Starting /dee2/code/volunteer_pipeline.sh SRR13165374 current disk space = 1541703843840 free memory = 1595987332 SRR13165374 SRAfilesize a339cd2f68873d05a093d1ab9b06fa50 SRR13165374.sra SRR13165374.sra file validated SRR13165374 is paired end SRR13165374 is conventional basespace SRR13165374 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR13165374_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 50 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.6215 37.0 37.0 37.0 37.0 37.0 2 36.02325 37.0 37.0 37.0 37.0 37.0 3 36.515 37.0 37.0 37.0 37.0 37.0 4 36.5145 37.0 37.0 37.0 37.0 37.0 5 36.567 37.0 37.0 37.0 37.0 37.0 6 36.564 37.0 37.0 37.0 37.0 37.0 7 36.481 37.0 37.0 37.0 37.0 37.0 8 36.528 37.0 37.0 37.0 37.0 37.0 9 36.5695 37.0 37.0 37.0 37.0 37.0 10-14 36.528800000000004 37.0 37.0 37.0 37.0 37.0 15-19 36.5003 37.0 37.0 37.0 37.0 37.0 20-24 36.4524 37.0 37.0 37.0 37.0 37.0 25-29 36.443200000000004 37.0 37.0 37.0 37.0 37.0 30-34 36.41760000000001 37.0 37.0 37.0 37.0 37.0 35-39 36.3851 37.0 37.0 37.0 37.0 37.0 40-44 36.3738 37.0 37.0 37.0 37.0 37.0 45-49 36.3521 37.0 37.0 37.0 37.0 37.0 50-54 36.3626 37.0 37.0 37.0 37.0 37.0 55-59 36.333600000000004 37.0 37.0 37.0 37.0 37.0 60-64 36.3092 37.0 37.0 37.0 37.0 37.0 65-69 36.2166 37.0 37.0 37.0 37.0 37.0 70-74 36.2496 37.0 37.0 37.0 37.0 37.0 75-79 36.277499999999996 37.0 37.0 37.0 37.0 37.0 80-84 36.269999999999996 37.0 37.0 37.0 37.0 37.0 85-89 36.25 37.0 37.0 37.0 37.0 37.0 90-94 36.1508 37.0 37.0 37.0 37.0 37.0 95-99 36.182 37.0 37.0 37.0 37.0 37.0 100-104 36.1328 37.0 37.0 37.0 37.0 37.0 105-109 36.1446 37.0 37.0 37.0 37.0 37.0 110-114 36.0991 37.0 37.0 37.0 37.0 37.0 115-119 36.0837 37.0 37.0 37.0 37.0 37.0 120-124 36.02419999999999 37.0 37.0 37.0 37.0 37.0 125-129 35.9637 37.0 37.0 37.0 37.0 37.0 130-134 35.945899999999995 37.0 37.0 37.0 37.0 37.0 135-139 35.8939 37.0 37.0 37.0 37.0 37.0 140-144 35.761399999999995 37.0 37.0 37.0 37.0 37.0 145-149 35.593199999999996 37.0 37.0 37.0 37.0 37.0 150-151 35.355000000000004 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 1.0 21 0.0 22 1.0 23 1.0 24 0.0 25 0.0 26 6.0 27 7.0 28 21.0 29 14.0 30 24.0 31 33.0 32 52.0 33 88.0 34 186.0 35 331.0 36 2767.0 37 468.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 52.1 9.475 5.8500000000000005 32.574999999999996 2 22.643416729845843 11.599696739954512 29.946929492039427 35.80995703816022 3 20.5 16.1 28.349999999999998 35.05 4 24.675 23.125 22.925 29.275000000000002 5 28.1 27.55 21.6 22.75 6 25.025 31.825 21.475 21.675 7 19.25 26.150000000000002 36.6 18.0 8 20.925 23.75 27.975 27.35 9 19.575 21.65 32.824999999999996 25.95 10-14 23.095 27.08 24.825 25.0 15-19 22.470000000000002 25.825 25.665 26.040000000000003 20-24 23.935000000000002 25.95 24.959999999999997 25.155 25-29 23.625 26.0 24.465 25.91 30-34 22.805 25.45 25.590000000000003 26.155 35-39 23.03 25.779999999999998 25.03 26.16 40-44 23.75 25.635 25.230000000000004 25.385 45-49 23.61 25.2 25.275 25.915 50-54 23.645 24.404999999999998 25.66 26.290000000000003 55-59 23.9 25.629999999999995 24.490000000000002 25.979999999999997 60-64 24.03 25.61 24.395 25.965 65-69 23.915 25.71 24.935 25.44 70-74 23.990000000000002 25.119999999999997 24.86 26.029999999999998 75-79 24.145 24.315 25.580000000000002 25.96 80-84 24.235 24.94 25.224999999999998 25.6 85-89 24.16 24.97 24.665 26.205000000000002 90-94 24.224999999999998 25.779999999999998 23.91 26.085 95-99 24.6 24.945 24.715 25.740000000000002 100-104 24.785 24.775 24.43 26.009999999999998 105-109 25.165 25.474999999999998 23.78 25.580000000000002 110-114 24.215 25.77 23.56 26.455000000000002 115-119 25.069999999999997 25.430000000000003 23.549999999999997 25.95 120-124 24.44 25.564999999999998 23.695 26.3 125-129 24.615000000000002 25.874999999999996 23.064999999999998 26.445 130-134 24.88 25.455 24.07 25.595000000000002 135-139 24.62 26.06 23.23 26.090000000000003 140-144 25.169999999999998 23.96 23.825 27.045 145-149 24.805 25.19 23.315 26.69 150-151 23.9875 25.8625 22.7625 27.3875 >>END_MODULE >>Per sequence GC content fail #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 0.0 25 0.0 26 0.5 27 0.5 28 1.5 29 3.5 30 8.0 31 14.0 32 13.0 33 16.0 34 21.5 35 32.5 36 40.5 37 48.0 38 75.5 39 95.5 40 116.5 41 142.5 42 168.0 43 185.5 44 189.0 45 184.5 46 196.5 47 204.5 48 188.5 49 188.0 50 175.5 51 153.0 52 135.5 53 121.5 54 111.5 55 104.5 56 95.5 57 90.5 58 82.0 59 72.0 60 79.5 61 73.5 62 56.0 63 65.0 64 67.0 65 53.5 66 45.5 67 40.5 68 39.5 69 29.5 70 27.5 71 33.0 72 24.5 73 13.0 74 16.0 75 19.5 76 13.5 77 6.5 78 6.5 79 6.0 80 4.5 81 2.5 82 0.5 83 0.5 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 1.075 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 73.075 #Duplication Level Percentage of deduplicated Percentage of total 1 74.71775573041396 54.6 2 17.72151898734177 25.900000000000002 3 5.029079712624016 11.025 4 1.7105713308244956 5.0 5 0.4789599726308587 1.7500000000000002 6 0.23947998631542936 1.05 7 0.0 0.0 8 0.034211426616489904 0.2 9 0.034211426616489904 0.22499999999999998 >10 0.034211426616489904 0.25 >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 GATCGGAAGAGCACACGTCTGAACTCCAGTCACGCAAGATCATCTCGTAT 10 0.25 TruSeq Adapter, Index 6 (97% over 37bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACGCAAGATCATCGCGTAT 9 0.22499999999999998 TruSeq Adapter, Index 6 (97% over 37bp) AACACTTTCAGGCTGCTGGCTCATCTCCACAATACCACCAGCATTGTCAG 8 0.2 No Hit GGAATCATTTCGGCATTTCCACCATGGCAGGGTAGAAGTAAGCATACAGA 6 0.15 No Hit GTCTAGCTCAGCTTTCAGTTCATCATAGTCACTGAACTTTGAGAGATCAA 6 0.15 No Hit CCCAGGTGCAACCACAATCTCATAGAACATCCGCGTCTCGCCGTCTGTAG 6 0.15 No Hit GCCATGGCTAATTTTGCTGCTAATAACACTACTAGCTTAGTTGGGACCCC 6 0.15 No Hit CCCGTTGTCAACTCCTCCCCTGACACATAAACCAGCAGCACATATTAACT 6 0.15 No Hit GCCATCACAACATCAATTCCAAGGAGCTCAGACAAGCGTGGAACAAGAGG 6 0.15 No Hit CCCGCCTTCTTGTATATGTAGGAAGCAATCCTCCTCATCTCGAGCAATTC 6 0.15 No Hit GCCAATACGAGGAAGACGTCCCGGCCGCCCTCCTCGTGGTAGTAGCACAC 5 0.125 No Hit CTGCAAGGTGGCCAATACTCTTCCCATATATGCGATAGCATACAGAACAA 5 0.125 No Hit GCAAGCTAGCGGCCGTCCAAATCACTAACCAAATATTCCAAAAAATTACA 5 0.125 No Hit GTTGGATCTCGATCTATGCTTTGGGCGCTTGGAACTGTTCGTCGAAAGGA 5 0.125 No Hit CTCCTTGATAACCTTGCAGAGACCCTCAAACTTCTCCTTGAGCTCCTCCT 5 0.125 No Hit GTAGCGTCGATCAGGCGACGGGGGGCTTCTCGACGTCCTCGAGCGGGCGG 5 0.125 No Hit GCCTCATGCTAATTATCCTGTTAGCCATGCCCTTCAGCTCAATAGTCCAT 5 0.125 No Hit TCTGGGGATTCCCAATGGGCGTCGCGGCAGAGCCGATGTTGGAGCTCGTG 5 0.125 No Hit AGGGGAGTGAGCATAACCAAAGCACCAGGAGGAATCATCTCCTTGATGGA 5 0.125 No Hit CATCGGGTGGGTCTTGAATTCGGCGTCCTTGTGAGGCACACCCACCAGCA 5 0.125 No Hit GGATCAAGTTGACTGCAAGCTTCCTGAGATCAGAGTTCAGCTGGCCAGGG 5 0.125 No Hit GGTGTGCACCGAGATCAGGCCCACCACGAAGCCGCCGCATGTGAATTCTG 5 0.125 No Hit GCAGGAACGTTTGAGAACGTCTCCCCTTCCTTGTTCACGGCAATGTATGT 5 0.125 No Hit GCCAAGCTTATAATATCATGTGGCTTTGCATCCAGTTACACAACGCGGCA 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 0.025 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 0.025 0.0 0.0 0.0 0.0 52-53 0.037500000000000006 0.0 0.0 0.0 0.0 54-55 0.05 0.0 0.0 0.0 0.0 56-57 0.0625 0.0 0.0 0.0 0.0 58-59 0.11249999999999999 0.0 0.0 0.0 0.0 60-61 0.175 0.0 0.0 0.0 0.0 62-63 0.21250000000000002 0.0 0.0 0.0 0.0 64-65 0.225 0.0 0.0 0.0 0.0 66-67 0.275 0.0 0.0 0.0 0.0 68-69 0.3375 0.0 0.0 0.0 0.0 70-71 0.4375 0.0 0.0 0.0 0.0 72-73 0.45 0.0 0.0 0.0 0.0 74-75 0.475 0.0 0.0 0.0 0.0 76-77 0.5625 0.0 0.0 0.0 0.0 78-79 0.7 0.0 0.0 0.0 0.0 80-81 0.9375 0.0 0.0 0.0 0.0 82-83 1.175 0.0 0.0 0.0 0.0 84-85 1.4375 0.0 0.0 0.0 0.0 86-87 1.6125 0.0 0.0 0.0 0.0 88-89 2.0375 0.0 0.0 0.0 0.0 90-91 2.5 0.0 0.0 0.0 0.0 92-93 2.8375 0.0 0.0 0.0 0.0 94-95 3.125 0.0 0.0 0.0 0.0 96-97 3.625 0.0 0.0 0.0 0.0 98-99 4.2125 0.0 0.0 0.0 0.0 100-101 4.5875 0.0 0.0 0.0 0.0 102-103 5.0125 0.0 0.0 0.0 0.0 104-105 5.262499999999999 0.0 0.0 0.0 0.0 106-107 5.775 0.0 0.0 0.0 0.0 108-109 6.3625 0.0 0.0 0.0 0.0 110-111 7.125 0.0 0.0 0.0 0.0 112-113 7.725 0.0 0.0 0.0 0.0 114-115 8.6375 0.0 0.0 0.0 0.0 116-117 9.4375 0.0 0.0 0.0 0.0 118-119 10.125 0.0 0.0 0.0 0.0 120-121 10.8625 0.0 0.0 0.0 0.0 122-123 11.7125 0.0 0.0 0.0 0.0 124-125 13.0375 0.0 0.0 0.0 0.0 126-127 13.7625 0.0 0.0 0.0 0.0 128-129 14.787500000000001 0.0 0.0 0.0 0.0 130-131 15.475 0.0 0.0 0.0 0.0 132-133 16.3375 0.0 0.0 0.0 0.0 134-135 17.15 0.0 0.0 0.0 0.0 136-137 17.975 0.0 0.0 0.0 0.0 138-139 18.925 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AGCCTCA 10 0.006830828 145.0 4 GCCTCAT 10 0.006830828 145.0 5 CCTCATA 10 0.006830828 145.0 6 CTCATAT 10 0.006830828 145.0 7 >>END_MODULE SRR13165374 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR13165374_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 51 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.00625 37.0 37.0 37.0 37.0 37.0 2 36.166 37.0 37.0 37.0 37.0 37.0 3 36.1515 37.0 37.0 37.0 37.0 37.0 4 36.1585 37.0 37.0 37.0 37.0 37.0 5 36.3135 37.0 37.0 37.0 37.0 37.0 6 36.2445 37.0 37.0 37.0 37.0 37.0 7 36.187 37.0 37.0 37.0 37.0 37.0 8 36.1385 37.0 37.0 37.0 37.0 37.0 9 36.1855 37.0 37.0 37.0 37.0 37.0 10-14 36.1685 37.0 37.0 37.0 37.0 37.0 15-19 36.0822 37.0 37.0 37.0 37.0 37.0 20-24 36.048500000000004 37.0 37.0 37.0 37.0 37.0 25-29 35.9474 37.0 37.0 37.0 37.0 37.0 30-34 35.9523 37.0 37.0 37.0 37.0 37.0 35-39 35.898900000000005 37.0 37.0 37.0 37.0 37.0 40-44 35.855500000000006 37.0 37.0 37.0 37.0 37.0 45-49 35.845549999999996 37.0 37.0 37.0 37.0 37.0 50-54 35.781 37.0 37.0 37.0 37.0 37.0 55-59 35.9007 37.0 37.0 37.0 37.0 37.0 60-64 35.837 37.0 37.0 37.0 37.0 37.0 65-69 35.80575 37.0 37.0 37.0 37.0 37.0 70-74 35.751799999999996 37.0 37.0 37.0 37.0 37.0 75-79 35.67575 37.0 37.0 37.0 37.0 37.0 80-84 35.75945 37.0 37.0 37.0 37.0 37.0 85-89 35.7053 37.0 37.0 37.0 37.0 37.0 90-94 35.69465 37.0 37.0 37.0 37.0 37.0 95-99 35.638850000000005 37.0 37.0 37.0 37.0 37.0 100-104 35.6596 37.0 37.0 37.0 37.0 37.0 105-109 35.5746 37.0 37.0 37.0 37.0 37.0 110-114 35.5441 37.0 37.0 37.0 37.0 37.0 115-119 35.5068 37.0 37.0 37.0 37.0 37.0 120-124 35.425 37.0 37.0 37.0 37.0 37.0 125-129 35.41225 37.0 37.0 37.0 37.0 37.0 130-134 35.2059 37.0 37.0 37.0 32.2 37.0 135-139 35.21755 37.0 37.0 37.0 32.2 37.0 140-144 35.0896 37.0 37.0 37.0 29.8 37.0 145-149 34.91365 37.0 37.0 37.0 25.0 37.0 150-151 34.73525 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 6 1.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 3.0 13 4.0 14 5.0 15 7.0 16 10.0 17 4.0 18 6.0 19 6.0 20 5.0 21 8.0 22 11.0 23 12.0 24 6.0 25 8.0 26 13.0 27 18.0 28 9.0 29 16.0 30 23.0 31 27.0 32 57.0 33 104.0 34 156.0 35 500.0 36 2688.0 37 293.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 46.91978878551672 19.78878551672115 8.95147095800855 24.339954739753583 2 31.674999999999997 21.375 24.4 22.55 3 25.025 23.849999999999998 28.199999999999996 22.925 4 28.025 29.95 18.9 23.125 5 29.275000000000002 31.05 18.5 21.175 6 26.0 32.65 18.375 22.975 7 22.825 22.275 34.35 20.549999999999997 8 23.799999999999997 22.025 24.075 30.099999999999998 9 26.700000000000003 20.825 25.85 26.625 10-14 27.075 25.290000000000003 22.895 24.740000000000002 15-19 26.979999999999997 24.91 23.445 24.665 20-24 26.57563025210084 24.359743897559024 23.90956382553021 25.155062024809926 25-29 27.31731731731732 24.544544544544543 23.20820820820821 24.92992992992993 30-34 26.36345441809266 24.887421194836385 23.911738216751726 24.837386170319224 35-39 25.535214085634255 25.270108043217288 23.52941176470588 25.665266106442573 40-44 26.878815170619436 24.452116481537075 23.976783748624037 24.69228459921945 45-49 26.634649056981342 23.627995397468606 24.788633748561708 24.948721796988345 50-54 26.850740296118445 24.90996398559424 23.634453781512605 24.60484193677471 55-59 26.22122122122122 25.25025025025025 23.563563563563562 24.964964964964963 60-64 27.00080032012805 25.595238095238095 23.46438575430172 23.93957583033213 65-69 26.809021353202983 25.118767815172276 24.59868980347052 23.473521028154224 70-74 26.72172172172172 25.16016016016016 23.403403403403402 24.714714714714713 75-79 27.705779334500875 25.364023017262948 23.422566925193898 23.50763072304228 80-84 27.62190547636909 24.96124031007752 23.710927731932983 23.705926481620406 85-89 26.85416875187669 25.933340006005405 23.54619157241517 23.66629966970273 90-94 26.962132959831926 25.326396878595368 24.250912910809863 23.460557250762843 95-99 27.069474316010606 25.979092682438854 23.30315610463662 23.64827689691392 100-104 27.26226226226226 25.105105105105107 24.004004004004003 23.62862862862863 105-109 27.177177177177175 25.195195195195197 24.284284284284286 23.343343343343342 110-114 28.38135254101641 25.08503401360544 23.41936774709884 23.114245698279312 115-119 29.194194194194196 25.900900900900904 22.812812812812812 22.09209209209209 120-124 28.673673673673672 25.59059059059059 23.66866866866867 22.067067067067068 125-129 29.520092078266526 25.932042235900514 22.70429865385578 21.84356703197718 130-134 29.70862120756984 26.01381796335236 22.314008210673876 21.963552618403924 135-139 30.60519597537168 24.82354707914101 22.891325023777345 21.679931921709965 140-144 31.992797118847538 24.719887955182074 22.54901960784314 20.73829531812725 145-149 32.797717374981225 24.68839165039796 21.99028883215698 20.523602142463833 150-151 32.90758827948911 25.43200601051841 21.68795391935888 19.97245179063361 >>END_MODULE >>Per sequence GC content fail #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 0.5 8 0.5 9 0.5 10 1.0 11 0.5 12 0.5 13 2.0 14 2.0 15 0.5 16 0.5 17 1.5 18 1.5 19 1.0 20 2.0 21 2.0 22 1.0 23 1.0 24 0.5 25 0.5 26 1.5 27 2.0 28 3.0 29 4.0 30 5.5 31 4.5 32 8.0 33 14.5 34 16.0 35 25.5 36 42.0 37 47.0 38 65.5 39 85.5 40 100.5 41 119.0 42 134.5 43 160.5 44 172.0 45 164.0 46 180.5 47 197.5 48 167.0 49 157.0 50 184.5 51 179.0 52 148.0 53 114.5 54 108.0 55 117.0 56 100.5 57 83.0 58 88.0 59 90.0 60 84.0 61 75.5 62 61.5 63 65.5 64 64.0 65 57.0 66 56.0 67 58.0 68 64.5 69 56.5 70 44.5 71 36.0 72 27.5 73 25.5 74 23.0 75 15.5 76 9.0 77 8.5 78 8.0 79 7.0 80 4.0 81 2.0 82 1.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.5 88 0.5 89 0.0 90 0.0 91 0.0 92 0.0 93 0.5 94 0.5 95 1.0 96 2.0 97 2.0 98 2.5 99 6.5 100 13.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.575 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 0.04 25-29 0.1 30-34 0.06999999999999999 35-39 0.04 40-44 0.06999999999999999 45-49 0.055 50-54 0.04 55-59 0.1 60-64 0.04 65-69 0.015 70-74 0.1 75-79 0.075 80-84 0.025 85-89 0.09 90-94 0.045 95-99 0.034999999999999996 100-104 0.1 105-109 0.1 110-114 0.04 115-119 0.1 120-124 0.1 125-129 0.08499999999999999 130-134 0.13 135-139 0.11499999999999999 140-144 0.04 145-149 0.11499999999999999 150-151 0.17500000000000002 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 73.5 #Duplication Level Percentage of deduplicated Percentage of total 1 75.578231292517 55.55 2 16.972789115646258 24.95 3 4.965986394557823 10.95 4 1.7006802721088436 5.0 5 0.44217687074829937 1.625 6 0.2380952380952381 1.05 7 0.0 0.0 8 0.06802721088435373 0.4 9 0.0 0.0 >10 0.03401360544217687 0.475 >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 19 0.475 No Hit CGTACCTCTGGCTTGGTAGATGAGTCTGGTAACCCAACTGGTGGTCTTTT 8 0.2 No Hit CCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGCAA 8 0.2 No Hit AAAACAATGTGGTTGTGATATTTTTGCCGAGTACCCAAGTCTGTATGCTT 6 0.15 No Hit GCTTCCTTCGCATTTCTCACTCCAATCCCCCCTGCCCAGATCGCCGCCGA 6 0.15 No Hit GAGCAACATGAACGACCTGGTCTCCGAGTACCAACAGTACCAGGATGCGA 6 0.15 No Hit GCGATTCCATTTTATATAATCAACTTGTCAGTACAAACTTGCAGGCCTCA 6 0.15 No Hit CATGCACAAACTGATTGTTTTCCTGAGGTATCTGTAAGCACTGGTGGAAC 6 0.15 No Hit GGAAATGTCATATAACAACTACTTGGACGCCGATGCTGCATGGAACTGTG 6 0.15 No Hit CTTGTGAAACCGTACATGGTTGCAGTTCAGAGCAACAATGTATCTGCTGT 6 0.15 No Hit TCGTGGTGGACGAGGAAGGGGAGGTGGGCGTGAAGTGCAGCGGCGAGGGG 5 0.125 No Hit GCTAGCTTCGCCCCAACAGAGCCTCGCTTGCGCTTTGGTCACTGAGAAAG 5 0.125 No Hit GAACAACCGAAGGAGACTATTCCCAGAAACCATCAGCCCAGTTTGATACA 5 0.125 No Hit GTACAGGTGAGATTACACATGTACGGTGGATTACACAGCGAGGATTTGAG 5 0.125 No Hit CCGAGGAGGGCCGTGCACGCGTCGGCGTACGACAAGAACGTGGAGGAGCA 5 0.125 No Hit CCTTTGACCTCTTTGACACCAAGAAGAAGGCCAACAACATCAAGCTCTAT 5 0.125 No Hit GTCCAGGCAAGGGGCGGCCTCTCGCAGGGCAAGAAGCTGTCCCCTGCCGC 5 0.125 No Hit GTTTGTTGCTGACGGTGGTGAATTGCTCATGGCTCAAAGCTATGCTAAGA 5 0.125 No Hit CGTCACCCAAGGTTTCAGACACAGTTGTTGAACCCTACAACGCCACACTC 5 0.125 No Hit GTTGGAAGTGCTGCTCTCAAGATGGTTGAGGAGGTTCGCAGGCAGTTCAA 5 0.125 No Hit CTCGCAGTTCCCCACCGGAAGCTCTCCGTGGCGTCTCCCTCGCGCGCAGA 5 0.125 No Hit CGCCGACATGTTCAAGTACCTGGGCAACCTGCTGCAGTGGAAGTCCCGTG 5 0.125 No Hit GGGGCTCGACATTCCCGACAGGAACAGCATCGAGACCCTGCGCCTGAGGT 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 0.025 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 0.025 0.0 0.0 0.0 0.0 52-53 0.037500000000000006 0.0 0.0 0.0 0.0 54-55 0.05 0.0 0.0 0.0 0.0 56-57 0.0625 0.0 0.0 0.0 0.0 58-59 0.11249999999999999 0.0 0.0 0.0 0.0 60-61 0.175 0.0 0.0 0.0 0.0 62-63 0.21250000000000002 0.0 0.0 0.0 0.0 64-65 0.225 0.0 0.0 0.0 0.0 66-67 0.275 0.0 0.0 0.0 0.0 68-69 0.3375 0.0 0.0 0.0 0.0 70-71 0.4375 0.0 0.0 0.0 0.0 72-73 0.45 0.0 0.0 0.0 0.0 74-75 0.475 0.0 0.0 0.0 0.0 76-77 0.5625 0.0 0.0 0.0 0.0 78-79 0.7 0.0 0.0 0.0 0.0 80-81 0.9375 0.0 0.0 0.0 0.0 82-83 1.175 0.0 0.0 0.0 0.0 84-85 1.4375 0.0 0.0 0.0 0.0 86-87 1.6125 0.0 0.0 0.0 0.0 88-89 2.0375 0.0 0.0 0.0 0.0 90-91 2.5 0.0 0.0 0.0 0.0 92-93 2.8125 0.0 0.0 0.0 0.0 94-95 3.1 0.0 0.0 0.0 0.0 96-97 3.5625 0.0 0.0 0.0 0.0 98-99 4.1 0.0 0.0 0.0 0.0 100-101 4.4625 0.0 0.0 0.0 0.0 102-103 4.925000000000001 0.0 0.0 0.0 0.0 104-105 5.175 0.0 0.0 0.0 0.0 106-107 5.675 0.0 0.0 0.0 0.0 108-109 6.2625 0.0 0.0 0.0 0.0 110-111 7.050000000000001 0.0 0.0 0.0 0.0 112-113 7.7 0.0 0.0 0.0 0.0 114-115 8.575 0.0 0.0 0.0 0.0 116-117 9.325 0.0 0.0 0.0 0.0 118-119 10.0 0.0 0.0 0.0 0.0 120-121 10.7375 0.0 0.0 0.0 0.0 122-123 11.5625 0.0 0.0 0.0 0.0 124-125 12.8625 0.0 0.0 0.0 0.0 126-127 13.649999999999999 0.0 0.0 0.0 0.0 128-129 14.6125 0.0 0.0 0.0 0.0 130-131 15.325 0.0 0.0 0.0 0.0 132-133 16.200000000000003 0.0 0.0 0.0 0.0 134-135 17.0375 0.0 0.0 0.0 0.0 136-137 17.887500000000003 0.0 0.0 0.0 0.0 138-139 18.8125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GTCATTC 10 0.006830828 145.0 8 GTCATGA 10 0.006830828 145.0 8 GCAGGTC 10 0.006830828 145.0 4 GGATTTT 10 0.006830828 145.0 9 GGACAGA 10 0.006830828 145.0 145 CGAGCAG 10 0.006830828 145.0 1 TCATTCC 10 0.006830828 145.0 9 >>END_MODULE Read 1564541 spots for SRR13165374.sra Written 1564541 spots for SRR13165374.sra Read 1564541 spots for SRR13165374.sra Written 1564541 spots for SRR13165374.sra Read 1564541 spots for SRR13165374.sra Written 1564541 spots for SRR13165374.sra Read 1564541 spots for SRR13165374.sra Written 1564541 spots for SRR13165374.sra Read 1564541 spots for SRR13165374.sra Written 1564541 spots for SRR13165374.sra Read 1564541 spots for SRR13165374.sra Written 1564541 spots for SRR13165374.sra Read 1564541 spots for SRR13165374.sra Written 1564541 spots for SRR13165374.sra Read 1564541 spots for SRR13165374.sra Written 1564541 spots for SRR13165374.sra Read 1564541 spots for SRR13165374.sra Written 1564541 spots for SRR13165374.sra Read 1564541 spots for SRR13165374.sra Written 1564541 spots for SRR13165374.sra Read 1564541 spots for SRR13165374.sra Written 1564541 spots for SRR13165374.sra Read 1564541 spots for SRR13165374.sra Written 1564541 spots for SRR13165374.sra Read 1564541 spots for SRR13165374.sra Written 1564541 spots for SRR13165374.sra Read 1564541 spots for SRR13165374.sra Written 1564541 spots for SRR13165374.sra Read 1564541 spots for SRR13165374.sra Written 1564541 spots for SRR13165374.sra Read 1564541 spots for SRR13165374.sra Written 1564541 spots for SRR13165374.sra Read 1564541 spots for SRR13165374.sra Written 1564541 spots for SRR13165374.sra Read 1564541 spots for SRR13165374.sra Written 1564541 spots for SRR13165374.sra Read 1564559 spots for SRR13165374.sra Written 1564559 spots for SRR13165374.sra Read 1564541 spots for SRR13165374.sra Written 1564541 spots for SRR13165374.sra SRR ids: ['SRR13165374.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_u3lxx756 SRR13165374.sra spots: 31290838 blocks: [[1, 1564541], [1564542, 3129082], [3129083, 4693623], [4693624, 6258164], [6258165, 7822705], [7822706, 9387246], [9387247, 10951787], [10951788, 12516328], [12516329, 14080869], [14080870, 15645410], [15645411, 17209951], [17209952, 18774492], [18774493, 20339033], [20339034, 21903574], [21903575, 23468115], [23468116, 25032656], [25032657, 26597197], [26597198, 28161738], [28161739, 29726279], [29726280, 31290838]] SRR13165374 file size 10612295 SRR13165374 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 SRR13165374 SRR13165374_1.fastq SRR13165374_2.fastq Input file: SRR13165374_1.fastq Paired file: SRR13165374_2.fastq trimmed: SRR13165374-trimmed-pair1.fastq, SRR13165374-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 Sat Dec 7 16:46:23 2024 >> started Sat Dec 7 16:46:58 2024 >> done (35.484s) 31290838 read pairs processed; of these: 731 ( 0.00%) short read pairs filtered out after trimming by size control 146646 ( 0.47%) empty read pairs filtered out after trimming by size control 31143461 (99.53%) read pairs available; of these: 6941114 (22.29%) trimmed read pairs available after processing 24202347 (77.71%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 35 0.00% 19 48 0.00% 20 54 0.00% 21 71 0.00% 22 88 0.00% 23 93 0.00% 24 127 0.00% 25 137 0.00% 26 140 0.00% 27 168 0.00% 28 175 0.00% 29 216 0.00% 30 261 0.00% 31 209 0.00% 32 238 0.00% 33 263 0.00% 34 257 0.00% 35 259 0.00% 36 286 0.00% 37 332 0.00% 38 301 0.00% 39 374 0.00% 40 430 0.00% 41 462 0.00% 42 488 0.00% 43 490 0.00% 44 493 0.00% 45 531 0.00% 46 634 0.00% 47 730 0.00% 48 887 0.00% 49 895 0.00% 50 975 0.00% 51 1132 0.00% 52 1211 0.00% 53 1293 0.00% 54 1360 0.00% 55 1470 0.00% 56 1575 0.01% 57 1837 0.01% 58 2096 0.01% 59 2377 0.01% 60 2801 0.01% 61 3071 0.01% 62 3672 0.01% 63 3910 0.01% 64 4137 0.01% 65 4584 0.01% 66 4948 0.02% 67 5240 0.02% 68 5982 0.02% 69 6857 0.02% 70 7749 0.02% 71 8800 0.03% 72 10437 0.03% 73 11357 0.04% 74 12582 0.04% 75 13720 0.04% 76 14540 0.05% 77 15900 0.05% 78 17191 0.06% 79 19223 0.06% 80 21312 0.07% 81 23789 0.08% 82 26396 0.08% 83 29007 0.09% 84 31975 0.10% 85 34135 0.11% 86 35187 0.11% 87 37804 0.12% 88 40294 0.13% 89 41680 0.13% 90 44705 0.14% 91 48504 0.16% 92 52126 0.17% 93 56220 0.18% 94 59651 0.19% 95 62690 0.20% 96 66320 0.21% 97 67416 0.22% 98 69085 0.22% 99 71722 0.23% 100 73546 0.24% 101 75082 0.24% 102 79757 0.26% 103 82128 0.26% 104 86285 0.28% 105 88231 0.28% 106 90041 0.29% 107 90284 0.29% 108 92976 0.30% 109 94267 0.30% 110 95368 0.31% 111 97605 0.31% 112 100163 0.32% 113 101482 0.33% 114 106403 0.34% 115 108350 0.35% 116 108917 0.35% 117 110496 0.35% 118 111014 0.36% 119 111486 0.36% 120 112952 0.36% 121 113537 0.36% 122 113799 0.37% 123 116958 0.38% 124 120457 0.39% 125 120327 0.39% 126 123357 0.40% 127 122320 0.39% 128 122365 0.39% 129 123299 0.40% 130 122869 0.39% 131 121677 0.39% 132 124613 0.40% 133 126220 0.41% 134 125912 0.40% 135 128981 0.41% 136 129272 0.42% 137 128197 0.41% 138 129877 0.42% 139 129443 0.42% 140 129782 0.42% 141 130125 0.42% 142 130696 0.42% 143 130493 0.42% 144 131880 0.42% 145 134347 0.43% 146 133997 0.43% 147 136428 0.44% 148 132426 0.43% 149 134354 0.43% 150 134056 0.43% 151 24202347 77.71% 31143461 reads passed initial QC criterion=sequence-density sequence-density=0.19 sequence-density-rank=1 fanout-score=16.38 fanout-score-rank=9 prefix-density=0.15 prefix-fanout=16.4 sequence=GGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCAAGATCATCTCGTATGCCGTCTTCTGCTTGAAAA criterion=fanout-score sequence-density=0.04 sequence-density-rank=36 fanout-score=218.35 fanout-score-rank=1 prefix-density=0.50 prefix-fanout=19.3 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.14 sequence-density-rank=1 fanout-score=9.35 fanout-score-rank=15 prefix-density=0.23 prefix-fanout=5.8 sequence=GGCAAGACCATCACCCTTGAGGTGGAGTCATCTGACACCAT criterion=fanout-score sequence-density=0.09 sequence-density-rank=21 fanout-score=184.47 fanout-score-rank=1 prefix-density=0.77 prefix-fanout=22.3 sequence=CGCCGCCGCCGC SRR13165374 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 16:48:13 Started mapping on | Dec 07 16:48:14 Finished on | Dec 07 16:50:53 Mapping speed, Million of reads per hour | 705.13 Number of input reads | 31143461 Average input read length | 288 UNIQUE READS: Uniquely mapped reads number | 28985616 Uniquely mapped reads % | 93.07% Average mapped length | 287.32 Number of splices: Total | 25884920 Number of splices: Annotated (sjdb) | 24174691 Number of splices: GT/AG | 25546001 Number of splices: GC/AG | 275692 Number of splices: AT/AC | 17003 Number of splices: Non-canonical | 46224 Mismatch rate per base, % | 0.22% Deletion rate per base | 0.01% Deletion average length | 2.66 Insertion rate per base | 0.01% Insertion average length | 2.25 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 315009 % of reads mapped to multiple loci | 1.01% Number of reads mapped to too many loci | 149451 % of reads mapped to too many loci | 0.48% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.30% % of reads unmapped: other | 2.14% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1843150 1843150 1843150 N_multimapping 315009 315009 315009 N_noFeature 1002453 28186232 1274414 N_ambiguous 601830 3922 75774 UnstrandedReadsAssigned:27381333 PositiveStrandReadsAssigned:795462 NegativeStrandReadsAssigned:27635428 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=145 echo kmer=141 SRR13165374 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: 52,972 [index] number of k-mers: 66,720,672 [index] number of equivalence classes: 111,837 [quant] running in paired-end mode [quant] will process pair 1: SRR13165374-trimmed-pair1.fastq SRR13165374-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 31,143,461 reads, 28,092,805 reads pseudoaligned [quant] estimated average fragment length: 231.644 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,116 rounds 52973 SRR13165374.ke.tsv 35125 SRR13165374.se.tsv 88098 total ==> SRR13165374.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 705.975 0 0 PNS24247 1044 813.356 95.1409 6.37801 PNS24249 1928 1697.36 203.655 6.54216 PNS24246 1044 813.356 95.1409 6.37801 PNS24248 1044 813.356 95.1409 6.37801 PNS24244 1471 1240.36 184.922 8.12908 PNS24243 293 115.051 0 0 KQK14069 1603 1372.36 2177.29 86.5065 KQK14071 474 261.494 92.1893 19.2229 ==> SRR13165374.se.tsv <== BRADI_1g14170v3 2419 BRADI_1g53295v3 289 BRADI_1g59795v3 875 BRADI_1g07683v3 0 BRADI_1g00485v3 226 BRADI_1g20270v3 3344 BRADI_1g74790v3 309 BRADI_1g09890v3 7 BRADI_1g77505v3 319 BRADI_1g48960v3 0 SRR13165374 completed mapping pipeline successfully