Starting /dee2/code/volunteer_pipeline.sh SRR5579248 current disk space = 1523252269056 free memory = 1563066608 SRR5579248 SRAfilesize 5a4174279ef574bbbaee09383b992462 SRR5579248.sra SRR5579248.sra file validated SRR5579248 is paired end SRR5579248 is conventional basespace SRR5579248 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR5579248_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 49 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 30.527 34.0 33.0 34.0 25.0 34.0 2 32.785 34.0 33.0 34.0 28.0 34.0 3 32.967 34.0 33.0 34.0 32.0 34.0 4 33.16525 34.0 33.0 34.0 32.0 34.0 5 33.26775 34.0 33.0 34.0 33.0 34.0 6 36.972 38.0 37.0 38.0 36.0 38.0 7 37.2895 38.0 38.0 38.0 37.0 38.0 8 37.35475 38.0 38.0 38.0 37.0 38.0 9 37.50125 38.0 38.0 38.0 37.0 38.0 10-14 37.46205 38.0 38.0 38.0 37.2 38.0 15-19 37.466300000000004 38.0 38.0 38.0 37.6 38.0 20-24 37.43365 38.0 38.0 38.0 37.2 38.0 25-29 37.38765 38.0 38.0 38.0 37.0 38.0 30-34 37.36195 38.0 38.0 38.0 37.0 38.0 35-39 37.19775 38.0 38.0 38.0 36.8 38.0 40-44 36.79745 38.0 38.0 38.0 35.2 38.0 45-49 37.0021 38.0 38.0 38.0 36.0 38.0 50-54 36.883849999999995 38.0 38.0 38.0 35.6 38.0 55-59 36.88905 38.0 38.0 38.0 35.4 38.0 60-64 36.8413 38.0 38.0 38.0 35.0 38.0 65-69 36.6404 38.0 38.0 38.0 34.4 38.0 70-74 36.1975 38.0 38.0 38.0 33.6 38.0 75-79 35.132999999999996 38.0 38.0 38.0 29.8 38.0 80-84 35.07525 38.0 38.0 38.0 30.2 38.0 85-89 34.8572 38.0 37.6 38.0 28.6 38.0 90-94 34.77725 38.0 37.4 38.0 28.2 38.0 95-99 34.6582 38.0 37.2 38.0 27.8 38.0 100-104 34.5004 38.0 37.0 38.0 26.6 38.0 105-109 34.3298 38.0 37.0 38.0 25.0 38.0 110-114 34.152699999999996 38.0 36.0 38.0 23.6 38.0 115-119 33.853300000000004 38.0 35.8 38.0 20.6 38.0 120-124 33.69425 38.0 35.4 38.0 16.2 38.0 125-129 33.518 38.0 35.0 38.0 15.0 38.0 130-134 33.404 38.0 35.2 38.0 15.6 38.0 135-139 33.07395 38.0 35.0 38.0 14.0 38.0 140-144 32.79185 38.0 35.0 38.0 13.8 38.0 145-149 32.0991 38.0 34.2 38.0 6.4 38.0 150-151 29.128625 36.5 27.5 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 1.0 3 0.0 4 0.0 5 0.0 6 1.0 7 1.0 8 0.0 9 0.0 10 0.0 11 3.0 12 1.0 13 2.0 14 5.0 15 8.0 16 10.0 17 17.0 18 96.0 19 64.0 20 19.0 21 10.0 22 16.0 23 15.0 24 14.0 25 11.0 26 19.0 27 25.0 28 36.0 29 41.0 30 42.0 31 55.0 32 70.0 33 93.0 34 139.0 35 186.0 36 517.0 37 2483.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 46.926454445664106 11.63556531284303 11.2788144895719 30.159165751920963 2 23.65 19.375 31.85 25.124999999999996 3 21.95 20.325 28.275 29.45 4 24.65 26.75 20.724999999999998 27.875 5 29.049999999999997 30.025000000000002 22.375 18.55 6 25.900000000000002 31.65 22.825 19.625 7 16.275000000000002 26.775 36.575 20.375 8 19.85 26.224999999999998 27.175 26.75 9 25.575 20.275000000000002 29.375 24.775 10-14 23.599999999999998 27.084999999999997 23.39 25.924999999999997 15-19 22.905 25.240000000000002 25.900000000000002 25.955000000000002 20-24 23.185 26.224999999999998 25.485000000000003 25.105 25-29 23.0 25.455 25.374999999999996 26.169999999999998 30-34 21.85 25.855 24.82 27.474999999999998 35-39 23.380000000000003 25.740000000000002 24.91 25.97 40-44 22.725 25.679999999999996 25.745 25.85 45-49 24.5 25.185000000000002 26.455000000000002 23.86 50-54 24.224999999999998 24.72 24.325 26.729999999999997 55-59 23.244999999999997 24.515 27.075 25.165 60-64 23.35 25.240000000000002 26.68 24.73 65-69 22.465 29.065 24.005000000000003 24.465 70-74 23.09 29.26 23.805 23.845 75-79 23.31 27.500000000000004 24.125 25.064999999999998 80-84 22.96 26.13 25.080000000000002 25.83 85-89 24.240000000000002 25.369999999999997 25.074999999999996 25.314999999999998 90-94 23.535 25.365 25.650000000000002 25.45 95-99 23.51 25.15 25.905 25.435000000000002 100-104 23.98 26.875 23.885 25.259999999999998 105-109 22.865 28.765 23.665 24.705 110-114 23.86 27.405 23.880000000000003 24.855 115-119 23.674999999999997 27.58 23.66 25.085 120-124 24.4 27.150000000000002 23.01 25.44 125-129 24.07 27.175 23.02 25.735000000000003 130-134 24.485 26.58 22.869999999999997 26.064999999999998 135-139 23.785 26.965 23.735 25.515 140-144 23.915 25.900000000000002 23.165 27.02 145-149 23.355 26.99 23.3 26.355 150-151 23.5 27.0625 22.5875 26.85 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.5 4 0.5 5 0.5 6 0.5 7 0.0 8 0.0 9 0.5 10 0.5 11 0.0 12 0.5 13 0.5 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.5 21 0.5 22 0.5 23 1.0 24 1.0 25 0.5 26 2.0 27 4.5 28 5.5 29 10.5 30 21.5 31 29.5 32 35.0 33 42.0 34 51.0 35 56.5 36 68.0 37 86.0 38 97.0 39 103.5 40 109.5 41 116.5 42 127.5 43 143.0 44 152.0 45 163.5 46 173.0 47 175.5 48 166.0 49 157.5 50 162.5 51 172.0 52 168.5 53 160.0 54 147.0 55 131.0 56 118.0 57 91.5 58 85.5 59 80.5 60 65.5 61 58.0 62 50.5 63 52.5 64 48.0 65 40.0 66 36.0 67 29.5 68 34.0 69 35.0 70 25.0 71 18.0 72 19.0 73 19.5 74 13.0 75 7.5 76 6.0 77 7.0 78 5.0 79 3.0 80 2.5 81 1.5 82 1.0 83 0.5 84 0.5 85 0.0 86 0.5 87 0.5 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 warn #Base N-Count 1 8.9 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 86.3 #Duplication Level Percentage of deduplicated Percentage of total 1 93.2502896871379 80.475 2 4.692931633835458 8.1 3 1.0428736964078795 2.7 4 0.5214368482039398 1.7999999999999998 5 0.28968713789107764 1.25 6 0.057937427578215524 0.3 7 0.028968713789107762 0.17500000000000002 8 0.0 0.0 9 0.0 0.0 >10 0.08690614136732329 0.9249999999999999 >50 0.0 0.0 >100 0.028968713789107762 4.275 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences fail #Sequence Count Percentage Possible Source GATCGGAAGAGCACACGTCTGAACTCCAGTCACCCCATGATCTCGTATGC 171 4.275 TruSeq Adapter, Index 6 (97% over 37bp) NATCGGAAGAGCACACGTCTGAACTCCAGTCACCCCATGATCTCGTATGC 16 0.4 TruSeq Adapter, Index 16 (97% over 35bp) GCCTTATGTGATAGATGCCTCTTTAAAATATCTAAGTGCTGGGGTTATGA 11 0.27499999999999997 No Hit GGATAATTGCGCGGTTTTGACTGCGGAAGGAAGCCAAGGCCCACCTAAAG 10 0.25 No Hit GTCCTTACAAGTCCGCTCCTCGGGGAGCTTGATTGATAATTCTGTATAAG 7 0.17500000000000002 No Hit GGGAACAGTCGCATGACGAGGCAGTTTCCAGAAACGTGTATCACATCTAG 6 0.15 No Hit GTTGGAACTCTACCAATTGGAGCTTTCTTAGCTGTCTTAGCAGTAGTTTA 6 0.15 No Hit GTAAAACGCAAGCACCGGCTGTCGAGTTGTACGGCCGTTCAGCCACGAGT 5 0.125 No Hit GTGATAGATGCCTCTTTAAAATATCTAAGTGCTGGGGTTATGAGTAGGGA 5 0.125 No Hit GTTTTTCTGAGACCTATCCGAGTTCAGTGCGACCGTACAGCTCTGGAACC 5 0.125 No Hit CTTACAAGTCCGCTCCTCGGGGAGCTTGATTGATAATTCTGTATAAGGTG 5 0.125 No Hit CTTATGTGATAGATGCCTCTTTAAAATATCTAAGTGCTGGGGTTATGAGT 5 0.125 No Hit CCGCAGACCCGAGCGAAAGCGGCGGTCCTTACAAGTCCGCTCCTCGGGGA 5 0.125 No Hit GCCATTCGGACCTACCGTAAGCCTATATTTCGTTTTTCTGAGACCTATCC 5 0.125 No Hit GTCGAGTTGTACGGCCGTTCAGCCACGAGTCACGGGGTCTAACGCCTACC 5 0.125 No Hit GGAAGCTATACTATATAGGTGGCTATCTATCCCTACCAAGGCTTATATTG 5 0.125 No Hit GTCGAGACTGAAAAGCTATAACCCGCAGACCCGAGCGAAAGCGGCGGTCC 5 0.125 No Hit >>END_MODULE >>Adapter Content fail #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.05 0.0 0.0 0.0 0.0 68-69 0.05 0.0 0.0 0.0 0.0 70-71 0.1 0.0 0.0 0.0 0.0 72-73 0.1125 0.0 0.0 0.0 0.0 74-75 0.2 0.0 0.0 0.0 0.0 76-77 0.25 0.0 0.0 0.0 0.0 78-79 0.3125 0.0 0.0 0.0 0.0 80-81 0.36250000000000004 0.0 0.0 0.0 0.0 82-83 0.475 0.0 0.0 0.0 0.0 84-85 0.6375 0.0 0.0 0.0 0.0 86-87 0.925 0.0 0.0 0.0 0.0 88-89 1.0875 0.0 0.0 0.0 0.0 90-91 1.3250000000000002 0.0 0.0 0.0 0.0 92-93 1.475 0.0 0.0 0.0 0.0 94-95 1.7375 0.0 0.0 0.0 0.0 96-97 1.9625 0.0 0.0 0.0 0.0 98-99 2.2625 0.0 0.0 0.0 0.0 100-101 2.6875 0.0 0.0 0.0 0.0 102-103 3.1625 0.0 0.0 0.0 0.0 104-105 3.625 0.0 0.0 0.0 0.0 106-107 4.1 0.0 0.0 0.0 0.0 108-109 4.7 0.0 0.0 0.0 0.0 110-111 5.3125 0.0 0.0 0.0 0.0 112-113 5.775 0.0 0.0 0.0 0.0 114-115 6.375 0.0 0.0 0.0 0.0 116-117 7.15 0.0 0.0 0.0 0.0 118-119 7.7375 0.0 0.0 0.0 0.0 120-121 8.5375 0.0 0.0 0.0 0.0 122-123 9.125 0.0 0.0 0.0 0.0 124-125 9.8125 0.0 0.0 0.0 0.0 126-127 10.4875 0.0 0.0 0.0 0.0 128-129 11.337499999999999 0.0 0.0 0.0 0.0 130-131 12.0125 0.0 0.0 0.0 0.0 132-133 12.9375 0.0 0.0 0.0 0.0 134-135 13.8125 0.0 0.0 0.0 0.0 136-137 14.712499999999999 0.0 0.0 0.0 0.0 138-139 15.7625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GAAGTCC 10 0.006841402 144.925 5 TCGTCAG 10 0.006841402 144.925 9 AAGTCCT 10 0.006841402 144.925 6 >>END_MODULE SRR5579248 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR5579248_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 49 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.509 33.0 33.0 34.0 32.0 34.0 2 32.5245 33.0 33.0 34.0 32.0 34.0 3 32.50275 34.0 33.0 34.0 32.0 34.0 4 32.36525 34.0 33.0 34.0 32.0 34.0 5 32.37675 34.0 33.0 34.0 32.0 34.0 6 36.45825 38.0 38.0 38.0 35.0 38.0 7 36.3135 38.0 38.0 38.0 34.0 38.0 8 36.3515 38.0 38.0 38.0 34.0 38.0 9 36.30375 38.0 38.0 38.0 34.0 38.0 10-14 36.2822 38.0 38.0 38.0 34.2 38.0 15-19 36.1982 38.0 38.0 38.0 34.2 38.0 20-24 36.17285 38.0 38.0 38.0 34.4 38.0 25-29 36.13425 38.0 38.0 38.0 34.2 38.0 30-34 36.01199999999999 38.0 38.0 38.0 34.0 38.0 35-39 35.83115 38.0 38.0 38.0 33.2 38.0 40-44 35.826350000000005 38.0 38.0 38.0 33.6 38.0 45-49 35.4879 38.0 38.0 38.0 30.6 38.0 50-54 35.4822 38.0 38.0 38.0 30.6 38.0 55-59 35.56765 38.0 38.0 38.0 31.4 38.0 60-64 35.66545 38.0 38.0 38.0 33.2 38.0 65-69 35.18405 38.0 38.0 38.0 30.0 38.0 70-74 34.3944 38.0 38.0 38.0 24.8 38.0 75-79 34.34955 38.0 38.0 38.0 25.0 38.0 80-84 34.27635 38.0 38.0 38.0 24.4 38.0 85-89 34.23174999999999 38.0 38.0 38.0 24.4 38.0 90-94 34.036150000000006 38.0 38.0 38.0 18.4 38.0 95-99 33.9096 38.0 37.8 38.0 15.0 38.0 100-104 33.83555 38.0 37.0 38.0 16.2 38.0 105-109 33.61065 38.0 36.6 38.0 14.6 38.0 110-114 33.399350000000005 38.0 36.0 38.0 14.2 38.0 115-119 33.3498 38.0 36.0 38.0 14.0 38.0 120-124 33.09429999999999 38.0 35.2 38.0 13.4 38.0 125-129 32.8174 38.0 35.0 38.0 13.0 38.0 130-134 32.543549999999996 38.0 34.8 38.0 8.6 38.0 135-139 31.96925 38.0 34.0 38.0 2.0 38.0 140-144 31.480700000000002 38.0 34.0 38.0 2.0 38.0 145-149 30.544399999999996 38.0 32.4 38.0 2.0 38.0 150-151 26.655625 34.5 16.5 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 45.0 3 19.0 4 14.0 5 7.0 6 9.0 7 2.0 8 11.0 9 9.0 10 9.0 11 7.0 12 13.0 13 14.0 14 30.0 15 37.0 16 57.0 17 36.0 18 7.0 19 5.0 20 9.0 21 12.0 22 12.0 23 6.0 24 21.0 25 24.0 26 25.0 27 23.0 28 22.0 29 39.0 30 43.0 31 61.0 32 73.0 33 109.0 34 115.0 35 199.0 36 439.0 37 2437.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 45.375 15.375 13.975000000000001 25.275 2 26.8 25.525 25.55 22.125 3 24.3 22.975 29.675 23.05 4 28.425 29.325000000000003 17.349999999999998 24.9 5 31.35 30.775000000000002 18.575 19.3 6 26.400000000000002 31.35 21.15 21.099999999999998 7 21.4 22.625 33.324999999999996 22.650000000000002 8 22.85 27.025 21.25 28.875 9 28.1 21.9 24.349999999999998 25.650000000000002 10-14 26.384999999999998 25.52 23.080000000000002 25.014999999999997 15-19 26.900000000000002 24.18 24.505 24.415 20-24 27.625 26.325 22.575 23.474999999999998 25-29 27.76 26.08 22.384999999999998 23.775 30-34 27.029999999999998 24.535 24.83 23.605 35-39 24.884999999999998 24.545 24.959999999999997 25.61 40-44 29.075 23.56 24.065 23.3 45-49 26.419999999999998 22.95 24.635 25.995 50-54 25.27 24.495 25.47 24.765 55-59 25.174999999999997 25.56 25.855 23.41 60-64 24.325 28.16 24.169999999999998 23.345 65-69 24.66 28.705000000000002 23.93 22.705000000000002 70-74 24.595 27.36 24.104999999999997 23.94 75-79 25.61 26.419999999999998 24.39 23.580000000000002 80-84 25.665 26.029999999999998 24.385 23.919999999999998 85-89 25.009999999999998 26.619999999999997 24.87 23.5 90-94 26.14 26.015 24.855 22.99 95-99 25.56 26.14 25.174999999999997 23.125 100-104 25.629999999999995 26.72 24.55 23.1 105-109 25.759999999999998 27.47 23.89 22.88 110-114 26.19 27.455000000000002 23.200000000000003 23.155 115-119 27.005000000000003 27.36 23.22 22.415 120-124 26.645000000000003 27.045 23.685000000000002 22.625 125-129 26.724999999999998 27.77 23.11 22.395 130-134 27.35 26.825 23.9 21.925 135-139 27.450000000000003 26.875 23.830000000000002 21.845 140-144 27.725 26.72 24.01 21.545 145-149 27.779999999999998 27.250000000000004 23.465 21.505 150-151 28.5875 26.387500000000003 24.275 20.75 >>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 0.5 7 0.5 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 0.5 20 1.5 21 1.0 22 0.5 23 1.5 24 1.5 25 0.5 26 1.5 27 5.5 28 7.5 29 7.5 30 13.5 31 18.0 32 20.0 33 22.5 34 30.0 35 41.0 36 52.5 37 78.0 38 102.5 39 113.5 40 130.5 41 119.0 42 103.0 43 121.5 44 143.0 45 142.5 46 142.0 47 154.5 48 162.0 49 167.5 50 145.0 51 146.5 52 176.0 53 168.5 54 156.0 55 141.5 56 124.0 57 120.0 58 113.5 59 101.5 60 89.5 61 76.0 62 58.0 63 55.0 64 54.0 65 43.5 66 37.0 67 39.5 68 45.5 69 39.0 70 30.5 71 27.5 72 23.5 73 18.5 74 13.5 75 12.0 76 10.5 77 6.0 78 4.5 79 6.5 80 4.5 81 2.0 82 2.0 83 1.0 84 0.0 85 0.0 86 0.5 87 0.5 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 0.0 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 85.02499999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 93.149073801823 79.2 2 3.822405174948545 6.5 3 1.4701558365186709 3.75 4 0.4704498676859747 1.6 5 0.5586592178770949 2.375 6 0.17641870038224053 0.8999999999999999 7 0.08820935019112026 0.525 8 0.058806233460746836 0.4 9 0.058806233460746836 0.44999999999999996 >10 0.11761246692149367 1.225 >50 0.0 0.0 >100 0.029403116730373418 3.075 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences fail #Sequence Count Percentage Possible Source GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG 123 3.075 Illumina Single End PCR Primer 1 (100% over 50bp) GCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCC 19 0.475 No Hit GAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCCTCC 10 0.25 No Hit CGGGCGTCGGCATCCAGACCGTCGGCTGATCGTGGTTTTACTAGGCTAGA 10 0.25 No Hit GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGGCGCCG 10 0.25 Illumina Single End PCR Primer 1 (98% over 50bp) TAGGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGT 9 0.22499999999999998 No Hit GCCCAAGCTGCTCACAGTATACGGGCGTCGGCATCCAGACCGTCGGCTGA 9 0.22499999999999998 No Hit GCTGCTCACAGTATACGGGCGTCGGCATCCAGACCGTCGGCTGATCGTGG 8 0.2 No Hit ATTAATTAGGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATA 8 0.2 No Hit GGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTC 7 0.17500000000000002 No Hit ATTACTTCCATTTCCGCCCAAGCTGCTCACAGTATACGGGCGTCGGCATC 7 0.17500000000000002 No Hit TCCATTTCCGCCCAAGCTGCTCACAGTATACGGGCGTCGGCATCCAGACC 7 0.17500000000000002 No Hit CTTCACTGCCCCCTTTCAGCCTTTTGGGTCCTGTATCCCAATTCTCAGAG 6 0.15 No Hit GACGAATTGCCAGAATTATTAACTGCGCAGTTAGGGCAGCGTCTGAGGAA 6 0.15 No Hit GGGAGTATTTGCACTTGTGGTAACGGTATTTGCATTATTGATGGTTTTTA 6 0.15 No Hit GGAATGGGAGTATTTGCACTTGTGGTAACGGTATTTGCATTATTGATGGT 6 0.15 No Hit CGAATAGCTCGTAACCAAACATGCACAGCGGTCAAACAGTATGTCCCAAG 6 0.15 No Hit GCGGGTTATAGCTTTTCAGTCTCGACGGGCTAGCACACATCTGGTTGACT 6 0.15 No Hit GTCTGAGGAAGTTTGCTGCGGTTTCGCCTTGACCGCGGGAAGGAGACATA 5 0.125 No Hit GTCCGAATGGCACAAAGCTTGTTCCGTTAGCTGGCATAAGATTCCATGCC 5 0.125 No Hit GTTGAGTCCGTCCGACTTCACTGCCCCCTTTCAGCCTTTTGGGTCCTGTA 5 0.125 No Hit AAGCTGCTCACAGTATACGGGCGTCGGCATCCAGACCGTCGGCTGATCGT 5 0.125 No Hit AATTAGGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGA 5 0.125 No Hit GGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTT 5 0.125 No Hit TGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCCTC 5 0.125 No Hit AAAGAATATCCCAATTATCCATAAAACTGTAACTAAGTGAGGCTCTCTCA 5 0.125 No Hit ATTAGGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAG 5 0.125 No Hit GCCGTACGCTGAGGACCACCTGAAACGGGCATCGTCGCTCTTCGTTGTTC 5 0.125 No Hit GCGGTGTACACCCTTTTGAGCAATGATTGCACAACCTGCGATCACCTTAT 5 0.125 No Hit CTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCCT 5 0.125 No Hit GTTAGGGCAGCGTCTGAGGAAGTTTGCTGCGGTTTCGCCTTGACCGCGGG 5 0.125 No Hit CCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCCTCCTATGGT 5 0.125 No Hit CACAGGCGTCATACTTCCCAAGAAGCGGCCATAGCCCAGATGCGAGGTGG 5 0.125 No Hit GGAAGTTTGCTGCGGTTTCGCCTTGACCGCGGGAAGGAGACATAACGATA 5 0.125 No Hit GGGAGGTATCCCAATAGGAGGTTTCCTCCTATGGTTTTCAAAACAATCAC 5 0.125 No Hit CTGAGGACCACCTGAAACGGGCATCGTCGCTCTTCGTTGTTCGTCGACTT 5 0.125 No Hit GGAGTATTTGCACTTGTGGTAACGGTATTTGCATTATTGATGGTTTTTAC 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 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.05 0.0 0.0 0.0 0.0 62-63 0.05 0.0 0.0 0.0 0.0 64-65 0.05 0.0 0.0 0.0 0.0 66-67 0.075 0.0 0.0 0.0 0.0 68-69 0.075 0.0 0.0 0.0 0.0 70-71 0.15 0.0 0.0 0.0 0.0 72-73 0.16249999999999998 0.0 0.0 0.0 0.0 74-75 0.25 0.0 0.0 0.0 0.0 76-77 0.275 0.0 0.0 0.0 0.0 78-79 0.3625 0.0 0.0 0.0 0.0 80-81 0.4125 0.0 0.0 0.0 0.0 82-83 0.5249999999999999 0.0 0.0 0.0 0.0 84-85 0.7 0.0 0.0 0.0 0.0 86-87 1.0 0.0 0.0 0.0 0.0 88-89 1.175 0.0 0.0 0.0 0.0 90-91 1.4 0.0 0.0 0.0 0.0 92-93 1.5499999999999998 0.0 0.0 0.0 0.0 94-95 1.8375 0.0 0.0 0.0 0.0 96-97 2.0875 0.0 0.0 0.0 0.0 98-99 2.3625 0.0 0.0 0.0 0.0 100-101 2.8 0.0 0.0 0.0 0.0 102-103 3.325 0.0 0.0 0.0 0.0 104-105 3.8625000000000003 0.0 0.0 0.0 0.0 106-107 4.4125 0.0 0.0 0.0 0.0 108-109 5.0125 0.0 0.0 0.0 0.0 110-111 5.7 0.0 0.0 0.0 0.0 112-113 6.1625 0.0 0.0 0.0 0.0 114-115 6.775 0.0 0.0 0.0 0.0 116-117 7.5375 0.0 0.0 0.0 0.0 118-119 8.0875 0.0 0.0 0.0 0.0 120-121 8.8 0.0 0.0 0.0 0.0 122-123 9.3625 0.0 0.0 0.0 0.0 124-125 10.087499999999999 0.0 0.0 0.0 0.0 126-127 10.8125 0.0 0.0 0.0 0.0 128-129 11.675 0.0 0.0 0.0 0.0 130-131 12.3375 0.0 0.0 0.0 0.0 132-133 13.274999999999999 0.0 0.0 0.0 0.0 134-135 14.212499999999999 0.0 0.0 0.0 0.0 136-137 15.1 0.0 0.0 0.0 0.0 138-139 16.1375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AAAAAAA 145 1.4678336E-4 10.0 60-64 >>END_MODULE Read 830867 spots for SRR5579248.sra Written 830867 spots for SRR5579248.sra Read 830867 spots for SRR5579248.sra Written 830867 spots for SRR5579248.sra Read 830867 spots for SRR5579248.sra Written 830867 spots for SRR5579248.sra Read 830867 spots for SRR5579248.sra Written 830867 spots for SRR5579248.sra Read 830867 spots for SRR5579248.sra Written 830867 spots for SRR5579248.sra Read 830867 spots for SRR5579248.sra Written 830867 spots for SRR5579248.sra Read 830867 spots for SRR5579248.sra Written 830867 spots for SRR5579248.sra Read 830867 spots for SRR5579248.sra Written 830867 spots for SRR5579248.sra Read 830867 spots for SRR5579248.sra Written 830867 spots for SRR5579248.sra Read 830867 spots for SRR5579248.sra Written 830867 spots for SRR5579248.sra Read 830878 spots for SRR5579248.sra Written 830878 spots for SRR5579248.sra Read 830867 spots for SRR5579248.sra Written 830867 spots for SRR5579248.sra Read 830867 spots for SRR5579248.sra Written 830867 spots for SRR5579248.sra Read 830867 spots for SRR5579248.sra Written 830867 spots for SRR5579248.sra Read 830867 spots for SRR5579248.sra Written 830867 spots for SRR5579248.sra Read 830867 spots for SRR5579248.sra Written 830867 spots for SRR5579248.sra Read 830867 spots for SRR5579248.sra Written 830867 spots for SRR5579248.sra Read 830867 spots for SRR5579248.sra Written 830867 spots for SRR5579248.sra Read 830867 spots for SRR5579248.sra Written 830867 spots for SRR5579248.sra Read 830867 spots for SRR5579248.sra Written 830867 spots for SRR5579248.sra SRR ids: ['SRR5579248.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_s8vksrhu SRR5579248.sra spots: 16617351 blocks: [[1, 830867], [830868, 1661734], [1661735, 2492601], [2492602, 3323468], [3323469, 4154335], [4154336, 4985202], [4985203, 5816069], [5816070, 6646936], [6646937, 7477803], [7477804, 8308670], [8308671, 9139537], [9139538, 9970404], [9970405, 10801271], [10801272, 11632138], [11632139, 12463005], [12463006, 13293872], [13293873, 14124739], [14124740, 14955606], [14955607, 15786473], [15786474, 16617351]] SRR5579248 file size 5609374 SRR5579248 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 SRR5579248 SRR5579248_1.fastq SRR5579248_2.fastq Input file: SRR5579248_1.fastq Paired file: SRR5579248_2.fastq trimmed: SRR5579248-trimmed-pair1.fastq, SRR5579248-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 Dec 9 23:29:12 2024 >> started Mon Dec 9 23:29:31 2024 >> done (19.213s) 16617351 read pairs processed; of these: 68363 ( 0.41%) short read pairs filtered out after trimming by size control 823536 ( 4.96%) empty read pairs filtered out after trimming by size control 15725452 (94.63%) read pairs available; of these: 7954838 (50.59%) trimmed read pairs available after processing 7770614 (49.41%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 21 0.00% 19 25 0.00% 20 29 0.00% 21 16 0.00% 22 23 0.00% 23 21 0.00% 24 40 0.00% 25 32 0.00% 26 43 0.00% 27 49 0.00% 28 42 0.00% 29 53 0.00% 30 44 0.00% 31 69 0.00% 32 47 0.00% 33 60 0.00% 34 52 0.00% 35 82 0.00% 36 76 0.00% 37 89 0.00% 38 77 0.00% 39 102 0.00% 40 117 0.00% 41 116 0.00% 42 156 0.00% 43 177 0.00% 44 273 0.00% 45 453 0.00% 46 515 0.00% 47 506 0.00% 48 535 0.00% 49 559 0.00% 50 730 0.00% 51 847 0.01% 52 868 0.01% 53 848 0.01% 54 779 0.00% 55 891 0.01% 56 1022 0.01% 57 1106 0.01% 58 1295 0.01% 59 1237 0.01% 60 1462 0.01% 61 1545 0.01% 62 1899 0.01% 63 2244 0.01% 64 2371 0.02% 65 3205 0.02% 66 5908 0.04% 67 13124 0.08% 68 16437 0.10% 69 18984 0.12% 70 22729 0.14% 71 9491 0.06% 72 6593 0.04% 73 6373 0.04% 74 6394 0.04% 75 7038 0.04% 76 7527 0.05% 77 8351 0.05% 78 8929 0.06% 79 10088 0.06% 80 11327 0.07% 81 12538 0.08% 82 14207 0.09% 83 15413 0.10% 84 19283 0.12% 85 20842 0.13% 86 22099 0.14% 87 23696 0.15% 88 26359 0.17% 89 28294 0.18% 90 29609 0.19% 91 30487 0.19% 92 32801 0.21% 93 33276 0.21% 94 35359 0.22% 95 37873 0.24% 96 39077 0.25% 97 38316 0.24% 98 39786 0.25% 99 42014 0.27% 100 43659 0.28% 101 45344 0.29% 102 47679 0.30% 103 50023 0.32% 104 51783 0.33% 105 54217 0.34% 106 56046 0.36% 107 56387 0.36% 108 57015 0.36% 109 56285 0.36% 110 57348 0.36% 111 61031 0.39% 112 64065 0.41% 113 68015 0.43% 114 68750 0.44% 115 70794 0.45% 116 72536 0.46% 117 69793 0.44% 118 70584 0.45% 119 72872 0.46% 120 72977 0.46% 121 75280 0.48% 122 78044 0.50% 123 81382 0.52% 124 82189 0.52% 125 84250 0.54% 126 85619 0.54% 127 83922 0.53% 128 83591 0.53% 129 86139 0.55% 130 86239 0.55% 131 88017 0.56% 132 94106 0.60% 133 95224 0.61% 134 95140 0.61% 135 98129 0.62% 136 101454 0.65% 137 101986 0.65% 138 101879 0.65% 139 106351 0.68% 140 106358 0.68% 141 109904 0.70% 142 116974 0.74% 143 121431 0.77% 144 131371 0.84% 145 143476 0.91% 146 162568 1.03% 147 194086 1.23% 148 259381 1.65% 149 451250 2.87% 150 2454425 15.61% 151 7770614 49.41% 15725452 reads passed initial QC criterion=sequence-density sequence-density=0.48 sequence-density-rank=1 fanout-score=21.32 fanout-score-rank=1 prefix-density=5.18 prefix-fanout=2.0 sequence=TTCGTTTTTTTTCTTG criterion=fanout-score sequence-density=0.48 sequence-density-rank=1 fanout-score=21.32 fanout-score-rank=1 prefix-density=5.18 prefix-fanout=2.0 sequence=TTCGTTTTTTTTCTTG criterion=sequence-density sequence-density=0.81 sequence-density-rank=1 fanout-score=4.63 fanout-score-rank=8 prefix-density=3.75 prefix-fanout=1.0 sequence=CAAGAAAAAAAACGAA criterion=fanout-score sequence-density=0.01 sequence-density-rank=36 fanout-score=20.89 fanout-score-rank=1 prefix-density=0.05 prefix-fanout=2.9 sequence=CATCTCCTCTAACTTTGGAGAGGTAGGAATGGGAGTATTTGCACTTGTGGTAACGGTATTTGCATTATTGATGGTTTTTACTATGTTGGGTATGCTGTTCGATTTCTTAAAGGACTGAATATTCGGTGGCAGTATGGGATTTCTAAAAATAATGTTAAGAATTTTTGCTGGTTTTTTGCGACGTTGGTGTTGTATTCTATAGCTCCATTATGGCCGTTATATGGAATCATTGGAGTGCCAGTAATTCTACCACGCCTTATATTTAAAGACAAAAAGAAGTGTCTAACAACAACATCCACACTACTACTCCTTGTCATATTTCTTCCTGAATTGCTGATTCTTATTGGATTTCTGATATTTCCTATTGTTATGGGCTATTACATCTCTAAGGAATTGGTGAAGTAAAATGGTGAAGCTTATGAATTTGTGGAGTGAGAGGATTAAAGATAGGGAAGTTGTTGAAGTTATTGGCTGTGAGAGAGTGCCATTGATGAAACGT SRR5579248 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 09 23:31:07 Started mapping on | Dec 09 23:31:07 Finished on | Dec 09 23:56:20 Mapping speed, Million of reads per hour | 37.42 Number of input reads | 15725452 Average input read length | 283 UNIQUE READS: Uniquely mapped reads number | 8546468 Uniquely mapped reads % | 54.35% Average mapped length | 283.74 Number of splices: Total | 7638720 Number of splices: Annotated (sjdb) | 7123084 Number of splices: GT/AG | 7540397 Number of splices: GC/AG | 89255 Number of splices: AT/AC | 3526 Number of splices: Non-canonical | 5542 Mismatch rate per base, % | 0.10% Deletion rate per base | 0.00% Deletion average length | 1.37 Insertion rate per base | 0.00% Insertion average length | 1.20 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 250647 % of reads mapped to multiple loci | 1.59% Number of reads mapped to too many loci | 88453 % of reads mapped to too many loci | 0.56% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 40.07% % of reads unmapped: other | 3.43% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 6944922 6944922 6944922 N_multimapping 250647 250647 250647 N_noFeature 342845 8261971 441184 N_ambiguous 230193 1208 44462 UnstrandedReadsAssigned:7973430 PositiveStrandReadsAssigned:283289 NegativeStrandReadsAssigned:8060822 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=136 echo kmer=131 SRR5579248 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: SRR5579248-trimmed-pair1.fastq SRR5579248-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 15,725,452 reads, 8,171,936 reads pseudoaligned [quant] estimated average fragment length: 206.636 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,117 rounds 52973 SRR5579248.ke.tsv 35125 SRR5579248.se.tsv 88098 total ==> SRR5579248.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 730.572 42.9437 8.67256 PNS24247 1044 838.364 7.94427 1.39808 PNS24249 1928 1722.36 90.4524 7.7483 PNS24246 1044 838.364 7.94427 1.39808 PNS24248 1044 838.364 7.94427 1.39808 PNS24244 1471 1265.36 32.7712 3.82109 PNS24243 293 117.841 0 0 KQK14069 1603 1397.36 1240.95 131.026 KQK14071 474 275.967 8.67993 4.64055 ==> SRR5579248.se.tsv <== BRADI_1g14170v3 1281 BRADI_1g53295v3 28 BRADI_1g59795v3 90 BRADI_1g07683v3 0 BRADI_1g00485v3 7 BRADI_1g20270v3 908 BRADI_1g74790v3 136 BRADI_1g09890v3 0 BRADI_1g77505v3 216 BRADI_1g48960v3 0 SRR5579248 completed mapping pipeline successfully