Starting /dee2/code/volunteer_pipeline.sh SRR12670172 current disk space = 3055770714112 free memory = 1271716268 SRR12670172 SRAfilesize 09c11d9c565d23ecbd27189edbd9b8a7 SRR12670172.sra SRR12670172.sra file validated SRR12670172 is paired end SRR12670172 is conventional basespace SRR12670172 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670172_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 36.618 37.0 37.0 37.0 37.0 37.0 2 36.5165 37.0 37.0 37.0 37.0 37.0 3 36.6105 37.0 37.0 37.0 37.0 37.0 4 36.6375 37.0 37.0 37.0 37.0 37.0 5 36.73 37.0 37.0 37.0 37.0 37.0 6 36.6875 37.0 37.0 37.0 37.0 37.0 7 36.535 37.0 37.0 37.0 37.0 37.0 8 36.723 37.0 37.0 37.0 37.0 37.0 9 36.5875 37.0 37.0 37.0 37.0 37.0 10-14 36.627500000000005 37.0 37.0 37.0 37.0 37.0 15-19 36.595 37.0 37.0 37.0 37.0 37.0 20-24 36.5555 37.0 37.0 37.0 37.0 37.0 25-29 36.5532 37.0 37.0 37.0 37.0 37.0 30-34 36.5249 37.0 37.0 37.0 37.0 37.0 35-39 36.528800000000004 37.0 37.0 37.0 37.0 37.0 40-44 36.4962 37.0 37.0 37.0 37.0 37.0 45-49 36.4521 37.0 37.0 37.0 37.0 37.0 50-54 36.4638 37.0 37.0 37.0 37.0 37.0 55-59 36.4251 37.0 37.0 37.0 37.0 37.0 60-64 36.3848 37.0 37.0 37.0 37.0 37.0 65-69 36.400099999999995 37.0 37.0 37.0 37.0 37.0 70-74 36.3156 37.0 37.0 37.0 37.0 37.0 75-79 36.301 37.0 37.0 37.0 37.0 37.0 80-84 36.3087 37.0 37.0 37.0 37.0 37.0 85-89 36.3278 37.0 37.0 37.0 37.0 37.0 90-94 36.336299999999994 37.0 37.0 37.0 37.0 37.0 95-99 36.2457 37.0 37.0 37.0 37.0 37.0 100-104 36.2328 37.0 37.0 37.0 37.0 37.0 105-109 36.2568 37.0 37.0 37.0 37.0 37.0 110-114 36.1765 37.0 37.0 37.0 37.0 37.0 115-119 36.078900000000004 37.0 37.0 37.0 37.0 37.0 120-124 35.959700000000005 37.0 37.0 37.0 37.0 37.0 125-129 35.80290000000001 37.0 37.0 37.0 37.0 37.0 130-134 35.6395 37.0 37.0 37.0 37.0 37.0 135-139 35.383799999999994 37.0 37.0 37.0 37.0 37.0 140-144 35.0021 37.0 37.0 37.0 29.8 37.0 145-149 34.76469999999999 37.0 37.0 37.0 25.0 37.0 150-151 34.479 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 22 1.0 23 1.0 24 1.0 25 0.0 26 5.0 27 3.0 28 10.0 29 15.0 30 18.0 31 49.0 32 90.0 33 104.0 34 155.0 35 316.0 36 2854.0 37 378.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 40.550000000000004 10.6 7.249999999999999 41.6 2 18.972431077694235 13.032581453634084 35.0125313283208 32.98245614035088 3 17.849999999999998 15.525 27.175 39.45 4 22.375 24.7 23.05 29.875 5 23.825 31.974999999999998 22.7 21.5 6 20.4 34.0 25.05 20.549999999999997 7 14.224999999999998 25.275 42.625 17.875 8 17.525 26.424999999999997 31.2 24.85 9 17.599999999999998 24.575 33.875 23.95 10-14 19.650000000000002 28.910000000000004 28.360000000000003 23.080000000000002 15-19 19.564999999999998 28.275 28.015 24.145 20-24 20.44 28.15 27.83 23.580000000000002 25-29 19.29 28.28 28.189999999999998 24.240000000000002 30-34 20.665 27.900000000000002 27.905 23.53 35-39 20.255000000000003 28.175 27.665 23.905 40-44 19.79 28.17 28.139999999999997 23.9 45-49 20.119999999999997 28.215 27.860000000000003 23.805 50-54 20.485 28.63 27.13 23.755000000000003 55-59 20.1 27.98 28.194999999999997 23.724999999999998 60-64 21.05 27.41 28.16 23.380000000000003 65-69 20.025000000000002 27.755000000000003 28.544999999999998 23.674999999999997 70-74 19.919999999999998 27.875 28.444999999999997 23.76 75-79 20.51 27.57 27.935 23.985 80-84 21.305 27.505000000000003 27.54 23.65 85-89 20.365 27.400000000000002 28.665000000000003 23.57 90-94 21.275 28.375 26.85 23.5 95-99 20.955 28.105000000000004 26.93 24.01 100-104 20.875 28.825 26.534999999999997 23.765 105-109 21.62 28.065 26.47 23.845 110-114 21.495 28.405 25.955000000000002 24.145 115-119 21.505 28.34 25.96 24.195 120-124 21.77 28.505000000000003 25.319999999999997 24.404999999999998 125-129 21.525 28.050000000000004 26.115 24.310000000000002 130-134 21.84 27.905 25.790000000000003 24.465 135-139 22.56 28.01 24.92 24.51 140-144 23.07 28.035 25.074999999999996 23.82 145-149 24.205 27.77 24.169999999999998 23.855 150-151 23.6875 27.450000000000003 24.375 24.4875 >>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 2.0 23 2.5 24 5.0 25 6.5 26 4.0 27 6.0 28 7.0 29 5.0 30 12.0 31 20.0 32 33.5 33 44.0 34 44.0 35 55.0 36 85.5 37 106.0 38 123.0 39 146.0 40 170.5 41 213.0 42 237.0 43 260.0 44 270.5 45 273.5 46 263.5 47 234.0 48 228.0 49 227.5 50 199.0 51 149.5 52 129.5 53 111.5 54 79.0 55 62.5 56 46.5 57 33.0 58 25.5 59 21.5 60 18.0 61 10.0 62 6.5 63 4.5 64 3.5 65 4.5 66 4.0 67 1.5 68 0.5 69 0.0 70 1.0 71 1.5 72 0.5 73 0.5 74 0.5 75 0.0 76 0.5 77 0.5 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 0.25 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 80.7 #Duplication Level Percentage of deduplicated Percentage of total 1 81.84634448574968 66.05 2 13.661710037174721 22.05 3 3.5315985130111525 8.55 4 0.6505576208178439 2.1 5 0.30978934324659235 1.25 6 0.0 0.0 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 GCCCAGCCGACCCACTTTGAACCAACTTCCTCAAACCAGTTCCATTCGGA 5 0.125 No Hit GGGGGGAACAACTACAGCAGTCACTGTGTCACTGAACCATTCCTCCTTTT 5 0.125 No Hit TTTTGTTTTTAGGATTCTCAAAGCTTCTCAGTTCTCCAATTGTAGTGGAG 5 0.125 No Hit GGAAGGACGAGGGCCACTGCCTTTGCTGCGCCGGTTGAGGTTGGAACAAT 5 0.125 No Hit ACCAAAAGCATCTGGCTGCCCAGGAATTCTAACCAACTTATACTTGAATA 5 0.125 No Hit CCCCGGTTGTCTTCTCGTATGCGTCCGACGTAGACCTTCTTCGAAACCGA 5 0.125 No Hit CGTATACGAAGACTCCCTCCAATGTGATTTAAGTTTTTTAATTCTCTTAG 5 0.125 No Hit GGCGTAGGGTTTGGGCCCTTTTGGTTTCGAGGATGTAAATGTAAAGGTGC 5 0.125 No Hit GTCACGTTAGGCAACGGGATCTCGTTATCGGCGCAGTCATCTTCAATCAT 5 0.125 No Hit GCTCCTTCAACTTCAGCTTCAGCTTGAACTTCCTCTTCCTCACTCCCTTC 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 0.05 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 0.15 0.0 0.0 0.0 0.0 60-61 0.15 0.0 0.0 0.0 0.0 62-63 0.16249999999999998 0.0 0.0 0.0 0.0 64-65 0.175 0.0 0.0 0.0 0.0 66-67 0.1875 0.0 0.0 0.0 0.0 68-69 0.2625 0.0 0.0 0.0 0.0 70-71 0.575 0.0 0.0 0.0 0.0 72-73 0.7625 0.0 0.0 0.0 0.0 74-75 0.8625 0.0 0.0 0.0 0.0 76-77 0.975 0.0 0.0 0.0 0.0 78-79 1.125 0.0 0.0 0.0 0.0 80-81 1.375 0.0 0.0 0.0 0.0 82-83 1.6 0.0 0.0 0.0 0.0 84-85 2.025 0.0 0.0 0.0 0.0 86-87 2.4000000000000004 0.0 0.0 0.0 0.0 88-89 2.775 0.0 0.0 0.0 0.0 90-91 3.4 0.0 0.0 0.0 0.0 92-93 3.875 0.0 0.0 0.0 0.0 94-95 4.487500000000001 0.0 0.0 0.0 0.0 96-97 5.1125 0.0 0.0 0.0 0.0 98-99 5.737500000000001 0.0 0.0 0.0 0.0 100-101 6.4125 0.0 0.0 0.0 0.0 102-103 7.3125 0.0 0.0 0.0 0.0 104-105 8.149999999999999 0.0 0.0 0.0 0.0 106-107 8.8625 0.0 0.0 0.0 0.0 108-109 10.075 0.0 0.0 0.0 0.0 110-111 10.85 0.0 0.0 0.0 0.0 112-113 11.9375 0.0 0.0 0.0 0.0 114-115 12.825 0.0 0.0 0.0 0.0 116-117 13.899999999999999 0.0 0.0 0.0 0.0 118-119 14.775 0.0 0.0 0.0 0.0 120-121 15.7875 0.0 0.0 0.0 0.0 122-123 16.575000000000003 0.0 0.0 0.0 0.0 124-125 17.3125 0.0 0.0 0.0 0.0 126-127 17.9625 0.0 0.0 0.0 0.0 128-129 18.8375 0.0 0.0 0.0 0.0 130-131 19.875 0.0 0.0 0.0 0.0 132-133 20.6375 0.0 0.0 0.0 0.0 134-135 21.5375 0.0 0.0 0.0 0.0 136-137 22.625 0.0 0.0 0.0 0.0 138-139 23.575000000000003 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TAACAAT 10 0.006830828 145.0 7 GCTCCTT 15 1.1411342E-4 145.0 1 >>END_MODULE SRR12670172 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670172_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 36.179 37.0 37.0 37.0 37.0 37.0 2 36.1795 37.0 37.0 37.0 37.0 37.0 3 36.148 37.0 37.0 37.0 37.0 37.0 4 36.1925 37.0 37.0 37.0 37.0 37.0 5 36.339 37.0 37.0 37.0 37.0 37.0 6 36.2525 37.0 37.0 37.0 37.0 37.0 7 36.3545 37.0 37.0 37.0 37.0 37.0 8 36.201 37.0 37.0 37.0 37.0 37.0 9 36.292 37.0 37.0 37.0 37.0 37.0 10-14 36.3185 37.0 37.0 37.0 37.0 37.0 15-19 36.354699999999994 37.0 37.0 37.0 37.0 37.0 20-24 36.2509 37.0 37.0 37.0 37.0 37.0 25-29 36.251999999999995 37.0 37.0 37.0 37.0 37.0 30-34 36.195499999999996 37.0 37.0 37.0 37.0 37.0 35-39 36.1464 37.0 37.0 37.0 37.0 37.0 40-44 36.1656 37.0 37.0 37.0 37.0 37.0 45-49 36.1927 37.0 37.0 37.0 37.0 37.0 50-54 36.0664 37.0 37.0 37.0 37.0 37.0 55-59 36.140299999999996 37.0 37.0 37.0 37.0 37.0 60-64 36.057900000000004 37.0 37.0 37.0 37.0 37.0 65-69 36.0188 37.0 37.0 37.0 37.0 37.0 70-74 35.9528 37.0 37.0 37.0 37.0 37.0 75-79 35.9535 37.0 37.0 37.0 37.0 37.0 80-84 35.9203 37.0 37.0 37.0 37.0 37.0 85-89 35.851 37.0 37.0 37.0 37.0 37.0 90-94 35.9486 37.0 37.0 37.0 37.0 37.0 95-99 35.8783 37.0 37.0 37.0 37.0 37.0 100-104 35.8344 37.0 37.0 37.0 37.0 37.0 105-109 35.769200000000005 37.0 37.0 37.0 37.0 37.0 110-114 35.7352 37.0 37.0 37.0 37.0 37.0 115-119 35.6938 37.0 37.0 37.0 37.0 37.0 120-124 35.568 37.0 37.0 37.0 37.0 37.0 125-129 35.42 37.0 37.0 37.0 37.0 37.0 130-134 35.2645 37.0 37.0 37.0 34.6 37.0 135-139 35.16930000000001 37.0 37.0 37.0 34.6 37.0 140-144 34.875600000000006 37.0 37.0 37.0 25.0 37.0 145-149 34.5877 37.0 37.0 37.0 25.0 37.0 150-151 34.203 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 1.0 13 3.0 14 2.0 15 2.0 16 1.0 17 3.0 18 0.0 19 0.0 20 3.0 21 3.0 22 8.0 23 5.0 24 9.0 25 6.0 26 9.0 27 10.0 28 9.0 29 18.0 30 18.0 31 45.0 32 72.0 33 112.0 34 217.0 35 592.0 36 2571.0 37 281.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 36.7 23.549999999999997 11.25 28.499999999999996 2 24.75 26.424999999999997 31.6 17.224999999999998 3 20.349999999999998 27.400000000000002 32.550000000000004 19.7 4 24.175 33.175 24.45 18.2 5 25.025 35.775 21.95 17.25 6 21.9 36.975 23.175 17.95 7 20.424999999999997 20.05 39.45 20.075000000000003 8 21.55 25.775 29.025000000000002 23.65 9 22.575 23.724999999999998 29.325000000000003 24.375 10-14 24.085 28.985 26.26 20.669999999999998 15-19 23.369999999999997 27.705000000000002 27.875 21.05 20-24 23.73 28.335 27.72 20.215 25-29 23.18 29.12 27.169999999999998 20.53 30-34 23.39 28.315 27.985 20.31 35-39 23.53 28.455000000000002 27.37 20.645 40-44 22.895 28.49 27.994999999999997 20.62 45-49 23.544999999999998 27.935 27.815 20.705000000000002 50-54 23.51 27.76 27.900000000000002 20.830000000000002 55-59 23.1 27.99 27.42 21.490000000000002 60-64 23.044999999999998 27.91 27.435 21.61 65-69 23.985 27.825 27.500000000000004 20.69 70-74 23.41 28.105000000000004 27.83 20.655 75-79 23.150000000000002 27.944999999999997 27.834999999999997 21.07 80-84 23.505000000000003 28.54 26.950000000000003 21.005 85-89 24.38 28.255000000000003 27.034999999999997 20.330000000000002 90-94 25.34 27.525 27.11 20.025000000000002 95-99 24.94 28.660000000000004 26.205000000000002 20.195 100-104 25.474999999999998 26.955000000000002 27.18 20.39 105-109 25.564999999999998 27.839999999999996 26.115 20.48 110-114 25.619999999999997 29.005 25.72 19.655 115-119 26.3 28.88 25.380000000000003 19.439999999999998 120-124 26.8 28.199999999999996 25.3 19.7 125-129 27.365000000000002 29.054999999999996 24.675 18.905 130-134 27.694999999999997 27.98 25.495 18.83 135-139 28.134999999999998 28.535 24.595 18.735 140-144 28.435 27.935 25.195 18.435000000000002 145-149 29.830000000000002 27.735 24.855 17.580000000000002 150-151 31.337500000000002 27.425 23.925 17.3125 >>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 0.5 6 0.5 7 0.0 8 0.0 9 0.0 10 0.5 11 0.5 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.5 18 1.0 19 0.5 20 0.0 21 0.0 22 1.0 23 2.0 24 1.0 25 0.5 26 2.5 27 6.0 28 8.0 29 9.5 30 12.0 31 14.5 32 25.0 33 34.0 34 50.0 35 65.5 36 82.5 37 104.5 38 135.5 39 162.5 40 183.0 41 208.5 42 238.5 43 258.0 44 269.0 45 301.0 46 303.0 47 266.0 48 239.5 49 220.5 50 180.0 51 121.5 52 91.0 53 86.0 54 72.5 55 52.5 56 38.0 57 35.5 58 31.0 59 25.5 60 16.0 61 8.0 62 6.5 63 7.0 64 3.5 65 0.0 66 0.5 67 0.5 68 0.0 69 0.0 70 2.0 71 2.5 72 0.5 73 0.0 74 0.5 75 1.0 76 0.5 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.5 83 1.5 84 1.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.5 90 0.5 91 0.0 92 0.5 93 1.0 94 1.0 95 0.5 96 0.0 97 1.0 98 1.0 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 81.125 #Duplication Level Percentage of deduplicated Percentage of total 1 82.40369799691834 66.85 2 13.127889060092448 21.3 3 3.5439137134052388 8.625 4 0.6471494607087828 2.1 5 0.2773497688751926 1.125 6 0.0 0.0 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 GCTGGTTCTACTCCTCCGGTGTCTCCTTTCTCTGGAAGCAGAGAGTCCTT 5 0.125 No Hit GGCGAAATCTGGTTGCAATATATTCAAGTATAAGTTGGTTAGAATTCCTG 5 0.125 No Hit CCGGATTGTTGGTTTAGGTGTGGCCTTCATACCAAAGGGAATAGAGAGGA 5 0.125 No Hit ACTTGTTCCTGCAACTTGCTTTCTTCAACATTATTACCAAACTCCCCAAT 5 0.125 No Hit CCACCACTCACTCATACACCGGTGATCAGAGACTACTTGATGCTAGTCAC 5 0.125 No Hit GCGACACCATGTGTAATTGGTCACCAGATGGCGAATGGATTGCTTTTGCA 5 0.125 No Hit GAATGGGGAGTAGATGTGGCTTTAACTGGCTCTCAAAAGGCTCTTTCTCT 5 0.125 No Hit CTTTTATCTCTTTCCCAATATGTCAGAATCAAAGAAAATCACCCTCAAAT 5 0.125 No Hit ATTGTCTTCGACAAGTCCACTTCCACCTTATTTGTGGCTTCTGACCAATT 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 0.05 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 0.15 0.0 0.0 0.0 0.0 60-61 0.15 0.0 0.0 0.0 0.0 62-63 0.16249999999999998 0.0 0.0 0.0 0.0 64-65 0.175 0.0 0.0 0.0 0.0 66-67 0.1875 0.0 0.0 0.0 0.0 68-69 0.2625 0.0 0.0 0.0 0.0 70-71 0.575 0.0 0.0 0.0 0.0 72-73 0.7625 0.0 0.0 0.0 0.0 74-75 0.8625 0.0 0.0 0.0 0.0 76-77 0.975 0.0 0.0 0.0 0.0 78-79 1.125 0.0 0.0 0.0 0.0 80-81 1.375 0.0 0.0 0.0 0.0 82-83 1.6 0.0 0.0 0.0 0.0 84-85 2.025 0.0 0.0 0.0 0.0 86-87 2.4000000000000004 0.0 0.0 0.0 0.0 88-89 2.75 0.0 0.0 0.0 0.0 90-91 3.375 0.0 0.0 0.0 0.0 92-93 3.85 0.0 0.0 0.0 0.0 94-95 4.4625 0.0 0.0 0.0 0.0 96-97 5.0875 0.0 0.0 0.0 0.0 98-99 5.6875 0.0 0.0 0.0 0.0 100-101 6.3875 0.0 0.0 0.0 0.0 102-103 7.2875 0.0 0.0 0.0 0.0 104-105 8.125 0.0 0.0 0.0 0.0 106-107 8.8625 0.0 0.0 0.0 0.0 108-109 10.100000000000001 0.0 0.0 0.0 0.0 110-111 10.875 0.0 0.0 0.0 0.0 112-113 11.95 0.0 0.0 0.0 0.0 114-115 12.825 0.0 0.0 0.0 0.0 116-117 13.899999999999999 0.0 0.0 0.0 0.0 118-119 14.775 0.0 0.0 0.0 0.0 120-121 15.7625 0.0 0.0 0.0 0.0 122-123 16.575000000000003 0.0 0.0 0.0 0.0 124-125 17.3125 0.0 0.0 0.0 0.0 126-127 17.9625 0.0 0.0 0.0 0.0 128-129 18.8125 0.0 0.0 0.0 0.0 130-131 19.875 0.0 0.0 0.0 0.0 132-133 20.6375 0.0 0.0 0.0 0.0 134-135 21.5375 0.0 0.0 0.0 0.0 136-137 22.65 0.0 0.0 0.0 0.0 138-139 23.575000000000003 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AGGTGGA 10 0.006830828 145.0 7 ACAGAGT 45 0.008957279 48.333332 145 >>END_MODULE Read 646460 spots for SRR12670172.sra Written 646460 spots for SRR12670172.sra Read 646460 spots for SRR12670172.sra Written 646460 spots for SRR12670172.sra Read 646460 spots for SRR12670172.sra Written 646460 spots for SRR12670172.sra Read 646460 spots for SRR12670172.sra Written 646460 spots for SRR12670172.sra Read 646460 spots for SRR12670172.sra Written 646460 spots for SRR12670172.sra Read 646460 spots for SRR12670172.sra Written 646460 spots for SRR12670172.sra Read 646460 spots for SRR12670172.sra Written 646460 spots for SRR12670172.sra Read 646460 spots for SRR12670172.sra Written 646460 spots for SRR12670172.sra Read 646460 spots for SRR12670172.sra Written 646460 spots for SRR12670172.sra Read 646460 spots for SRR12670172.sra Written 646460 spots for SRR12670172.sra Read 646460 spots for SRR12670172.sra Written 646460 spots for SRR12670172.sra Read 646460 spots for SRR12670172.sra Written 646460 spots for SRR12670172.sra Read 646460 spots for SRR12670172.sra Written 646460 spots for SRR12670172.sra Read 646460 spots for SRR12670172.sra Written 646460 spots for SRR12670172.sra Read 646460 spots for SRR12670172.sra Written 646460 spots for SRR12670172.sra Read 646460 spots for SRR12670172.sra Written 646460 spots for SRR12670172.sra Read 646460 spots for SRR12670172.sra Written 646460 spots for SRR12670172.sra Read 646462 spots for SRR12670172.sra Written 646462 spots for SRR12670172.sra Read 646460 spots for SRR12670172.sra Written 646460 spots for SRR12670172.sra Read 646460 spots for SRR12670172.sra Written 646460 spots for SRR12670172.sra SRR ids: ['SRR12670172.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_g84hetg9 SRR12670172.sra spots: 12929202 blocks: [[1, 646460], [646461, 1292920], [1292921, 1939380], [1939381, 2585840], [2585841, 3232300], [3232301, 3878760], [3878761, 4525220], [4525221, 5171680], [5171681, 5818140], [5818141, 6464600], [6464601, 7111060], [7111061, 7757520], [7757521, 8403980], [8403981, 9050440], [9050441, 9696900], [9696901, 10343360], [10343361, 10989820], [10989821, 11636280], [11636281, 12282740], [12282741, 12929202]] SRR12670172 file size 4372208 SRR12670172 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 SRR12670172 SRR12670172_1.fastq SRR12670172_2.fastq Input file: SRR12670172_1.fastq Paired file: SRR12670172_2.fastq trimmed: SRR12670172-trimmed-pair1.fastq, SRR12670172-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- paired 3' end adapter sequence (-y): AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- end quality threshold (-q): 10 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- number of concurrent threads (-t): 20 Tue Feb 11 08:10:42 2025 >> started Tue Feb 11 08:11:03 2025 >> done (21.226s) 12929202 read pairs processed; of these: 59 ( 0.00%) short read pairs filtered out after trimming by size control 9819 ( 0.08%) empty read pairs filtered out after trimming by size control 12919324 (99.92%) read pairs available; of these: 3703146 (28.66%) trimmed read pairs available after processing 9216178 (71.34%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 5 0.00% 19 1 0.00% 20 6 0.00% 21 6 0.00% 22 9 0.00% 23 12 0.00% 24 19 0.00% 25 24 0.00% 26 22 0.00% 27 18 0.00% 28 23 0.00% 29 42 0.00% 30 60 0.00% 31 60 0.00% 32 46 0.00% 33 87 0.00% 34 72 0.00% 35 74 0.00% 36 94 0.00% 37 95 0.00% 38 128 0.00% 39 180 0.00% 40 169 0.00% 41 193 0.00% 42 182 0.00% 43 229 0.00% 44 213 0.00% 45 213 0.00% 46 264 0.00% 47 310 0.00% 48 390 0.00% 49 506 0.00% 50 547 0.00% 51 641 0.00% 52 686 0.01% 53 763 0.01% 54 769 0.01% 55 875 0.01% 56 873 0.01% 57 1057 0.01% 58 1296 0.01% 59 1537 0.01% 60 1844 0.01% 61 2127 0.02% 62 2300 0.02% 63 2524 0.02% 64 2859 0.02% 65 3173 0.02% 66 3353 0.03% 67 3921 0.03% 68 4128 0.03% 69 4900 0.04% 70 5655 0.04% 71 6464 0.05% 72 7088 0.05% 73 8164 0.06% 74 9007 0.07% 75 9504 0.07% 76 10543 0.08% 77 11373 0.09% 78 12291 0.10% 79 13448 0.10% 80 14694 0.11% 81 16449 0.13% 82 18394 0.14% 83 19919 0.15% 84 21579 0.17% 85 23285 0.18% 86 24571 0.19% 87 25751 0.20% 88 27051 0.21% 89 28186 0.22% 90 30245 0.23% 91 31823 0.25% 92 33469 0.26% 93 36064 0.28% 94 38057 0.29% 95 40522 0.31% 96 41169 0.32% 97 42941 0.33% 98 42827 0.33% 99 43464 0.34% 100 45172 0.35% 101 45563 0.35% 102 47650 0.37% 103 49605 0.38% 104 50969 0.39% 105 52319 0.40% 106 53499 0.41% 107 53940 0.42% 108 53478 0.41% 109 54016 0.42% 110 53290 0.41% 111 54748 0.42% 112 56009 0.43% 113 56141 0.43% 114 57840 0.45% 115 58885 0.46% 116 59920 0.46% 117 59561 0.46% 118 59908 0.46% 119 59220 0.46% 120 59615 0.46% 121 59702 0.46% 122 59358 0.46% 123 60678 0.47% 124 61316 0.47% 125 61752 0.48% 126 62100 0.48% 127 61757 0.48% 128 61215 0.47% 129 61194 0.47% 130 60785 0.47% 131 60118 0.47% 132 60139 0.47% 133 60884 0.47% 134 60869 0.47% 135 61582 0.48% 136 61888 0.48% 137 61321 0.47% 138 60764 0.47% 139 62257 0.48% 140 60358 0.47% 141 60431 0.47% 142 60150 0.47% 143 59955 0.46% 144 60632 0.47% 145 60583 0.47% 146 60577 0.47% 147 60630 0.47% 148 60820 0.47% 149 59701 0.46% 150 60360 0.47% 151 9216178 71.34% 12919324 reads passed initial QC criterion=sequence-density sequence-density=0.38 sequence-density-rank=1 fanout-score=2.01 fanout-score-rank=28 prefix-density=0.38 prefix-fanout=2.0 sequence=TGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGGAGTATGAATGTGTTCTCTGTG criterion=fanout-score sequence-density=0.03 sequence-density-rank=33 fanout-score=134.61 fanout-score-rank=1 prefix-density=0.27 prefix-fanout=14.0 sequence=TGAAGAAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAG criterion=sequence-density sequence-density=0.74 sequence-density-rank=1 fanout-score=2.08 fanout-score-rank=28 prefix-density=0.74 prefix-fanout=2.1 sequence=CTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGGAGTGAACAAACAAAAGTGTCCGTGAGTGTCTTTATCTTTGTGTCTTCTTCA criterion=fanout-score sequence-density=0.01 sequence-density-rank=33 fanout-score=24.82 fanout-score-rank=1 prefix-density=0.11 prefix-fanout=2.7 sequence=CCACCACTAAACCCAAAGCTCAAAAAAAATCTTAACTGCACCCGCTCATCCAGCAATGGCAGCAGCAACAATGGCCCTCTCCTCCCCTTCGCTAGCCGGAAAGGCGGTGAAGCTCAACCCCTCCTCCTCTGAGATCATGGGCAATGGCCGTGTCTCCATGAGGAAAACCACCAAGCCTGTTCCCTCCGGGAGCCCATGGTACGGACCAGACCGTGTTAAATACTTGGGCCCGTTCTCTGGTGAGCCCCCATCCTACTTGACTGGTGAGTTCCCTGG SRR12670172 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 08:11:57 Started mapping on | Feb 11 08:11:57 Finished on | Feb 11 08:13:29 Mapping speed, Million of reads per hour | 505.54 Number of input reads | 12919324 Average input read length | 283 UNIQUE READS: Uniquely mapped reads number | 12059237 Uniquely mapped reads % | 93.34% Average mapped length | 281.80 Number of splices: Total | 11601147 Number of splices: Annotated (sjdb) | 11324695 Number of splices: GT/AG | 11366965 Number of splices: GC/AG | 183566 Number of splices: AT/AC | 7285 Number of splices: Non-canonical | 43331 Mismatch rate per base, % | 0.35% Deletion rate per base | 0.03% Deletion average length | 2.89 Insertion rate per base | 0.02% Insertion average length | 2.43 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 295834 % of reads mapped to multiple loci | 2.29% Number of reads mapped to too many loci | 75368 % of reads mapped to too many loci | 0.58% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.60% % of reads unmapped: other | 0.18% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 564253 564253 564253 N_multimapping 295834 295834 295834 N_noFeature 426674 11879272 504876 N_ambiguous 174555 763 72379 UnstrandedReadsAssigned:11458008 PositiveStrandReadsAssigned:179202 NegativeStrandReadsAssigned:11481982 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=132 echo kmer=127 SRR12670172 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: SRR12670172-trimmed-pair1.fastq SRR12670172-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 12,919,324 reads, 11,551,199 reads pseudoaligned [quant] estimated average fragment length: 204.502 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,039 rounds 52401 SRR12670172.ke.tsv 34699 SRR12670172.se.tsv 87100 total ==> SRR12670172.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1814.5 506 24.4252 Potri.005G024800.1.v4.1 1035 831.498 175 18.434 Potri.004G059700.1.v4.1 961 757.543 0 0 Potri.007G009000.2.v4.1 1416 1212.5 0 0 Potri.003G141000.2.v4.1 2943 2739.5 646 20.6541 Potri.016G087400.1.v4.1 270 110.626 583 461.589 Potri.015G069301.1.v4.1 564 367.363 0 0 Potri.010G195200.1.v4.1 1773 1569.5 80 4.4645 Potri.012G127500.1.v4.1 977 773.521 72 8.15275 ==> SRR12670172.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 112 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 184 Potri.001G212900.v4.1 5 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 21 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 7 SRR12670172 completed mapping pipeline successfully