59499 0.49% 118 58568 0.48% 119 57220 0.47% 120 57753 0.47% 121 58027 0.48% 122 57422 0.47% 123 58838 0.48% 124 59700 0.49% 125 59798 0.49% 126 59892 0.49% 127 58852 0.48% 128 58248 0.48% 129 57878 0.47% 130 57947 0.48% 131 56676 0.47% 132 57260 0.47% 133 57662 0.47% 134 57339 0.47% 135 57991 0.48% 136 57912 0.48% 137 56693 0.47% 138 56457 0.46% 139 57190 0.47% 140 55477 0.46% 141 54847 0.45% 142 55000 0.45% 143 55624 0.46% 144 55958 0.46% 145 55500 0.46% 146 55314 0.45% 147 56011 0.46% 148 55292 0.45% 149 54079 0.44% 150 54104 0.44% 151 8568309 70.31% 12185679 reads passed initial QC criterion=sequence-density sequence-density=0.39 sequence-density-rank=1 fanout-score=1.99 fanout-score-rank=25 prefix-density=0.39 prefix-fanout=2.0 sequence=TGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGGAGTATGAATGTGTTCTCTGTGT criterion=fanout-score sequence-density=0.03 sequence-density-rank=28 fanout-score=172.48 fanout-score-rank=1 prefix-density=0.28 prefix-fanout=15.8 sequence=TGAAGAAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTC criterion=sequence-density sequence-density=0.73 sequence-density-rank=1 fanout-score=2.03 fanout-score-rank=30 prefix-density=0.73 prefix-fanout=2.0 sequence=CTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGAC criterion=fanout-score sequence-density=0.12 sequence-density-rank=20 fanout-score=36.33 fanout-score-rank=1 prefix-density=0.35 prefix-fanout=12.6 sequence=AAAGAAAAGAAAA SRR12670118 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 10 23:38:34 Started mapping on | Feb 10 23:38:34 Finished on | Feb 10 23:39:51 Mapping speed, Million of reads per hour | 569.72 Number of input reads | 12185679 Average input read length | 281 UNIQUE READS: Uniquely mapped reads number | 11447947 Uniquely mapped reads % | 93.95% Average mapped length | 280.58 Number of splices: Total | 10848539 Number of splices: Annotated (sjdb) | 10602771 Number of splices: GT/AG | 10632305 Number of splices: GC/AG | 172283 Number of splices: AT/AC | 7267 Number of splices: Non-canonical | 36684 Mismatch rate per base, % | 0.35% Deletion rate per base | 0.03% Deletion average length | 2.85 Insertion rate per base | 0.02% Insertion average length | 2.39 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 281095 % of reads mapped to multiple loci | 2.31% Number of reads mapped to too many loci | 59760 % of reads mapped to too many loci | 0.49% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.09% % of reads unmapped: other | 0.17% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 456637 456637 456637 N_multimapping 281095 281095 281095 N_noFeature 438493 11289960 502798 N_ambiguous 159161 642 65187 UnstrandedReadsAssigned:10850293 PositiveStrandReadsAssigned:157345 NegativeStrandReadsAssigned:10879962 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=130 echo kmer=125 SRR12670118 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: SRR12670118-trimmed-pair1.fastq SRR12670118-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 12,185,679 reads, 10,909,440 reads pseudoaligned [quant] estimated average fragment length: 203.865 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,066 rounds 52401 SRR12670118.ke.tsv 34699 SRR12670118.se.tsv 87100 total ==> SRR12670118.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1815.14 611 31.7053 Potri.005G024800.1.v4.1 1035 832.135 165 18.6762 Potri.004G059700.1.v4.1 961 758.222 7 0.869563 Potri.007G009000.2.v4.1 1416 1213.14 0 0 Potri.003G141000.2.v4.1 2943 2740.14 701.545 24.1147 Potri.016G087400.1.v4.1 270 113.179 495 411.945 Potri.015G069301.1.v4.1 564 367.986 0 0 Potri.010G195200.1.v4.1 1773 1570.14 87 5.21893 Potri.012G127500.1.v4.1 977 774.172 56 6.81317 ==> SRR12670118.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 186 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 141 Potri.001G212900.v4.1 7 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 6 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 0 SRR12670118 completed mapping pipeline successfully