Starting /dee2/code/volunteer_pipeline.sh SRR7230822 current disk space = 3053022003200 free memory = 1507964524 SRR7230822 SRAfilesize 9d1c580a6a70d0a6119c14fd4bab8408 SRR7230822.sra SRR7230822.sra file validated SRR7230822 is paired end SRR7230822 is conventional basespace SRR7230822 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7230822_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 48 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 33.43475 34.0 33.0 34.0 33.0 34.0 2 33.471 34.0 34.0 34.0 33.0 34.0 3 33.56125 34.0 34.0 34.0 33.0 34.0 4 33.5075 34.0 34.0 34.0 33.0 34.0 5 33.47425 34.0 34.0 34.0 33.0 34.0 6 37.1775 38.0 37.0 38.0 36.0 38.0 7 37.4915 38.0 38.0 38.0 37.0 38.0 8 37.42575 38.0 38.0 38.0 37.0 38.0 9 37.5195 38.0 38.0 38.0 38.0 38.0 10-14 37.46659999999999 38.0 38.0 38.0 38.0 38.0 15-19 37.4711 38.0 38.0 38.0 38.0 38.0 20-24 37.3163 38.0 38.0 38.0 37.2 38.0 25-29 37.1377 38.0 38.0 38.0 36.4 38.0 30-34 36.99325 38.0 38.0 38.0 36.0 38.0 35-39 36.95515 38.0 38.0 38.0 36.0 38.0 40-44 36.7133 38.0 38.0 38.0 35.2 38.0 45-49 36.74345 38.0 37.8 38.0 34.6 38.0 50-54 36.9072 38.0 37.8 38.0 35.6 38.0 55-59 37.0364 38.0 38.0 38.0 36.0 38.0 60-64 37.019549999999995 38.0 38.0 38.0 36.0 38.0 65-69 37.052949999999996 38.0 38.0 38.0 36.0 38.0 70-74 33.72735 38.0 36.6 38.0 15.6 38.0 75-79 34.05030000000001 38.0 37.2 38.0 22.6 38.0 80-84 35.714600000000004 38.0 38.0 38.0 32.2 38.0 85-89 36.3757 38.0 38.0 38.0 35.0 38.0 90-94 36.366499999999995 38.0 38.0 38.0 35.0 38.0 95-99 36.3774 38.0 38.0 38.0 35.0 38.0 100-104 36.1556 38.0 38.0 38.0 34.0 38.0 105-109 36.023199999999996 38.0 38.0 38.0 33.8 38.0 110-114 35.6882 38.0 37.6 38.0 32.2 38.0 115-119 34.540000000000006 38.0 35.0 38.0 25.4 38.0 120-124 35.07215 38.0 36.4 38.0 29.2 38.0 125-129 34.563100000000006 38.0 35.4 38.0 25.8 38.0 130-134 34.348499999999994 38.0 35.0 38.0 24.4 38.0 135-139 34.6876 38.0 35.6 38.0 28.2 38.0 140-144 34.0327 38.0 34.8 38.0 24.4 38.0 145-149 33.4107 38.0 33.0 38.0 22.2 38.0 150-151 29.528750000000002 35.5 27.0 38.0 7.5 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 4 1.0 5 0.0 6 0.0 7 0.0 8 2.0 9 0.0 10 0.0 11 2.0 12 1.0 13 4.0 14 2.0 15 8.0 16 3.0 17 11.0 18 25.0 19 14.0 20 7.0 21 6.0 22 6.0 23 10.0 24 10.0 25 13.0 26 15.0 27 23.0 28 22.0 29 33.0 30 38.0 31 58.0 32 73.0 33 135.0 34 227.0 35 386.0 36 822.0 37 2043.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 41.035258814703674 12.203050762690673 10.352588147036759 36.40910227556889 2 20.75 16.650000000000002 33.1 29.5 3 20.599999999999998 20.0 26.625 32.775 4 24.224999999999998 27.35 21.25 27.175 5 25.924999999999997 31.7 22.1 20.275000000000002 6 19.15 30.599999999999998 28.299999999999997 21.95 7 13.125 21.65 44.55 20.674999999999997 8 17.0 21.925 30.975 30.099999999999998 9 18.7 20.674999999999997 31.45 29.175 10-14 20.465 26.064999999999998 25.235000000000003 28.235 15-19 20.836041802090104 25.6262813140657 27.071353567678386 26.466323316165806 20-24 21.325 26.125 25.945 26.605 25-29 20.53 25.795 27.215 26.46 30-34 19.919999999999998 25.6 26.450000000000003 28.03 35-39 21.293004156442485 25.454454404326704 27.142070208823675 26.11047123040713 40-44 21.355029882979256 25.62402691979308 26.588318015167495 26.432625182060164 45-49 21.549697363813717 25.3564103846731 26.646991146015708 26.44690110549747 50-54 20.674999999999997 26.009999999999998 26.735 26.58 55-59 20.595 24.665 27.589999999999996 27.150000000000002 60-64 20.630000000000003 24.43 28.084999999999997 26.855 65-69 19.650000000000002 26.174999999999997 26.445 27.73 70-74 20.277428867893615 26.836327890339142 25.547485118234942 27.3387581235323 75-79 20.073537248214855 27.304699989342428 25.013321965256313 27.6084407971864 80-84 20.590781767252356 26.442577030812327 26.172650878533233 26.793990323402088 85-89 20.86655634120656 26.071912140815407 25.47515169750765 27.586379820470384 90-94 21.12 24.94 25.564999999999998 28.375 95-99 20.66 26.25 26.02 27.07 100-104 21.560000000000002 27.089999999999996 24.625 26.724999999999998 105-109 21.47 25.81 25.295 27.425 110-114 21.265 25.900000000000002 25.595000000000002 27.24 115-119 21.165 25.89 25.965 26.979999999999997 120-124 21.175 26.029999999999998 25.669999999999998 27.125 125-129 22.185 25.365 26.279999999999998 26.169999999999998 130-134 21.95 27.089999999999996 24.73 26.229999999999997 135-139 22.03 26.205000000000002 24.995 26.77 140-144 23.135 25.685000000000002 24.215 26.965 145-149 22.445 25.94 24.875 26.740000000000002 150-151 21.2 26.674999999999997 25.0375 27.0875 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 1.0 1 1.0 2 1.0 3 0.5 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 0.5 14 0.5 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 1.0 23 3.5 24 6.5 25 6.0 26 5.5 27 8.0 28 10.5 29 14.5 30 16.5 31 25.0 32 35.5 33 40.0 34 52.5 35 64.0 36 73.0 37 81.0 38 101.0 39 117.0 40 95.5 41 108.0 42 140.5 43 144.5 44 171.0 45 170.5 46 152.5 47 159.5 48 157.5 49 156.0 50 150.5 51 161.5 52 187.0 53 215.5 54 236.5 55 215.0 56 152.0 57 114.5 58 114.5 59 103.5 60 76.0 61 50.0 62 36.0 63 19.0 64 7.0 65 3.5 66 4.0 67 3.5 68 2.0 69 3.5 70 2.5 71 1.0 72 5.5 73 7.0 74 2.5 75 0.5 76 1.0 77 1.5 78 1.0 79 1.0 80 1.0 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 warn #Base N-Count 1 0.025 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 0.005 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.155 40-44 0.445 45-49 0.045 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 8.445 75-79 6.17 80-84 1.825 85-89 0.295 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 80.65 #Duplication Level Percentage of deduplicated Percentage of total 1 90.01859888406696 72.6 2 5.7036577805331685 9.2 3 1.7048977061376318 4.125 4 0.9299442033477991 3.0 5 0.402975821450713 1.625 6 0.3099814011159331 1.5 7 0.3719776813391197 2.1 8 0.09299442033477992 0.6 9 0.12399256044637322 0.8999999999999999 >10 0.3409795412275264 4.35 >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 fail #Sequence Count Percentage Possible Source GATCGGAAGAGCACACGTCTGAACTCCAGTCACCTGCTGATCTCGTATGC 49 1.225 TruSeq Adapter, Index 7 (97% over 36bp) GTCGGTTCGGTCCTCCAGTTAGTGTTACCCAACCTTCAACCTGCCCATGG 25 0.625 No Hit GGCCAACATAGCCTTCTCCGTCCCCCCTTCGCAGTAACACCAAGTACAGG 14 0.35000000000000003 No Hit CTTCGCAGTAACACCAAGTACAGGAATATTAACCTGTTTCCCATCGACTA 12 0.3 No Hit CCCCACTGCTGCCTCCCGTAGGAGTCTGGACCGTGTCTCAGTTCCAGTGT 12 0.3 No Hit GTCAGTCTTCGTCCAGGGGGCCGCCTTCGCCACCGGTATTCCTCCAGATC 11 0.27499999999999997 No Hit CCCATATTCAGACAGGATACCACGTGTCCCGCCCTACTCATCGAGCTCAC 11 0.27499999999999997 No Hit GGGGATTTCACATCTGACTTAACAAACCGCCTGCGTGCGCTTTACGCCCA 10 0.25 No Hit CGGGAACGTATTCACCGTGGCATTCTGATCCACGATTACTAGCGATTCCG 10 0.25 No Hit GTTCGGTCCTCCAGTTAGTGTTACCCAACCTTCAACCTGCCCATGGCTAG 10 0.25 No Hit CCGGTATTCCTCCAGATCTCTACGCATTTCACCGCTACACCTGGAATTCT 10 0.25 No Hit GTCCCCCCTTCGCAGTAACACCAAGTACAGGAATATTAACCTGTTTCCCA 9 0.22499999999999998 No Hit CCCCTTCGCAGTAACACCAAGTACAGGAATATTAACCTGTTTCCCATCGA 9 0.22499999999999998 No Hit GCTTCTTCTGCGGGTAACGTCAATGAGCAAAGGTATTAACTTTACTCCCT 9 0.22499999999999998 No Hit CGGGGATTTCACATCTGACTTAACAAACCGCCTGCGTGCGCTTTACGCCC 9 0.22499999999999998 No Hit GTTGATTTCTTTTCCTCGGGGTACTTAGATGTTTCAGTTCCCCCGGTTCG 8 0.2 No Hit ACGAGACTCAAGCTTGCCAGTATCAGATGCAGTTCCCAGGTTGAGCCCGG 8 0.2 No Hit CTGAGCGTCAGTCTTCGTCCAGGGGGCCGCCTTCGCCACCGGTATTCCTC 8 0.2 No Hit CCACTGCTGCCTCCCGTAGGAGTCTGGACCGTGTCTCAGTTCCAGTGTGG 7 0.17500000000000002 No Hit GTGCTTCTTCTGCGGGTAACGTCAATGAGCAAAGGTATTAACTTTACTCC 7 0.17500000000000002 No Hit CCGATTAACGCTTGCACCCTCCGTATTACCGCGGCTGCTGGCACGGAGTT 7 0.17500000000000002 No Hit CCCGGTTCGCCTCATTAACCTATGGATTCAGTTAATGATAGTGTGTCGAA 7 0.17500000000000002 No Hit GTCAGCATTCGCACTTCTGATACCTCCAGCATGCCTCACAGCACACCTTC 7 0.17500000000000002 No Hit CCACGCTTTCGCACCTGAGCGTCAGTCTTCGTCCAGGGGGCCGCCTTCGC 7 0.17500000000000002 No Hit CGATTAACGCTTGCACCCTCCGTATTACCGCGGCTGCTGGCACGGAGTTA 7 0.17500000000000002 No Hit GTTTGCTCCCCACGCTTTCGCACCTGAGCGTCAGTCTTCGTCCAGGGGGC 7 0.17500000000000002 No Hit CCGGGAACGTATTCACCGTGGCATTCTGATCCACGATTACTAGCGATTCC 7 0.17500000000000002 No Hit CACGCTTTCGCACCTGAGCGTCAGTCTTCGTCCAGGGGGCCGCCTTCGCC 7 0.17500000000000002 No Hit CTTTGGTCTTGCGACGTTATGCGGTATTAGCTACCGTTTCCAGTAGTTAT 7 0.17500000000000002 No Hit GCCGGTGCTTCTTCTGCGGGTAACGTCAATGAGCAAAGGTATTAACTTTA 7 0.17500000000000002 No Hit GTTTGATTGGCCTTTCACCCCCAGCCACAAGTCATCCGCTAATTTTTCAA 6 0.15 No Hit CTTTCCCTCACGGTACTGGTTCACTATCGGTCAGTCAGGAGTATTTAGCC 6 0.15 No Hit GATTAACGCTTGCACCCTCCGTATTACCGCGGCTGCTGGCACGGAGTTAG 6 0.15 No Hit GTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTAGGTGAGCC 6 0.15 No Hit CCCCGGTTCGCCTCATTAACCTATGGATTCAGTTAATGATAGTGTGTCGA 6 0.15 No Hit GTCGGTTTGGGGTACGATTTGATGTTACCTGATGCTTAGAGGCTTTTCCT 6 0.15 No Hit GCCAACATAGCCTTCTCCGTCCCCCCTTCGCAGTAACACCAAGTACAGGA 6 0.15 No Hit CCCACTGCTGCCTCCCGTAGGAGTCTGGACCGTGTCTCAGTTCCAGTGTG 6 0.15 No Hit CGTCAATTCATTTGAGTTTTAACCTTGCGGCCGTACTCCCCAGGCGGTCG 6 0.15 No Hit CAGTAATTCCGATTAACGCTTGCACCCTCCGTATTACCGCGGCTGCTGGC 6 0.15 No Hit GCGACGTTATGCGGTATTAGCTACCGTTTCCAGTAGTTATCCCCCTCCAT 5 0.125 No Hit TCCGATTAACGCTTGCACCCTCCGTATTACCGCGGCTGCTGGCACGGAGT 5 0.125 No Hit GCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTAGGTGAGCCGTT 5 0.125 No Hit GGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTAGGTGAGCCGT 5 0.125 No Hit ATTCCGATTAACGCTTGCACCCTCCGTATTACCGCGGCTGCTGGCACGGA 5 0.125 No Hit CCCACGCTTTCGCACCTGAGCGTCAGTCTTCGTCCAGGGGGCCGCCTTCG 5 0.125 No Hit GTCCAGGGGGCCGCCTTCGCCACCGGTATTCCTCCAGATCTCTACGCATT 5 0.125 No Hit CCCCCCTCTACGAGACTCAAGCTTGCCAGTATCAGATGCAGTTCCCAGGT 5 0.125 No Hit CTTGCACCCTCCGTATTACCGCGGCTGCTGGCACGGAGTTAGCCGGTGCT 5 0.125 No Hit CGGTATTCCTCCAGATCTCTACGCATTTCACCGCTACACCTGGAATTCTA 5 0.125 No Hit GCGCCATTGTAGCACGTGTGTAGCCCTGGTCGTAAGGGCCATGATGACTT 5 0.125 No Hit CTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCG 5 0.125 No Hit GCGGTATTAGCTACCGTTTCCAGTAGTTATCCCCCTCCATCAGGCAGTTT 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 0.05 0.0 0.0 0.0 0.0 42-43 0.05 0.0 0.0 0.0 0.0 44-45 0.05 0.0 0.0 0.0 0.0 46-47 0.05 0.0 0.0 0.0 0.0 48-49 0.05 0.0 0.0 0.0 0.0 50-51 0.0625 0.0 0.0 0.0 0.0 52-53 0.075 0.0 0.0 0.0 0.0 54-55 0.0875 0.0 0.0 0.0 0.0 56-57 0.1 0.0 0.0 0.0 0.0 58-59 0.1 0.0 0.0 0.0 0.0 60-61 0.125 0.0 0.0 0.0 0.0 62-63 0.125 0.0 0.0 0.0 0.0 64-65 0.15 0.0 0.0 0.0 0.0 66-67 0.15 0.0 0.0 0.0 0.0 68-69 0.15 0.0 0.0 0.0 0.0 70-71 0.15 0.0 0.0 0.0 0.0 72-73 0.175 0.0 0.0 0.0 0.0 74-75 0.2375 0.0 0.0 0.0 0.0 76-77 0.2625 0.0 0.0 0.0 0.0 78-79 0.3625 0.0 0.0 0.0 0.0 80-81 0.4375 0.0 0.0 0.0 0.0 82-83 0.4875 0.0 0.0 0.0 0.0 84-85 0.6000000000000001 0.0 0.0 0.0 0.0 86-87 0.725 0.0 0.0 0.0 0.0 88-89 0.85 0.0 0.0 0.0 0.0 90-91 0.95 0.0 0.0 0.0 0.0 92-93 1.125 0.0 0.0 0.0 0.0 94-95 1.3624999999999998 0.0 0.0 0.0 0.0 96-97 1.5875 0.0 0.0 0.0 0.0 98-99 1.8375 0.0 0.0 0.0 0.0 100-101 2.025 0.0 0.0 0.0 0.0 102-103 2.3 0.0 0.0 0.0 0.0 104-105 2.5625 0.0 0.0 0.0 0.0 106-107 2.95 0.0 0.0 0.0 0.0 108-109 3.3125 0.0 0.0 0.0 0.0 110-111 3.8875 0.0 0.0 0.0 0.0 112-113 4.3125 0.0 0.0 0.0 0.0 114-115 4.9 0.0 0.0 0.0 0.0 116-117 5.575 0.0 0.0 0.0 0.0 118-119 6.15 0.0 0.0 0.0 0.0 120-121 6.85 0.0 0.0 0.0 0.0 122-123 7.3375 0.0 0.0 0.0 0.0 124-125 8.125 0.0 0.0 0.0 0.0 126-127 8.9 0.0 0.0 0.0 0.0 128-129 9.8875 0.0 0.0 0.0 0.0 130-131 10.475000000000001 0.0 0.0 0.0 0.0 132-133 11.45 0.0 0.0 0.0 0.0 134-135 12.175 0.0 0.0 0.0 0.0 136-137 13.0625 0.0 0.0 0.0 0.0 138-139 14.2 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CCCCTTC 10 0.0071167517 143.025 3 TAATACC 10 0.0071167517 143.025 6 AATACCA 10 0.0071167517 143.025 7 ATACCAG 10 0.0071167517 143.025 8 >>END_MODULE SRR7230822 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7230822_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 48 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.814 34.0 33.0 34.0 32.0 34.0 2 33.02675 34.0 33.0 34.0 32.0 34.0 3 32.98375 34.0 33.0 34.0 33.0 34.0 4 32.893 34.0 33.0 34.0 32.0 34.0 5 32.9615 34.0 33.0 34.0 33.0 34.0 6 36.99225 38.0 38.0 38.0 37.0 38.0 7 36.8955 38.0 38.0 38.0 37.0 38.0 8 36.8175 38.0 38.0 38.0 37.0 38.0 9 36.84825 38.0 38.0 38.0 37.0 38.0 10-14 36.5851 38.0 38.0 38.0 35.6 38.0 15-19 36.81845 38.0 38.0 38.0 36.8 38.0 20-24 36.864 38.0 38.0 38.0 37.0 38.0 25-29 36.87295 38.0 38.0 38.0 37.2 38.0 30-34 36.877599999999994 38.0 38.0 38.0 37.0 38.0 35-39 36.67835 38.0 38.0 38.0 36.2 38.0 40-44 36.7021 38.0 38.0 38.0 36.4 38.0 45-49 36.599599999999995 38.0 38.0 38.0 36.4 38.0 50-54 36.67595 38.0 38.0 38.0 36.8 38.0 55-59 36.4105 38.0 38.0 38.0 35.6 38.0 60-64 36.62835 38.0 38.0 38.0 36.6 38.0 65-69 36.36315 38.0 38.0 38.0 35.6 38.0 70-74 36.059 38.0 38.0 38.0 35.0 38.0 75-79 36.07015 38.0 38.0 38.0 35.0 38.0 80-84 36.0538 38.0 38.0 38.0 34.8 38.0 85-89 36.055200000000006 38.0 38.0 38.0 35.0 38.0 90-94 35.92145 38.0 38.0 38.0 34.6 38.0 95-99 35.7551 38.0 38.0 38.0 34.0 38.0 100-104 35.6333 38.0 38.0 38.0 33.8 38.0 105-109 35.519149999999996 38.0 38.0 38.0 33.2 38.0 110-114 35.344199999999994 38.0 38.0 38.0 32.2 38.0 115-119 35.28945 38.0 38.0 38.0 32.2 38.0 120-124 34.9217 38.0 37.4 38.0 30.0 38.0 125-129 34.77745 38.0 36.4 38.0 28.8 38.0 130-134 34.431200000000004 38.0 36.0 38.0 25.0 38.0 135-139 34.070899999999995 38.0 35.8 38.0 23.8 38.0 140-144 33.47305 38.0 34.0 38.0 19.8 38.0 145-149 32.00365 38.0 31.8 38.0 9.0 38.0 150-151 26.709125 34.5 16.5 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 23.0 3 7.0 4 3.0 5 2.0 6 3.0 7 5.0 8 5.0 9 6.0 10 4.0 11 3.0 12 7.0 13 6.0 14 8.0 15 9.0 16 17.0 17 29.0 18 13.0 19 10.0 20 4.0 21 7.0 22 10.0 23 6.0 24 17.0 25 12.0 26 13.0 27 16.0 28 26.0 29 35.0 30 39.0 31 32.0 32 63.0 33 81.0 34 123.0 35 201.0 36 485.0 37 2670.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 46.17706237424547 16.121730382293762 12.726358148893361 24.974849094567407 2 29.425 22.775000000000002 27.575 20.225 3 25.85 26.125 27.125 20.9 4 29.775000000000002 32.425 18.15 19.650000000000002 5 28.95 34.025 19.05 17.974999999999998 6 23.575 36.5 20.75 19.175 7 22.95 19.6 34.525 22.925 8 26.674999999999997 23.325000000000003 23.599999999999998 26.400000000000002 9 27.450000000000003 23.65 25.0 23.9 10-14 27.544999999999998 26.66 22.935 22.86 15-19 28.595 26.005 23.810000000000002 21.59 20-24 28.185 26.855 23.974999999999998 20.985 25-29 27.145000000000003 27.334999999999997 23.745 21.775 30-34 28.09 27.215 23.805 20.89 35-39 27.700000000000003 25.97 24.610000000000003 21.72 40-44 28.565 25.97 24.365000000000002 21.099999999999998 45-49 27.741321444672646 26.078244752792667 25.321845414015932 20.858588388518758 50-54 27.50175298006611 25.89401983371732 25.267955524391468 21.3362716618251 55-59 26.998945941876222 26.61245796315816 25.814385383727352 20.574210711238266 60-64 27.339999999999996 26.479999999999997 25.21 20.97 65-69 28.16005608974359 27.013221153846157 24.524238782051285 20.302483974358974 70-74 28.077753779697623 27.459942739464566 24.30559043648601 20.1567130443518 75-79 26.985 26.91 24.72 21.385 80-84 28.08 26.075 25.590000000000003 20.255000000000003 85-89 27.77 26.68 24.735 20.815 90-94 27.625 26.865 24.705 20.805 95-99 27.605 27.07 24.825 20.5 100-104 27.6 27.765 24.715 19.919999999999998 105-109 27.095000000000002 27.975 24.365000000000002 20.565 110-114 27.27 27.639999999999997 24.695 20.395 115-119 27.76 28.044999999999998 24.695 19.5 120-124 27.905 27.41 24.825 19.86 125-129 28.194999999999997 27.075 24.635 20.095 130-134 28.000000000000004 27.105 24.34 20.555 135-139 29.104999999999997 27.229999999999997 23.465 20.200000000000003 140-144 29.354999999999997 27.565 23.645 19.435 145-149 29.23 28.115000000000002 22.85 19.805 150-151 29.7125 28.7375 23.075000000000003 18.475 >>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 0.5 11 0.5 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 1.0 20 1.0 21 0.0 22 0.0 23 0.5 24 0.5 25 1.5 26 2.0 27 1.0 28 2.5 29 6.0 30 8.0 31 12.5 32 19.0 33 21.0 34 27.0 35 36.5 36 55.5 37 71.0 38 65.0 39 78.5 40 102.5 41 115.0 42 130.5 43 143.5 44 145.0 45 150.0 46 159.0 47 166.0 48 184.0 49 194.0 50 200.5 51 187.5 52 183.5 53 234.0 54 258.5 55 233.0 56 187.5 57 130.0 58 100.5 59 95.0 60 71.5 61 53.5 62 56.0 63 37.0 64 11.5 65 6.0 66 4.0 67 3.5 68 5.0 69 5.5 70 5.5 71 6.0 72 5.0 73 2.0 74 4.0 75 5.5 76 3.0 77 2.5 78 2.0 79 0.5 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 0.6 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 0.185 50-54 0.16999999999999998 55-59 0.385 60-64 0.0 65-69 0.16 70-74 0.455 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 82.5 #Duplication Level Percentage of deduplicated Percentage of total 1 89.60606060606061 73.925 2 6.666666666666667 11.0 3 1.9090909090909092 4.725 4 0.6060606060606061 2.0 5 0.5757575757575757 2.375 6 0.21212121212121215 1.05 7 0.09090909090909091 0.525 8 0.09090909090909091 0.6 9 0.0 0.0 >10 0.24242424242424243 3.8 >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 fail #Sequence Count Percentage Possible Source GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG 44 1.0999999999999999 Illumina Single End PCR Primer 1 (100% over 50bp) GCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAG 26 0.65 No Hit GCGACTTATATTCTGTAGCAAGGTTAACCGAATAGGGGAGCCGAAGGGAA 19 0.475 No Hit CTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAA 18 0.44999999999999996 No Hit GGTGGATGCCCTGGCAGTCAGAGGCGATGAAGGACGTGCTAATCTGCGAT 13 0.325 No Hit GGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTA 12 0.3 No Hit GGTGAGTCGACCCCTAAGGCGAGGCCGAAAGGCGTAGTCGATGGGAAACA 10 0.25 No Hit CTTATATTCTGTAGCAAGGTTAACCGAATAGGGGAGCCGAAGGGAAACCG 10 0.25 No Hit GTGAAAAGCCCGCTCGCCGGAAGACCAAGGGTTCCTGTCCAACGTTAATC 8 0.2 No Hit ATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGA 8 0.2 No Hit ACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCA 8 0.2 No Hit GGTTAACCGAATAGGGGAGCCGAAGGGAAACCGAGTCTTAACTGGGCGTT 7 0.17500000000000002 No Hit AAACCATGCACCGAAGCTGCGGCAGCGACGCTTATGCGTTGTTGGGTAGG 7 0.17500000000000002 No Hit GGGAAACCGAGTCTTAACTGGGCGTTAAGTTGCAGGGTATAGACCCGAAA 7 0.17500000000000002 No Hit GCCCGCTCGCCGGAAGACCAAGGGTTCCTGTCCAACGTTAATCGGGGCAG 6 0.15 No Hit GTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAA 6 0.15 No Hit GTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTT 6 0.15 No Hit GTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGG 6 0.15 No Hit CGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAG 6 0.15 No Hit CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGAT 6 0.15 No Hit GCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGC 6 0.15 No Hit AACACATGCAAGTCGAACGGTAACAGGAAGAAGCTTGCTTCTTTGCTGAC 5 0.125 No Hit GTAACATCAAATCGTACCCCAAACCGACACAGGTGGTCAGGTAGAGAATA 5 0.125 No Hit TGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAG 5 0.125 No Hit GCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGC 5 0.125 No Hit GTTTAAGCGTGTAGGCTGGTTTTCCAGGCAAATCCGGAAAATCAAGGCTG 5 0.125 No Hit GCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTT 5 0.125 No Hit CTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGT 5 0.125 No Hit CAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTA 5 0.125 No Hit CGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATG 5 0.125 No Hit CAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCC 5 0.125 No Hit GGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGC 5 0.125 No Hit GCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGT 5 0.125 No Hit GCCTAACACATGCAAGTCGAACGGTAACAGGAAGAAGCTTGCTTCTTTGC 5 0.125 No Hit AAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCA 5 0.125 No Hit AGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTT 5 0.125 No Hit GGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAGAAGCTTGCTTC 5 0.125 No Hit AGCGTACACGGTGGATGCCCTGGCAGTCAGAGGCGATGAAGGACGTGCTA 5 0.125 No Hit GGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCC 5 0.125 No Hit GTAGCGGCGAGCGAACGGGGAGCAGCCCAGAGCCTGAATCAGTGTGTGTG 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 0.05 0.0 0.0 0.0 0.0 42-43 0.05 0.0 0.0 0.0 0.0 44-45 0.05 0.0 0.0 0.0 0.0 46-47 0.05 0.0 0.0 0.0 0.0 48-49 0.05 0.0 0.0 0.0 0.0 50-51 0.05 0.0 0.0 0.0 0.0 52-53 0.05 0.0 0.0 0.0 0.0 54-55 0.0625 0.0 0.0 0.0 0.0 56-57 0.075 0.0 0.0 0.0 0.0 58-59 0.075 0.0 0.0 0.0 0.0 60-61 0.1 0.0 0.0 0.0 0.0 62-63 0.1 0.0 0.0 0.0 0.0 64-65 0.125 0.0 0.0 0.0 0.0 66-67 0.125 0.0 0.0 0.0 0.0 68-69 0.125 0.0 0.0 0.0 0.0 70-71 0.125 0.0 0.0 0.0 0.0 72-73 0.15 0.0 0.0 0.0 0.0 74-75 0.21250000000000002 0.0 0.0 0.0 0.0 76-77 0.25 0.0 0.0 0.0 0.0 78-79 0.3625 0.0 0.0 0.0 0.0 80-81 0.4375 0.0 0.0 0.0 0.0 82-83 0.4875 0.0 0.0 0.0 0.0 84-85 0.6000000000000001 0.0 0.0 0.0 0.0 86-87 0.725 0.0 0.0 0.0 0.0 88-89 0.85 0.0 0.0 0.0 0.0 90-91 0.975 0.0 0.0 0.0 0.0 92-93 1.1375000000000002 0.0 0.0 0.0 0.0 94-95 1.3624999999999998 0.0 0.0 0.0 0.0 96-97 1.5875 0.0 0.0 0.0 0.0 98-99 1.85 0.0 0.0 0.0 0.0 100-101 2.0125 0.0 0.0 0.0 0.0 102-103 2.2625 0.0 0.0 0.0 0.0 104-105 2.575 0.0 0.0 0.0 0.0 106-107 3.0374999999999996 0.0 0.0 0.0 0.0 108-109 3.4625000000000004 0.0 0.0 0.0 0.0 110-111 4.025 0.0 0.0 0.0 0.0 112-113 4.475 0.0 0.0 0.0 0.0 114-115 5.0875 0.0 0.0 0.0 0.0 116-117 5.75 0.0 0.0 0.0 0.0 118-119 6.3375 0.0 0.0 0.0 0.0 120-121 7.0375 0.0 0.0 0.0 0.0 122-123 7.575 0.0 0.0 0.0 0.0 124-125 8.4125 0.0 0.0 0.0 0.0 126-127 9.212499999999999 0.0 0.0 0.0 0.0 128-129 10.0875 0.0 0.0 0.0 0.0 130-131 10.7 0.0 0.0 0.0 0.0 132-133 11.662500000000001 0.0 0.0 0.0 0.0 134-135 12.45 0.0 0.0 0.0 0.0 136-137 13.3125 0.0 0.0 0.0 0.0 138-139 14.4375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GTAGCTT 10 0.006830828 145.0 1 AAAAAAA 35 0.0035366106 20.714287 140-144 >>END_MODULE Read 559632 spots for SRR7230822.sra Written 559632 spots for SRR7230822.sra Read 559632 spots for SRR7230822.sra Written 559632 spots for SRR7230822.sra Read 559632 spots for SRR7230822.sra Written 559632 spots for SRR7230822.sra Read 559632 spots for SRR7230822.sra Written 559632 spots for SRR7230822.sra Read 559632 spots for SRR7230822.sra Written 559632 spots for SRR7230822.sra Read 559632 spots for SRR7230822.sra Written 559632 spots for SRR7230822.sra Read 559632 spots for SRR7230822.sra Written 559632 spots for SRR7230822.sra Read 559632 spots for SRR7230822.sra Written 559632 spots for SRR7230822.sra Read 559632 spots for SRR7230822.sra Written 559632 spots for SRR7230822.sra Read 559632 spots for SRR7230822.sra Written 559632 spots for SRR7230822.sra Read 559632 spots for SRR7230822.sra Written 559632 spots for SRR7230822.sra Read 559632 spots for SRR7230822.sra Written 559632 spots for SRR7230822.sra Read 559632 spots for SRR7230822.sra Written 559632 spots for SRR7230822.sra Read 559632 spots for SRR7230822.sra Written 559632 spots for SRR7230822.sra Read 559632 spots for SRR7230822.sra Written 559632 spots for SRR7230822.sra Read 559632 spots for SRR7230822.sra Written 559632 spots for SRR7230822.sra Read 559632 spots for SRR7230822.sra Written 559632 spots for SRR7230822.sra Read 559632 spots for SRR7230822.sra Written 559632 spots for SRR7230822.sra Read 559638 spots for SRR7230822.sra Written 559638 spots for SRR7230822.sra Read 559632 spots for SRR7230822.sra Written 559632 spots for SRR7230822.sra SRR ids: ['SRR7230822.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_54429sb1 SRR7230822.sra spots: 11192646 blocks: [[1, 559632], [559633, 1119264], [1119265, 1678896], [1678897, 2238528], [2238529, 2798160], [2798161, 3357792], [3357793, 3917424], [3917425, 4477056], [4477057, 5036688], [5036689, 5596320], [5596321, 6155952], [6155953, 6715584], [6715585, 7275216], [7275217, 7834848], [7834849, 8394480], [8394481, 8954112], [8954113, 9513744], [9513745, 10073376], [10073377, 10633008], [10633009, 11192646]] SRR7230822 file size 3771120 SRR7230822 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 SRR7230822 SRR7230822_1.fastq SRR7230822_2.fastq Input file: SRR7230822_1.fastq Paired file: SRR7230822_2.fastq trimmed: SRR7230822-trimmed-pair1.fastq, SRR7230822-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 10:38:23 2025 >> started Tue Feb 11 10:38:37 2025 >> done (13.728s) 11192646 read pairs processed; of these: 35405 ( 0.32%) short read pairs filtered out after trimming by size control 155624 ( 1.39%) empty read pairs filtered out after trimming by size control 11001617 (98.29%) read pairs available; of these: 5790355 (52.63%) trimmed read pairs available after processing 5211262 (47.37%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 2 0.00% 19 5 0.00% 20 6 0.00% 21 10 0.00% 22 17 0.00% 23 11 0.00% 24 19 0.00% 25 18 0.00% 26 21 0.00% 27 28 0.00% 28 15 0.00% 29 30 0.00% 30 20 0.00% 31 38 0.00% 32 20 0.00% 33 22 0.00% 34 37 0.00% 35 49 0.00% 36 44 0.00% 37 45 0.00% 38 45 0.00% 39 68 0.00% 40 80 0.00% 41 67 0.00% 42 91 0.00% 43 102 0.00% 44 102 0.00% 45 135 0.00% 46 139 0.00% 47 149 0.00% 48 165 0.00% 49 164 0.00% 50 249 0.00% 51 242 0.00% 52 261 0.00% 53 268 0.00% 54 278 0.00% 55 325 0.00% 56 346 0.00% 57 417 0.00% 58 465 0.00% 59 507 0.00% 60 552 0.01% 61 643 0.01% 62 767 0.01% 63 794 0.01% 64 962 0.01% 65 1365 0.01% 66 2013 0.02% 67 3792 0.03% 68 5838 0.05% 69 16762 0.15% 70 13659 0.12% 71 3727 0.03% 72 2608 0.02% 73 2683 0.02% 74 2644 0.02% 75 2774 0.03% 76 2971 0.03% 77 3358 0.03% 78 3632 0.03% 79 4700 0.04% 80 4667 0.04% 81 5051 0.05% 82 5813 0.05% 83 6939 0.06% 84 10000 0.09% 85 10398 0.09% 86 11931 0.11% 87 11964 0.11% 88 13418 0.12% 89 14058 0.13% 90 14357 0.13% 91 15061 0.14% 92 14930 0.14% 93 17334 0.16% 94 16896 0.15% 95 18584 0.17% 96 19958 0.18% 97 19594 0.18% 98 19797 0.18% 99 22435 0.20% 100 23177 0.21% 101 22543 0.20% 102 24295 0.22% 103 26576 0.24% 104 29059 0.26% 105 33166 0.30% 106 29829 0.27% 107 29417 0.27% 108 32495 0.30% 109 39446 0.36% 110 37266 0.34% 111 33681 0.31% 112 36378 0.33% 113 42868 0.39% 114 38875 0.35% 115 42018 0.38% 116 42639 0.39% 117 39013 0.35% 118 42438 0.39% 119 42902 0.39% 120 46417 0.42% 121 45083 0.41% 122 48814 0.44% 123 50270 0.46% 124 51305 0.47% 125 50532 0.46% 126 51368 0.47% 127 52782 0.48% 128 54544 0.50% 129 54843 0.50% 130 58354 0.53% 131 57929 0.53% 132 60213 0.55% 133 64619 0.59% 134 67084 0.61% 135 69022 0.63% 136 69042 0.63% 137 75816 0.69% 138 75404 0.69% 139 76602 0.70% 140 75540 0.69% 141 86446 0.79% 142 82364 0.75% 143 89772 0.82% 144 95707 0.87% 145 106449 0.97% 146 121570 1.11% 147 150240 1.37% 148 201740 1.83% 149 366614 3.33% 150 2191238 19.92% 151 5211262 47.37% 11001617 reads passed initial QC criterion=sequence-density sequence-density=0.90 sequence-density-rank=1 fanout-score=2.60 fanout-score-rank=22 prefix-density=2.34 prefix-fanout=1.0 sequence=CACTCGTCAGCGAAACAGCAAGCTGTTTCCTGTTACC criterion=fanout-score sequence-density=0.04 sequence-density-rank=35 fanout-score=13.43 fanout-score-rank=1 prefix-density=0.14 prefix-fanout=4.1 sequence=AATGAAGAAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAGGTGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGG criterion=sequence-density sequence-density=3.68 sequence-density-rank=1 fanout-score=1.94 fanout-score-rank=37 prefix-density=3.69 prefix-fanout=1.9 sequence=GCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATG criterion=fanout-score sequence-density=0.14 sequence-density-rank=37 fanout-score=21.48 fanout-score-rank=1 prefix-density=2.94 prefix-fanout=1.0 sequence=GCCGCGGTAATTCCAGCTCCAATAGCGTATATTTAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGGACTTTGGGTTGGGTCGGCCGGTCCGCCTCAGGTGTGCACCGGTCGCCTCGTCCCTTCTACCGGCGATGCGCTCCTGGCCTTAACTGGCCGGGTCGTGCCTCCGGTGCTGTTACTTTGAAGAAATTAGAGTGCTCAAAGCAAGCCTACGCTCTGGATACATTAGCATGGGATAACATCATAGGATTTCGATCCTATTGTGTTGGCCTTCGGGATCGGAGTAATGATTAACAGGGACAGTCGGGGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTTTTCATTAATCAAGAACGAAAGTTGGGGGCTCGAAGACGATCAGATACCGTCCTAGTCTCAACCATAAACGATGCCGACCAGGGATTGGCGGATGTTGCTTTTAGGACTCCGCCAGCACCTTA Potential 3prime adapter identified. Now checking if in reference sequence /dee2/code/volunteer_pipeline.sh: line 905: -f: command not found /dee2/code/volunteer_pipeline.sh: line 906: -f: command not found Adapter seq not found in reference. Now shuffling file before clipping skewer v0.2.2 [April 4, 2016] COMMAND LINE: skewer -f sanger -l 18 -t 20 -x CACTCGTCAGCGAAACAGCAAGCTGTTTCCTGTTACC -y GCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATG -o SRR7230822 SRR7230822_1.fastq SRR7230822_2.fastq Input file: SRR7230822_1.fastq Paired file: SRR7230822_2.fastq trimmed: SRR7230822-trimmed-pair1.fastq, SRR7230822-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): CACTCGTCAGCGAAACAGCAAGCTGTTTCCTGTTACC -- paired 3' end adapter sequence (-y): GCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACT -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- 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 10:39:49 2025 >> started Tue Feb 11 10:39:54 2025 >> done (5.138s) 3667206 read pairs processed; of these: 32 ( 0.00%) short read pairs filtered out after trimming by size control 253 ( 0.01%) empty read pairs filtered out after trimming by size control 3666921 (99.99%) read pairs available; of these: 1505 ( 0.04%) trimmed read pairs available after processing 3665416 (99.96%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 1 0.00% 19 0 0.00% 20 4 0.00% 21 4 0.00% 22 3 0.00% 23 3 0.00% 24 9 0.00% 25 5 0.00% 26 8 0.00% 27 12 0.00% 28 4 0.00% 29 10 0.00% 30 4 0.00% 31 16 0.00% 32 9 0.00% 33 5 0.00% 34 5 0.00% 35 15 0.00% 36 14 0.00% 37 14 0.00% 38 16 0.00% 39 22 0.00% 40 29 0.00% 41 23 0.00% 42 28 0.00% 43 36 0.00% 44 29 0.00% 45 59 0.00% 46 40 0.00% 47 55 0.00% 48 51 0.00% 49 45 0.00% 50 76 0.00% 51 81 0.00% 52 78 0.00% 53 87 0.00% 54 99 0.00% 55 110 0.00% 56 123 0.00% 57 143 0.00% 58 169 0.00% 59 158 0.00% 60 186 0.01% 61 225 0.01% 62 259 0.01% 63 252 0.01% 64 319 0.01% 65 479 0.01% 66 606 0.02% 67 1296 0.04% 68 1930 0.05% 69 5641 0.15% 70 4533 0.12% 71 1296 0.04% 72 859 0.02% 73 940 0.03% 74 908 0.02% 75 868 0.02% 76 984 0.03% 77 1111 0.03% 78 1204 0.03% 79 1552 0.04% 80 1563 0.04% 81 1687 0.05% 82 1875 0.05% 83 2334 0.06% 84 3437 0.09% 85 3364 0.09% 86 3917 0.11% 87 3972 0.11% 88 4414 0.12% 89 4704 0.13% 90 4825 0.13% 91 4992 0.14% 92 4909 0.13% 93 5737 0.16% 94 5606 0.15% 95 6236 0.17% 96 6580 0.18% 97 6491 0.18% 98 6569 0.18% 99 7423 0.20% 100 7690 0.21% 101 7598 0.21% 102 8058 0.22% 103 8794 0.24% 104 9685 0.26% 105 10944 0.30% 106 9910 0.27% 107 9841 0.27% 108 10850 0.30% 109 13093 0.36% 110 12531 0.34% 111 11326 0.31% 112 12132 0.33% 113 14151 0.39% 114 13106 0.36% 115 13975 0.38% 116 14135 0.39% 117 13094 0.36% 118 14075 0.38% 119 14299 0.39% 120 15646 0.43% 121 15038 0.41% 122 16267 0.44% 123 16796 0.46% 124 17151 0.47% 125 16748 0.46% 126 17224 0.47% 127 17588 0.48% 128 18192 0.50% 129 18044 0.49% 130 19566 0.53% 131 19289 0.53% 132 20158 0.55% 133 21513 0.59% 134 22233 0.61% 135 22954 0.63% 136 23108 0.63% 137 25403 0.69% 138 25148 0.69% 139 25490 0.70% 140 25100 0.68% 141 28698 0.78% 142 27503 0.75% 143 30099 0.82% 144 32025 0.87% 145 35133 0.96% 146 40461 1.10% 147 50309 1.37% 148 67246 1.83% 149 122603 3.34% 150 731090 19.94% 151 1736026 47.34% criterion=sequence-density sequence-density=0.91 sequence-density-rank=1 fanout-score=2.60 fanout-score-rank=22 prefix-density=2.36 prefix-fanout=1.0 sequence=CACTCGTCAGCGAAACAGCAAGCTGTTTCCTGTTACC criterion=fanout-score sequence-density=0.04 sequence-density-rank=36 fanout-score=12.84 fanout-score-rank=1 prefix-density=0.14 prefix-fanout=4.1 sequence=AATGAAGAAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAGGTGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGG criterion=sequence-density sequence-density=3.70 sequence-density-rank=1 fanout-score=1.94 fanout-score-rank=37 prefix-density=3.72 prefix-fanout=1.9 sequence=GCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATG criterion=fanout-score sequence-density=0.14 sequence-density-rank=37 fanout-score=21.35 fanout-score-rank=1 prefix-density=2.95 prefix-fanout=1.0 sequence=GCCGCGGTAATTCCAGCTCCAATAGCGTATATTTAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGGACTTTGGGTTGGGTCGGCCGGTCCGCCTCAGGTGTGCACCGGTCGCCTCGTCCCTTCTACCGGCGATGCGCTCCTGGCCTTAACTGGCCGGGTCGTGCCTCCGGTGCTGTTACTTTGAAGAAATTAGAGTGCTCAAAGCAAGCCTACGCTCTGGATACATTAGCATGGGATAACATCATAGGATTTCGATCCTATTGTGTTGGCCTTCGGGATCGGAGTAATGATTAACAGGGACAGTCGGGGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTTTTCATTAATCAAGAACGAAAGTTGGGGGCTCGAAGACGATCAGATACCGTCCTAGTCTCAACCATAAACGATGCCGACCAGGGATTGGCGGATGTTGCTTTTAGGACTCCGCCAGCACCTTA SRR7230822 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 10:41:07 Started mapping on | Feb 11 10:41:08 Finished on | Feb 11 10:47:29 Mapping speed, Million of reads per hour | 103.95 Number of input reads | 11001332 Average input read length | 286 UNIQUE READS: Uniquely mapped reads number | 5625988 Uniquely mapped reads % | 51.14% Average mapped length | 289.92 Number of splices: Total | 4107028 Number of splices: Annotated (sjdb) | 4016860 Number of splices: GT/AG | 4018875 Number of splices: GC/AG | 72144 Number of splices: AT/AC | 2701 Number of splices: Non-canonical | 13308 Mismatch rate per base, % | 0.40% Deletion rate per base | 0.03% Deletion average length | 2.46 Insertion rate per base | 0.04% Insertion average length | 2.44 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 228288 % of reads mapped to multiple loci | 2.08% Number of reads mapped to too many loci | 523395 % of reads mapped to too many loci | 4.76% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 40.46% % of reads unmapped: other | 1.57% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 5166648 5166648 5166648 N_multimapping 228288 228288 228288 N_noFeature 309441 5427831 361367 N_ambiguous 187425 649 40845 UnstrandedReadsAssigned:5129122 PositiveStrandReadsAssigned:197508 NegativeStrandReadsAssigned:5223776 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=140 echo kmer=135 SRR7230822 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: SRR7230822-trimmed-pair1.fastq SRR7230822-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 11,001,332 reads, 5,723,434 reads pseudoaligned [quant] estimated average fragment length: 204.318 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,262 rounds 52401 SRR7230822.ke.tsv 34699 SRR7230822.se.tsv 87100 total ==> SRR7230822.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1814.68 176 11.3315 Potri.005G024800.1.v4.1 1035 831.682 40 5.61923 Potri.004G059700.1.v4.1 961 757.689 2 0.308399 Potri.007G009000.2.v4.1 1416 1212.68 0 0 Potri.003G141000.2.v4.1 2943 2739.68 330 14.073 Potri.016G087400.1.v4.1 270 91.7327 251.081 319.789 Potri.015G069301.1.v4.1 564 362.001 0 0 Potri.010G195200.1.v4.1 1773 1569.68 1 0.0744324 Potri.012G127500.1.v4.1 977 773.689 17 2.56718 ==> SRR7230822.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 169 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 201 Potri.001G212900.v4.1 8 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 0 SRR7230822 completed mapping pipeline successfully