Starting /dee2/code/volunteer_pipeline.sh SRR7230766 current disk space = 3057428168704 free memory = 1575440452 SRR7230766 SRAfilesize 2bade2a3e026b9707bbea70c3b7f2c36 SRR7230766.sra SRR7230766.sra file validated SRR7230766 is paired end SRR7230766 is conventional basespace SRR7230766 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7230766_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 33.50225 34.0 33.0 34.0 33.0 34.0 2 33.458 34.0 34.0 34.0 33.0 34.0 3 33.544 34.0 34.0 34.0 33.0 34.0 4 33.51775 34.0 34.0 34.0 33.0 34.0 5 33.46575 34.0 34.0 34.0 33.0 34.0 6 37.1815 38.0 37.0 38.0 36.0 38.0 7 37.38 38.0 38.0 38.0 37.0 38.0 8 37.447 38.0 38.0 38.0 37.0 38.0 9 37.523 38.0 38.0 38.0 38.0 38.0 10-14 37.43885000000001 38.0 38.0 38.0 37.6 38.0 15-19 37.399550000000005 38.0 38.0 38.0 37.4 38.0 20-24 37.251349999999995 38.0 38.0 38.0 37.2 38.0 25-29 36.893100000000004 38.0 38.0 38.0 35.6 38.0 30-34 36.836850000000005 38.0 38.0 38.0 35.6 38.0 35-39 36.7676 38.0 38.0 38.0 35.2 38.0 40-44 36.4487 38.0 38.0 38.0 34.2 38.0 45-49 36.45655000000001 38.0 37.8 38.0 33.6 38.0 50-54 36.60975 38.0 37.8 38.0 34.2 38.0 55-59 36.725300000000004 38.0 38.0 38.0 35.2 38.0 60-64 36.7363 38.0 38.0 38.0 35.4 38.0 65-69 36.75215 38.0 38.0 38.0 35.8 38.0 70-74 33.7366 38.0 36.2 38.0 15.2 38.0 75-79 34.2883 38.0 37.4 38.0 26.4 38.0 80-84 35.738150000000005 38.0 38.0 38.0 31.6 38.0 85-89 36.2744 38.0 38.0 38.0 34.4 38.0 90-94 36.2493 38.0 38.0 38.0 34.0 38.0 95-99 36.2341 38.0 38.0 38.0 34.2 38.0 100-104 36.05545 38.0 38.0 38.0 34.0 38.0 105-109 35.84605 38.0 38.0 38.0 33.2 38.0 110-114 35.48585 38.0 37.6 38.0 31.0 38.0 115-119 34.3679 38.0 35.0 38.0 23.2 38.0 120-124 35.07805 38.0 36.4 38.0 29.2 38.0 125-129 34.37505 38.0 35.4 38.0 23.6 38.0 130-134 34.26795 38.0 35.2 38.0 23.6 38.0 135-139 34.59325 38.0 35.6 38.0 27.4 38.0 140-144 33.79540000000001 38.0 34.6 38.0 22.4 38.0 145-149 33.2537 38.0 33.0 38.0 20.2 38.0 150-151 29.5775 35.5 27.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 5 1.0 6 0.0 7 2.0 8 1.0 9 2.0 10 2.0 11 2.0 12 6.0 13 5.0 14 4.0 15 7.0 16 11.0 17 7.0 18 18.0 19 12.0 20 9.0 21 9.0 22 11.0 23 10.0 24 12.0 25 18.0 26 18.0 27 18.0 28 25.0 29 38.0 30 39.0 31 62.0 32 93.0 33 135.0 34 224.0 35 333.0 36 805.0 37 2061.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 41.935483870967744 12.4031007751938 14.678669667416855 30.9827456864216 2 22.125 16.875 31.6 29.4 3 21.099999999999998 23.225 26.700000000000003 28.975 4 22.55 30.575000000000003 24.65 22.225 5 23.3 31.874999999999996 26.075 18.75 6 17.5 32.675 30.175 19.650000000000002 7 15.5 23.35 41.625 19.525000000000002 8 17.4 23.525 31.95 27.125 9 16.125 25.025 34.175 24.675 10-14 19.845 28.95 26.415 24.79 15-19 20.40306045906886 28.149222383357504 27.619142871430714 23.82857428614292 20-24 20.25 28.1 27.11 24.54 25-29 19.794999999999998 28.605000000000004 27.495000000000005 24.104999999999997 30-34 19.415 29.01 26.735 24.84 35-39 20.063104121800972 28.712375419442083 27.315069865277707 23.90945059347924 40-44 20.349274853214233 28.23305063481708 27.495358056907715 23.922316455060972 45-49 20.63341171761645 28.46350127582929 26.852454095161853 24.050632911392405 50-54 19.794999999999998 28.34 26.825 25.040000000000003 55-59 20.195 27.275 27.355 25.174999999999997 60-64 20.13 27.265 28.105000000000004 24.5 65-69 19.6 28.34 26.865 25.195 70-74 20.278620988725066 28.398742411101473 26.59366869037294 24.72896790980052 75-79 20.388503678611126 28.142698353887685 26.618324247075638 24.850473720425555 80-84 20.86085984348003 28.08212216688688 26.405122471795917 24.65189551783718 85-89 20.61566228817808 28.28637320766068 26.015241151107993 25.082723353053243 90-94 20.755000000000003 26.889999999999997 27.389999999999997 24.965 95-99 20.119999999999997 27.87 27.41 24.6 100-104 21.355 27.68 26.1 24.865000000000002 105-109 21.18 27.82 25.995 25.005 110-114 20.955 27.67 25.86 25.515 115-119 20.69 27.87 26.174999999999997 25.264999999999997 120-124 20.455000000000002 28.605000000000004 25.629999999999995 25.31 125-129 21.560000000000002 27.05 26.200000000000003 25.19 130-134 21.529999999999998 28.494999999999997 25.4 24.575 135-139 21.055 27.83 25.7 25.415 140-144 22.005 27.04 24.725 26.229999999999997 145-149 21.654999999999998 27.985 25.074999999999996 25.285000000000004 150-151 21.837500000000002 27.575 24.4125 26.174999999999997 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 9.0 1 7.5 2 3.5 3 1.5 4 1.5 5 1.0 6 1.0 7 2.0 8 1.5 9 0.0 10 1.0 11 1.5 12 0.5 13 0.0 14 0.0 15 0.0 16 0.0 17 0.5 18 1.0 19 0.5 20 0.5 21 1.0 22 3.0 23 3.0 24 3.5 25 7.5 26 8.5 27 11.5 28 15.5 29 24.0 30 32.5 31 40.0 32 56.0 33 68.0 34 86.0 35 104.0 36 111.5 37 130.0 38 137.5 39 148.0 40 156.5 41 159.0 42 182.0 43 190.5 44 180.5 45 165.5 46 159.5 47 165.0 48 169.5 49 150.0 50 138.0 51 136.5 52 139.0 53 167.5 54 168.0 55 141.5 56 96.5 57 66.5 58 68.0 59 58.5 60 37.5 61 25.5 62 22.0 63 13.5 64 8.0 65 3.5 66 1.0 67 1.5 68 2.0 69 2.0 70 1.0 71 1.0 72 1.0 73 0.0 74 0.0 75 0.5 76 0.5 77 0.0 78 0.0 79 0.5 80 0.5 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 0.015 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.165 40-44 0.365 45-49 0.065 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 7.76 75-79 5.535 80-84 1.6099999999999999 85-89 0.27 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 89.7 #Duplication Level Percentage of deduplicated Percentage of total 1 93.08807134894091 83.5 2 4.9052396878483835 8.799999999999999 3 1.1148272017837235 3.0 4 0.36231884057971014 1.3 5 0.055741360089186176 0.25 6 0.2229654403567447 1.2 7 0.08361204013377926 0.525 8 0.055741360089186176 0.4 9 0.055741360089186176 0.44999999999999996 >10 0.055741360089186176 0.575 >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 GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGGAATATCTCGTATGC 12 0.3 TruSeq Adapter, Index 7 (97% over 37bp) TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 11 0.27499999999999997 No Hit CCCGGTTCGCCTCATTAACCTATGGATTCAGTTAATGATAGTGTGTCGAA 9 0.22499999999999998 No Hit CCCATATTCAGACAGGATACCACGTGTCCCGCCCTACTCATCGAGCTCAC 9 0.22499999999999998 No Hit GTCGGTTCGGTCCTCCAGTTAGTGTTACCCAACCTTCAACCTGCCCATGG 8 0.2 No Hit CTTTGGTCTTGCGACGTTATGCGGTATTAGCTACCGTTTCCAGTAGTTAT 8 0.2 No Hit GTGCTTCTTCTGCGGGTAACGTCAATGAGCAAAGGTATTAACTTTACTCC 7 0.17500000000000002 No Hit CGGGAACGTATTCACCGTGGCATTCTGATCCACGATTACTAGCGATTCCG 7 0.17500000000000002 No Hit GGCCAACATAGCCTTCTCCGTCCCCCCTTCGCAGTAACACCAAGTACAGG 7 0.17500000000000002 No Hit CCCCCTTCGCAGTAACACCAAGTACAGGAATATTAACCTGTTTCCCATCG 6 0.15 No Hit TCCGATTAACGCTTGCACCCTCCGTATTACCGCGGCTGCTGGCACGGAGT 6 0.15 No Hit GGGGATTTCACATCTGACTTAACAAACCGCCTGCGTGCGCTTTACGCCCA 6 0.15 No Hit CTTCGCAGTAACACCAAGTACAGGAATATTAACCTGTTTCCCATCGACTA 6 0.15 No Hit CCCCGGTTCGCCTCATTAACCTATGGATTCAGTTAATGATAGTGTGTCGA 6 0.15 No Hit GCTTCTTCTGCGGGTAACGTCAATGAGCAAAGGTATTAACTTTACTCCCT 6 0.15 No Hit GCCAACATAGCCTTCTCCGTCCCCCCTTCGCAGTAACACCAAGTACAGGA 6 0.15 No Hit CTCCGTCCCCCCTTCGCAGTAACACCAAGTACAGGAATATTAACCTGTTT 6 0.15 No Hit CCGGTTCGCCTCATTAACCTATGGATTCAGTTAATGATAGTGTGTCGAAA 5 0.125 No Hit GTCCCCCCTTCGCAGTAACACCAAGTACAGGAATATTAACCTGTTTCCCA 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 0.0125 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 0.025 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 0.075 0.0 0.0 0.0 0.0 60-61 0.075 0.0 0.0 0.0 0.0 62-63 0.075 0.0 0.0 0.0 0.0 64-65 0.075 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 0.075 0.0 0.0 0.0 0.0 72-73 0.075 0.0 0.0 0.0 0.0 74-75 0.125 0.0 0.0 0.0 0.0 76-77 0.1375 0.0 0.0 0.0 0.0 78-79 0.1875 0.0 0.0 0.0 0.0 80-81 0.2625 0.0 0.0 0.0 0.0 82-83 0.35 0.0 0.0 0.0 0.0 84-85 0.5 0.0 0.0 0.0 0.0 86-87 0.675 0.0 0.0 0.0 0.0 88-89 0.775 0.0 0.0 0.0 0.0 90-91 0.9624999999999999 0.0 0.0 0.0 0.0 92-93 1.1875 0.0 0.0 0.0 0.0 94-95 1.3375 0.0 0.0 0.0 0.0 96-97 1.6749999999999998 0.0 0.0 0.0 0.0 98-99 2.125 0.0 0.0 0.0 0.0 100-101 2.5625 0.0 0.0 0.0 0.0 102-103 2.925 0.0 0.0 0.0 0.0 104-105 3.2125 0.0 0.0 0.0 0.0 106-107 3.6125 0.0 0.0 0.0 0.0 108-109 4.1 0.0 0.0 0.0 0.0 110-111 4.5875 0.0 0.0 0.0 0.0 112-113 5.1375 0.0 0.0 0.0 0.0 114-115 5.475 0.0 0.0 0.0 0.0 116-117 6.125 0.0 0.0 0.0 0.0 118-119 6.6375 0.0 0.0 0.0 0.0 120-121 7.199999999999999 0.0 0.0 0.0 0.0 122-123 7.7875 0.0 0.0 0.0 0.0 124-125 8.5 0.0 0.0 0.0 0.0 126-127 9.325 0.0 0.0 0.0 0.0 128-129 10.125 0.0 0.0 0.0 0.0 130-131 10.6625 0.0 0.0 0.0 0.0 132-133 11.3125 0.0 0.0 0.0 0.0 134-135 12.125 0.0 0.0 0.0 0.0 136-137 13.175 0.0 0.0 0.0 0.0 138-139 14.075 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CCAAGCC 10 0.0071260575 142.9625 7 CGGAAGA 140 0.0013756334 10.211607 4 >>END_MODULE SRR7230766 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7230766_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 46 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.4145 34.0 33.0 34.0 32.0 34.0 2 32.60075 34.0 33.0 34.0 32.0 34.0 3 32.53375 34.0 33.0 34.0 32.0 34.0 4 32.412 34.0 33.0 34.0 32.0 34.0 5 32.443 34.0 33.0 34.0 32.0 34.0 6 36.3725 38.0 38.0 38.0 36.0 38.0 7 36.31525 38.0 38.0 38.0 35.0 38.0 8 36.26475 38.0 38.0 38.0 35.0 38.0 9 36.26275 38.0 38.0 38.0 35.0 38.0 10-14 35.9234 38.0 38.0 38.0 32.8 38.0 15-19 36.14934999999999 38.0 38.0 38.0 35.0 38.0 20-24 36.1803 38.0 38.0 38.0 35.6 38.0 25-29 36.1268 38.0 38.0 38.0 35.2 38.0 30-34 36.10574999999999 38.0 38.0 38.0 35.4 38.0 35-39 35.86785 38.0 38.0 38.0 33.8 38.0 40-44 35.91425 38.0 38.0 38.0 34.2 38.0 45-49 35.85245 38.0 38.0 38.0 34.0 38.0 50-54 35.9449 38.0 38.0 38.0 34.8 38.0 55-59 35.657250000000005 38.0 38.0 38.0 33.0 38.0 60-64 35.93625 38.0 38.0 38.0 34.4 38.0 65-69 35.7148 38.0 38.0 38.0 33.4 38.0 70-74 35.486149999999995 38.0 38.0 38.0 32.8 38.0 75-79 35.547450000000005 38.0 38.0 38.0 32.6 38.0 80-84 35.53415 38.0 38.0 38.0 33.2 38.0 85-89 35.4831 38.0 38.0 38.0 33.2 38.0 90-94 35.35555 38.0 38.0 38.0 32.4 38.0 95-99 35.20185 38.0 38.0 38.0 31.0 38.0 100-104 35.1109 38.0 38.0 38.0 30.2 38.0 105-109 35.0178 38.0 38.0 38.0 29.8 38.0 110-114 34.86965 38.0 38.0 38.0 28.2 38.0 115-119 34.8178 38.0 38.0 38.0 29.2 38.0 120-124 34.4383 38.0 36.8 38.0 25.4 38.0 125-129 34.2309 38.0 36.0 38.0 23.8 38.0 130-134 33.967150000000004 38.0 36.0 38.0 21.8 38.0 135-139 33.5954 38.0 35.8 38.0 18.2 38.0 140-144 32.80795 38.0 33.4 38.0 13.0 38.0 145-149 31.358449999999998 38.0 31.2 38.0 4.2 38.0 150-151 26.345625 34.5 16.5 37.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 48.0 3 26.0 4 9.0 5 9.0 6 6.0 7 4.0 8 5.0 9 4.0 10 10.0 11 4.0 12 6.0 13 10.0 14 11.0 15 9.0 16 9.0 17 22.0 18 8.0 19 8.0 20 9.0 21 8.0 22 13.0 23 22.0 24 25.0 25 17.0 26 21.0 27 14.0 28 23.0 29 33.0 30 39.0 31 38.0 32 57.0 33 78.0 34 125.0 35 206.0 36 476.0 37 2588.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 43.871130128366474 16.486282406242132 15.932544676566826 23.710042788824566 2 27.275 23.175 27.325 22.225 3 24.05 25.674999999999997 28.050000000000004 22.225 4 27.800000000000004 31.05 21.2 19.950000000000003 5 27.025 34.2 20.875 17.9 6 22.95 34.0 22.95 20.1 7 21.425 20.025000000000002 37.45 21.099999999999998 8 25.575 24.0 24.224999999999998 26.200000000000003 9 25.324999999999996 26.075 25.15 23.45 10-14 26.534999999999997 27.334999999999997 23.849999999999998 22.28 15-19 26.534999999999997 26.605 25.619999999999997 21.240000000000002 20-24 26.200000000000003 27.185 25.779999999999998 20.835 25-29 25.81 27.61 25.900000000000002 20.68 30-34 26.83 26.669999999999998 26.125 20.375 35-39 25.755 26.56 26.290000000000003 21.395 40-44 26.424999999999997 26.8 26.150000000000002 20.625 45-49 26.245930378161788 26.82193839218633 26.506386175807663 20.425745053844228 50-54 25.617268493013473 26.57885511093304 27.02459057444784 20.77928582160565 55-59 25.439212930428674 26.859753036843692 27.28641702640297 20.41461700632467 60-64 25.564999999999998 27.155 26.815 20.465 65-69 26.057995692893275 27.109731056242804 26.608904692743025 20.2233685581209 70-74 25.406871609403254 26.883664858348403 26.91380349608198 20.795660036166367 75-79 25.230000000000004 27.189999999999998 26.69 20.89 80-84 25.369999999999997 27.415 26.634999999999998 20.580000000000002 85-89 25.64 26.735 27.235 20.39 90-94 25.345000000000002 27.125 27.235 20.294999999999998 95-99 25.36 27.845 26.96 19.835 100-104 25.21 27.229999999999997 26.86 20.7 105-109 25.25 27.72 26.61 20.419999999999998 110-114 26.02 27.689999999999998 26.369999999999997 19.919999999999998 115-119 25.55 27.915 27.215 19.32 120-124 25.955000000000002 27.800000000000004 26.68 19.564999999999998 125-129 26.07 28.15 26.375 19.405 130-134 26.31 27.41 26.75 19.53 135-139 26.685 27.889999999999997 26.075 19.35 140-144 27.35 27.6 26.009999999999998 19.040000000000003 145-149 28.03 27.91 25.019999999999996 19.040000000000003 150-151 27.85 28.1875 25.4 18.5625 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.0 2 0.5 3 0.5 4 0.5 5 0.5 6 0.0 7 0.5 8 0.5 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.5 15 0.5 16 0.0 17 0.0 18 1.0 19 1.0 20 0.0 21 1.5 22 2.5 23 1.0 24 1.0 25 3.5 26 3.5 27 2.5 28 4.0 29 6.5 30 12.5 31 20.0 32 24.0 33 29.5 34 45.0 35 60.5 36 76.0 37 90.5 38 110.5 39 132.5 40 149.5 41 152.5 42 154.5 43 177.0 44 175.5 45 174.5 46 190.0 47 194.0 48 200.5 49 201.0 50 188.0 51 164.0 52 175.0 53 198.5 54 192.5 55 174.0 56 129.5 57 85.0 58 67.0 59 62.0 60 45.5 61 33.5 62 32.0 63 20.0 64 9.5 65 5.0 66 1.5 67 1.0 68 1.0 69 3.5 70 3.0 71 0.0 72 0.5 73 1.0 74 0.5 75 1.0 76 1.0 77 0.0 78 1.0 79 1.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.5 86 0.5 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 0.675 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 0.17500000000000002 50-54 0.165 55-59 0.38999999999999996 60-64 0.0 65-69 0.165 70-74 0.45999999999999996 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 90.3 #Duplication Level Percentage of deduplicated Percentage of total 1 93.57696566998892 84.5 2 4.73421926910299 8.55 3 0.9413067552602437 2.55 4 0.3045404208194906 1.0999999999999999 5 0.1937984496124031 0.8750000000000001 6 0.02768549280177187 0.15 7 0.02768549280177187 0.17500000000000002 8 0.02768549280177187 0.2 9 0.02768549280177187 0.22499999999999998 >10 0.13842746400885936 1.675 >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 GGTGGATGCCCTGGCAGTCAGAGGCGATGAAGGACGTGCTAATCTGCGAT 16 0.4 No Hit GCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAG 15 0.375 No Hit GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG 14 0.35000000000000003 Illumina Single End PCR Primer 1 (100% over 50bp) GCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGC 12 0.3 No Hit CTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAA 10 0.25 No Hit GGTGAGTCGACCCCTAAGGCGAGGCCGAAAGGCGTAGTCGATGGGAAACA 9 0.22499999999999998 No Hit GCGACTTATATTCTGTAGCAAGGTTAACCGAATAGGGGAGCCGAAGGGAA 8 0.2 No Hit GCCTAACACATGCAAGTCGAACGGTAACAGGAAGAAGCTTGCTTCTTTGC 7 0.17500000000000002 No Hit GAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCCTCC 6 0.15 No Hit GCCCGCTCGCCGGAAGACCAAGGGTTCCTGTCCAACGTTAATCGGGGCAG 5 0.125 No Hit GTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAA 5 0.125 No Hit GCTCGCCGGAAGACCAAGGGTTCCTGTCCAACGTTAATCGGGGCAGGGTG 5 0.125 No Hit GGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTA 5 0.125 No Hit GCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGT 5 0.125 No Hit ACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCA 5 0.125 No Hit CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGAT 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 0.037500000000000006 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 0.05 0.0 0.0 0.0 0.0 56-57 0.05 0.0 0.0 0.0 0.0 58-59 0.075 0.0 0.0 0.0 0.0 60-61 0.075 0.0 0.0 0.0 0.0 62-63 0.075 0.0 0.0 0.0 0.0 64-65 0.075 0.0 0.0 0.0 0.0 66-67 0.075 0.0 0.0 0.0 0.0 68-69 0.0875 0.0 0.0 0.0 0.0 70-71 0.1 0.0 0.0 0.0 0.0 72-73 0.1 0.0 0.0 0.0 0.0 74-75 0.175 0.0 0.0 0.0 0.0 76-77 0.1875 0.0 0.0 0.0 0.0 78-79 0.2375 0.0 0.0 0.0 0.0 80-81 0.3125 0.0 0.0 0.0 0.0 82-83 0.4 0.0 0.0 0.0 0.0 84-85 0.5249999999999999 0.0 0.0 0.0 0.0 86-87 0.7 0.0 0.0 0.0 0.0 88-89 0.825 0.0 0.0 0.0 0.0 90-91 0.975 0.0 0.0 0.0 0.0 92-93 1.1875 0.0 0.0 0.0 0.0 94-95 1.3375 0.0 0.0 0.0 0.0 96-97 1.6875 0.0 0.0 0.0 0.0 98-99 2.1375 0.0 0.0 0.0 0.0 100-101 2.5625 0.0 0.0 0.0 0.0 102-103 2.9124999999999996 0.0 0.0 0.0 0.0 104-105 3.2375 0.0 0.0 0.0 0.0 106-107 3.6375 0.0 0.0 0.0 0.0 108-109 4.1375 0.0 0.0 0.0 0.0 110-111 4.6125 0.0 0.0 0.0 0.0 112-113 5.1875 0.0 0.0 0.0 0.0 114-115 5.625 0.0 0.0 0.0 0.0 116-117 6.2875 0.0 0.0 0.0 0.0 118-119 6.7875 0.0 0.0 0.0 0.0 120-121 7.45 0.0 0.0 0.0 0.0 122-123 8.075 0.0 0.0 0.0 0.0 124-125 8.85 0.0 0.0 0.0 0.0 126-127 9.712499999999999 0.0 0.0 0.0 0.0 128-129 10.537500000000001 0.0 0.0 0.0 0.0 130-131 11.0625 0.0 0.0 0.0 0.0 132-133 11.625 0.0 0.0 0.0 0.0 134-135 12.4875 0.0 0.0 0.0 0.0 136-137 13.5375 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 TGATTTT 10 0.006633489 146.40506 1 CGGAAGA 135 0.009814282 10.709259 4 >>END_MODULE Read 530940 spots for SRR7230766.sra Written 530940 spots for SRR7230766.sra Read 530940 spots for SRR7230766.sra Written 530940 spots for SRR7230766.sra Read 530940 spots for SRR7230766.sra Written 530940 spots for SRR7230766.sra Read 530940 spots for SRR7230766.sra Written 530940 spots for SRR7230766.sra Read 530940 spots for SRR7230766.sra Written 530940 spots for SRR7230766.sra Read 530940 spots for SRR7230766.sra Written 530940 spots for SRR7230766.sra Read 530940 spots for SRR7230766.sra Written 530940 spots for SRR7230766.sra Read 530940 spots for SRR7230766.sra Written 530940 spots for SRR7230766.sra Read 530940 spots for SRR7230766.sra Written 530940 spots for SRR7230766.sra Read 530940 spots for SRR7230766.sra Written 530940 spots for SRR7230766.sra Read 530940 spots for SRR7230766.sra Written 530940 spots for SRR7230766.sra Read 530940 spots for SRR7230766.sra Written 530940 spots for SRR7230766.sra Read 530940 spots for SRR7230766.sra Written 530940 spots for SRR7230766.sra Read 530940 spots for SRR7230766.sra Written 530940 spots for SRR7230766.sra Read 530940 spots for SRR7230766.sra Written 530940 spots for SRR7230766.sra Read 530940 spots for SRR7230766.sra Written 530940 spots for SRR7230766.sra Read 530940 spots for SRR7230766.sra Written 530940 spots for SRR7230766.sra Read 530940 spots for SRR7230766.sra Written 530940 spots for SRR7230766.sra Read 530947 spots for SRR7230766.sra Written 530947 spots for SRR7230766.sra Read 530940 spots for SRR7230766.sra Written 530940 spots for SRR7230766.sra SRR ids: ['SRR7230766.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_0vk5o03j SRR7230766.sra spots: 10618807 blocks: [[1, 530940], [530941, 1061880], [1061881, 1592820], [1592821, 2123760], [2123761, 2654700], [2654701, 3185640], [3185641, 3716580], [3716581, 4247520], [4247521, 4778460], [4778461, 5309400], [5309401, 5840340], [5840341, 6371280], [6371281, 6902220], [6902221, 7433160], [7433161, 7964100], [7964101, 8495040], [8495041, 9025980], [9025981, 9556920], [9556921, 10087860], [10087861, 10618807]] SRR7230766 file size 3576664 SRR7230766 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 SRR7230766 SRR7230766_1.fastq SRR7230766_2.fastq Input file: SRR7230766_1.fastq Paired file: SRR7230766_2.fastq trimmed: SRR7230766-trimmed-pair1.fastq, SRR7230766-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 00:15:33 2025 >> started Tue Feb 11 00:15:45 2025 >> done (11.654s) 10618807 read pairs processed; of these: 70187 ( 0.66%) short read pairs filtered out after trimming by size control 95913 ( 0.90%) empty read pairs filtered out after trimming by size control 10452707 (98.44%) read pairs available; of these: 5667502 (54.22%) trimmed read pairs available after processing 4785205 (45.78%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 3 0.00% 19 7 0.00% 20 15 0.00% 21 23 0.00% 22 32 0.00% 23 36 0.00% 24 33 0.00% 25 46 0.00% 26 39 0.00% 27 32 0.00% 28 42 0.00% 29 36 0.00% 30 41 0.00% 31 43 0.00% 32 48 0.00% 33 49 0.00% 34 42 0.00% 35 72 0.00% 36 56 0.00% 37 69 0.00% 38 82 0.00% 39 87 0.00% 40 105 0.00% 41 106 0.00% 42 98 0.00% 43 127 0.00% 44 152 0.00% 45 197 0.00% 46 194 0.00% 47 202 0.00% 48 243 0.00% 49 290 0.00% 50 308 0.00% 51 290 0.00% 52 307 0.00% 53 326 0.00% 54 358 0.00% 55 350 0.00% 56 397 0.00% 57 434 0.00% 58 506 0.00% 59 504 0.00% 60 553 0.01% 61 602 0.01% 62 758 0.01% 63 905 0.01% 64 1050 0.01% 65 1886 0.02% 66 2492 0.02% 67 3947 0.04% 68 5220 0.05% 69 13054 0.12% 70 17110 0.16% 71 8016 0.08% 72 4457 0.04% 73 3509 0.03% 74 3056 0.03% 75 3131 0.03% 76 3415 0.03% 77 3734 0.04% 78 3965 0.04% 79 4911 0.05% 80 4874 0.05% 81 5213 0.05% 82 6358 0.06% 83 7279 0.07% 84 11201 0.11% 85 12801 0.12% 86 14571 0.14% 87 15071 0.14% 88 16194 0.15% 89 16130 0.15% 90 16776 0.16% 91 17084 0.16% 92 17314 0.17% 93 18888 0.18% 94 18993 0.18% 95 20521 0.20% 96 21403 0.20% 97 21513 0.21% 98 22358 0.21% 99 24350 0.23% 100 25343 0.24% 101 25268 0.24% 102 27641 0.26% 103 29315 0.28% 104 31868 0.30% 105 34414 0.33% 106 32625 0.31% 107 33090 0.32% 108 34773 0.33% 109 39306 0.38% 110 38296 0.37% 111 36841 0.35% 112 38744 0.37% 113 42696 0.41% 114 41656 0.40% 115 43627 0.42% 116 43945 0.42% 117 42117 0.40% 118 44370 0.42% 119 45146 0.43% 120 47496 0.45% 121 46951 0.45% 122 49385 0.47% 123 50185 0.48% 124 52723 0.50% 125 52446 0.50% 126 53359 0.51% 127 53731 0.51% 128 55412 0.53% 129 56730 0.54% 130 58769 0.56% 131 58473 0.56% 132 60782 0.58% 133 64446 0.62% 134 64781 0.62% 135 67404 0.64% 136 68270 0.65% 137 72577 0.69% 138 73103 0.70% 139 73846 0.71% 140 74068 0.71% 141 80239 0.77% 142 81094 0.78% 143 85805 0.82% 144 93500 0.89% 145 104358 1.00% 146 118785 1.14% 147 145332 1.39% 148 195066 1.87% 149 349346 3.34% 150 2026869 19.39% 151 4785205 45.78% 10452707 reads passed initial QC criterion=sequence-density sequence-density=0.59 sequence-density-rank=1 fanout-score=2.06 fanout-score-rank=38 prefix-density=0.61 prefix-fanout=2.0 sequence=TTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAGGTGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGG criterion=fanout-score sequence-density=0.03 sequence-density-rank=33 fanout-score=40.77 fanout-score-rank=1 prefix-density=0.15 prefix-fanout=8.4 sequence=TGCTGCTGCTGCATTTATTAGAGAAGGAGATGCTGGTAATCTCCATTTCACAAGTTCATTAATCTCGATCGAAAATATGGCTCATTTAAGCATATACAAAGTACATCTGGGAAAGAAAGTTAAGAACCAAGATAGGGTCACTGATATTTGGATGATGTTCATACGGAGAGGGAGGGAGAAAGGCTGTACTCAAGCCCCCAGAGCTCAAAACTGCCTTTGACAAAATCATAATAACCACCCTTCAGTCCTAGAGTTTTGTTCACCAAGCCATCTCTCACAAACGGGTAGGTTAGCAAGTGTCCAAGGGACACGTTCACTGCCTCCTTTTCACATTGTGTACAGAGGTCTGGGAAAGGTGCATTGGCATGTTCTGCTAAAACCTTAGTCTTGGCAGGGTAGCAAACTTTGACCCAGTCTTCTATGAAATCAGTTGATGTTGTTCCATCATAAGGGAAGGACATGAGGCCCTTAATTCCACCACAGGCGCTGTGTCCAATGACCACAATGTATT criterion=sequence-density sequence-density=2.18 sequence-density-rank=1 fanout-score=2.23 fanout-score-rank=29 prefix-density=2.29 prefix-fanout=2.1 sequence=GCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATG criterion=fanout-score sequence-density=0.01 sequence-density-rank=40 fanout-score=29.26 fanout-score-rank=1 prefix-density=0.06 prefix-fanout=2.8 sequence=GGAGATTGTCTCGTACGGTTAAGAGCCTCCGCCCGTCTCTGGGACTATGGACGGGCACGCTCATATCAGGCTATATTTGGTCCGGGTTATTATCGTCGCGGTTACCGTAATACTTCAGATCAGTTAAGTAGGGCCATATGCCTCGGGAATAAGCTGACGGTGACAAGGTTTCCCCCTAATCGAGACGCTGCAATAACACAGGGGCATACAGTAACCAGGCAAGAGTTCAATCGCTTAGTTTCGTGGCGGGATTTGAGGAAAACTGCGACTGTTCTTTAACCAAACATCCGTGCGATTCGTGCCACTCGTAGACGGCATCTCACAGTCACTGAAGGCTATTAAAGAGTTAGCACCCACCATTGGATGAAGCCCAGGATAAGTGACCCCCCCGGACCTTGGAGTTTCATGC SRR7230766 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 00:16:50 Started mapping on | Feb 11 00:16:50 Finished on | Feb 11 00:22:21 Mapping speed, Million of reads per hour | 113.69 Number of input reads | 10452707 Average input read length | 285 UNIQUE READS: Uniquely mapped reads number | 6302991 Uniquely mapped reads % | 60.30% Average mapped length | 286.33 Number of splices: Total | 4017038 Number of splices: Annotated (sjdb) | 3923451 Number of splices: GT/AG | 3909101 Number of splices: GC/AG | 88050 Number of splices: AT/AC | 3391 Number of splices: Non-canonical | 16496 Mismatch rate per base, % | 0.41% Deletion rate per base | 0.04% Deletion average length | 2.72 Insertion rate per base | 0.03% Insertion average length | 2.06 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 190022 % of reads mapped to multiple loci | 1.82% Number of reads mapped to too many loci | 157065 % of reads mapped to too many loci | 1.50% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 35.74% % of reads unmapped: other | 0.64% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 4003938 4003938 4003938 N_multimapping 190022 190022 190022 N_noFeature 237926 6093340 304501 N_ambiguous 191605 676 48307 UnstrandedReadsAssigned:5873460 PositiveStrandReadsAssigned:208975 NegativeStrandReadsAssigned:5950183 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=138 echo kmer=133 SRR7230766 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: SRR7230766-trimmed-pair1.fastq SRR7230766-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 10,452,707 reads, 6,269,538 reads pseudoaligned [quant] estimated average fragment length: 196.149 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,271 rounds 52401 SRR7230766.ke.tsv 34699 SRR7230766.se.tsv 87100 total ==> SRR7230766.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1822.85 135 9.2552 Potri.005G024800.1.v4.1 1035 839.851 73 10.8624 Potri.004G059700.1.v4.1 961 765.87 1 0.163173 Potri.007G009000.2.v4.1 1416 1220.85 0 0 Potri.003G141000.2.v4.1 2943 2747.85 376 17.1001 Potri.016G087400.1.v4.1 270 96.0238 120.848 157.277 Potri.015G069301.1.v4.1 564 369.808 0 0 Potri.010G195200.1.v4.1 1773 1577.85 18 1.42564 Potri.012G127500.1.v4.1 977 781.87 15 2.39751 ==> SRR7230766.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 113 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 192 Potri.001G212900.v4.1 40 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 6 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 0 SRR7230766 completed mapping pipeline successfully