Starting /dee2/code/volunteer_pipeline.sh SRR7170006 current disk space = 3050947104768 free memory = 1580131852 SRR7170006 SRAfilesize 3ae9cdcb3121bf5f2e28862e1dc15712 SRR7170006.sra SRR7170006.sra file validated SRR7170006 is paired end SRR7170006 is conventional basespace SRR7170006 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7170006_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 43 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 33.138 34.0 34.0 34.0 33.0 34.0 2 33.51125 34.0 34.0 34.0 33.0 34.0 3 33.592 34.0 34.0 34.0 33.0 34.0 4 33.61475 34.0 34.0 34.0 33.0 34.0 5 33.6535 34.0 34.0 34.0 33.0 34.0 6 37.3545 38.0 38.0 38.0 36.0 38.0 7 37.56075 38.0 38.0 38.0 37.0 38.0 8 37.62625 38.0 38.0 38.0 38.0 38.0 9 37.6905 38.0 38.0 38.0 38.0 38.0 10-14 37.677 38.0 38.0 38.0 38.0 38.0 15-19 37.682849999999995 38.0 38.0 38.0 38.0 38.0 20-24 37.57935 38.0 38.0 38.0 38.0 38.0 25-29 37.57455 38.0 38.0 38.0 38.0 38.0 30-34 37.573 38.0 38.0 38.0 38.0 38.0 35-39 37.528549999999996 38.0 38.0 38.0 38.0 38.0 40-44 37.3966 38.0 38.0 38.0 38.0 38.0 45-49 37.35119999999999 38.0 38.0 38.0 37.0 38.0 50-54 37.348 38.0 38.0 38.0 37.0 38.0 55-59 37.3124 38.0 38.0 38.0 37.0 38.0 60-64 37.2952 38.0 38.0 38.0 37.0 38.0 65-69 37.237899999999996 38.0 38.0 38.0 37.0 38.0 70-74 37.165499999999994 38.0 38.0 38.0 36.8 38.0 75-79 36.9059 38.0 38.0 38.0 36.2 38.0 80-84 36.8333 38.0 38.0 38.0 36.0 38.0 85-89 36.75145 38.0 38.0 38.0 36.0 38.0 90-94 36.54875 38.0 38.0 38.0 35.4 38.0 95-99 36.3883 38.0 38.0 38.0 34.6 38.0 100-104 36.486599999999996 38.0 38.0 38.0 35.0 38.0 105-109 36.358000000000004 38.0 38.0 38.0 34.2 38.0 110-114 36.19255 38.0 38.0 38.0 34.0 38.0 115-119 36.0104 38.0 38.0 38.0 34.0 38.0 120-124 35.77265 38.0 37.6 38.0 32.8 38.0 125-129 35.568400000000004 38.0 37.0 38.0 31.6 38.0 130-134 35.28765 38.0 36.4 38.0 30.6 38.0 135-139 34.98055 38.0 36.0 38.0 29.4 38.0 140-144 34.64565 38.0 35.8 38.0 27.8 38.0 145-149 34.02075 38.0 35.0 38.0 23.8 38.0 150-151 30.967000000000002 36.5 30.0 38.0 11.5 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 6 1.0 7 1.0 8 0.0 9 1.0 10 0.0 11 0.0 12 2.0 13 1.0 14 2.0 15 2.0 16 1.0 17 7.0 18 10.0 19 20.0 20 3.0 21 5.0 22 8.0 23 10.0 24 6.0 25 7.0 26 12.0 27 29.0 28 22.0 29 21.0 30 29.0 31 32.0 32 48.0 33 64.0 34 126.0 35 167.0 36 496.0 37 2867.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 40.28411973617453 14.434297311009638 11.39015728056824 33.891425672247586 2 24.025 14.774999999999999 29.025000000000002 32.175 3 20.200000000000003 17.675 25.275 36.85 4 23.724999999999998 23.125 23.125 30.025000000000002 5 23.674999999999997 28.599999999999998 23.7 24.025 6 21.8 32.15 24.45 21.6 7 15.2 31.65 36.4 16.75 8 17.0 29.925 30.125 22.95 9 17.9 26.700000000000003 33.775 21.625 10-14 19.11 31.215 27.500000000000004 22.175 15-19 19.275000000000002 30.03 27.575 23.119999999999997 20-24 19.97 29.89 27.505000000000003 22.634999999999998 25-29 19.900000000000002 30.380000000000003 26.845000000000002 22.875 30-34 19.11 30.099999999999998 27.915 22.875 35-39 19.48 28.88 27.67 23.97 40-44 19.255 29.849999999999998 27.384999999999998 23.51 45-49 19.56684839693893 29.42529885459911 27.674686140149053 23.33316660831291 50-54 19.73 29.13 27.384999999999998 23.755000000000003 55-59 19.365 29.265 27.765 23.605 60-64 19.59 29.01 27.55 23.849999999999998 65-69 20.0 30.25 26.46 23.29 70-74 20.14 29.705 26.815 23.34 75-79 19.85 29.125 27.11 23.915 80-84 20.23 28.849999999999998 27.575 23.345 85-89 20.119172800560815 28.180862250262884 27.77026688698613 23.929698062190173 90-94 20.159871298577244 28.912573525715146 27.17812075813182 23.749434417575788 95-99 19.966822500377017 28.66837581058664 27.446840597194992 23.91796109184135 100-104 20.389175128807963 28.877995097794006 26.682006903106398 24.05082287029163 105-109 20.006000300015 28.66143307165358 27.02135106755338 24.311215560778038 110-114 20.205000000000002 28.63 27.279999999999998 23.885 115-119 20.200050012503127 28.73718429607402 27.35683920980245 23.705926481620406 120-124 20.674999999999997 28.349999999999998 26.715 24.26 125-129 21.095 28.444999999999997 26.86 23.599999999999998 130-134 20.722976017623793 28.258148500475645 27.186702047764484 23.832173434136084 135-139 20.962320004013847 27.926345893331995 26.707139631729465 24.40419447092469 140-144 20.597657423165483 28.035839423365704 27.069776754429874 24.296726399038942 145-149 20.58190194801943 28.72452301066653 26.471030096649805 24.22254494466423 150-151 20.0875 28.000000000000004 27.187499999999996 24.725 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.5 2 0.5 3 0.0 4 0.0 5 0.0 6 0.0 7 0.5 8 1.0 9 0.5 10 0.0 11 0.5 12 0.5 13 0.5 14 0.5 15 1.0 16 1.0 17 0.0 18 0.5 19 1.0 20 2.5 21 2.0 22 1.0 23 2.5 24 2.0 25 4.0 26 7.0 27 9.0 28 14.0 29 25.0 30 30.5 31 34.5 32 44.5 33 50.5 34 62.5 35 79.5 36 100.0 37 124.0 38 136.5 39 155.5 40 188.0 41 208.5 42 235.0 43 250.0 44 254.5 45 262.5 46 259.5 47 235.5 48 204.5 49 197.5 50 179.0 51 141.5 52 112.5 53 91.5 54 72.0 55 53.5 56 41.5 57 34.5 58 23.5 59 15.5 60 14.0 61 11.5 62 8.0 63 5.5 64 2.5 65 0.5 66 0.5 67 0.5 68 0.0 69 0.5 70 0.5 71 0.0 72 0.0 73 0.0 74 0.0 75 0.0 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 1.4500000000000002 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 0.034999999999999996 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 0.145 90-94 0.545 95-99 0.5349999999999999 100-104 0.045 105-109 0.005 110-114 0.0 115-119 0.025 120-124 0.0 125-129 0.0 130-134 0.135 135-139 0.345 140-144 0.11 145-149 0.155 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 97.8 #Duplication Level Percentage of deduplicated Percentage of total 1 98.31288343558282 96.15 2 1.5593047034764826 3.05 3 0.07668711656441718 0.22499999999999998 4 0.025562372188139063 0.1 5 0.0 0.0 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.025562372188139063 0.475 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences warn #Sequence Count Percentage Possible Source GATCGGAAGAGCACACGTCTGAACTCCAGTCACTCATTCATCTCGTATGC 19 0.475 TruSeq Adapter, Index 3 (97% over 36bp) >>END_MODULE >>Adapter Content warn #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 0.0 0.0 0.0 0.0 0.0 62-63 0.0125 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 0.05 0.0 0.0 0.0 0.0 72-73 0.0625 0.0 0.0 0.0 0.0 74-75 0.075 0.0 0.0 0.0 0.0 76-77 0.075 0.0 0.0 0.0 0.0 78-79 0.075 0.0 0.0 0.0 0.0 80-81 0.1 0.0 0.0 0.0 0.0 82-83 0.16249999999999998 0.0 0.0 0.0 0.0 84-85 0.1875 0.0 0.0 0.0 0.0 86-87 0.2875 0.0 0.0 0.0 0.0 88-89 0.42500000000000004 0.0 0.0 0.0 0.0 90-91 0.55 0.0 0.0 0.0 0.0 92-93 0.675 0.0 0.0 0.0 0.0 94-95 0.8 0.0 0.0 0.0 0.0 96-97 0.95 0.0 0.0 0.0 0.0 98-99 1.125 0.0 0.0 0.0 0.0 100-101 1.2999999999999998 0.0 0.0 0.0 0.0 102-103 1.4375 0.0 0.0 0.0 0.0 104-105 1.5625 0.0 0.0 0.0 0.0 106-107 1.7625000000000002 0.0 0.0 0.0 0.0 108-109 2.0625 0.0 0.0 0.0 0.0 110-111 2.325 0.0 0.0 0.0 0.0 112-113 2.5 0.0 0.0 0.0 0.0 114-115 2.8125 0.0 0.0 0.0 0.0 116-117 3.225 0.0 0.0 0.0 0.0 118-119 3.7125000000000004 0.0 0.0 0.0 0.0 120-121 4.2375 0.0 0.0 0.0 0.0 122-123 4.824999999999999 0.0 0.0 0.0 0.0 124-125 5.1875 0.0 0.0 0.0 0.0 126-127 5.7875 0.0 0.0 0.0 0.0 128-129 6.2625 0.0 0.0 0.0 0.0 130-131 6.75 0.0 0.0 0.0 0.0 132-133 7.2625 0.0 0.0 0.0 0.0 134-135 7.8125 0.0 0.0 0.0 0.0 136-137 8.45 0.0 0.0 0.0 0.0 138-139 9.1 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TAATGTC 10 0.006832588 144.9875 145 >>END_MODULE SRR7170006 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7170006_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 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.28025 33.0 33.0 34.0 32.0 34.0 2 32.382 34.0 33.0 34.0 32.0 34.0 3 32.4055 34.0 33.0 34.0 32.0 34.0 4 32.225 34.0 33.0 34.0 32.0 34.0 5 32.06025 34.0 33.0 34.0 32.0 34.0 6 36.13625 38.0 38.0 38.0 37.0 38.0 7 36.06375 38.0 38.0 38.0 36.0 38.0 8 36.07475 38.0 38.0 38.0 37.0 38.0 9 36.04275 38.0 38.0 38.0 36.0 38.0 10-14 35.989050000000006 38.0 38.0 38.0 36.2 38.0 15-19 35.8744 38.0 38.0 38.0 36.0 38.0 20-24 35.93445 38.0 38.0 38.0 36.0 38.0 25-29 36.01595 38.0 38.0 38.0 36.6 38.0 30-34 36.0558 38.0 38.0 38.0 37.0 38.0 35-39 35.97685 38.0 38.0 38.0 36.4 38.0 40-44 35.870099999999994 38.0 38.0 38.0 36.2 38.0 45-49 35.71005 38.0 38.0 38.0 35.8 38.0 50-54 35.94365 38.0 38.0 38.0 36.0 38.0 55-59 35.95715 38.0 38.0 38.0 36.0 38.0 60-64 35.92015 38.0 38.0 38.0 36.0 38.0 65-69 35.8639 38.0 38.0 38.0 36.0 38.0 70-74 35.6981 38.0 38.0 38.0 35.2 38.0 75-79 35.647999999999996 38.0 38.0 38.0 35.0 38.0 80-84 35.618849999999995 38.0 38.0 38.0 34.8 38.0 85-89 35.28435 38.0 38.0 38.0 34.0 38.0 90-94 34.907349999999994 38.0 38.0 38.0 30.8 38.0 95-99 35.30495 38.0 38.0 38.0 33.2 38.0 100-104 35.41435 38.0 38.0 38.0 33.8 38.0 105-109 35.28365 38.0 38.0 38.0 33.0 38.0 110-114 35.240300000000005 38.0 38.0 38.0 32.8 38.0 115-119 35.09995 38.0 38.0 38.0 31.4 38.0 120-124 34.97455 38.0 38.0 38.0 31.0 38.0 125-129 34.56785 38.0 37.6 38.0 26.8 38.0 130-134 33.48864999999999 38.0 36.2 38.0 14.0 38.0 135-139 32.55565 38.0 35.4 38.0 2.0 38.0 140-144 31.7685 38.0 34.6 38.0 2.0 38.0 145-149 31.46165 38.0 33.6 38.0 2.0 38.0 150-151 27.97075 35.5 17.5 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 147.0 3 5.0 4 1.0 5 2.0 6 1.0 7 0.0 8 0.0 9 3.0 10 0.0 11 4.0 12 3.0 13 3.0 14 3.0 15 4.0 16 3.0 17 16.0 18 8.0 19 4.0 20 4.0 21 5.0 22 9.0 23 12.0 24 8.0 25 8.0 26 15.0 27 29.0 28 28.0 29 31.0 30 44.0 31 61.0 32 78.0 33 102.0 34 104.0 35 124.0 36 333.0 37 2798.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 36.85427910562837 20.740169622205087 15.60010280133642 26.80544847083012 2 27.50126968004063 28.212290502793298 26.612493651599795 17.673946165566274 3 21.642363775901767 30.416986441545152 29.470452801227935 18.470196981325145 4 24.62570986060919 33.582860092927206 22.79297883324729 18.998451213216313 5 24.850843060959793 35.590142671854736 21.99740596627756 17.56160830090791 6 22.622441046903344 37.678154962425495 22.67426794506349 17.02513604560767 7 20.90248962655602 23.96265560165975 36.59232365145228 18.54253112033195 8 23.555325213785956 25.706141487431978 27.286861881316405 23.451671417465665 9 23.664516129032258 25.31612903225807 29.135483870967743 21.883870967741935 10-14 24.405812143227816 28.676699532952775 25.339906590555266 21.577581733264143 15-19 23.702160895600105 28.450924238479562 27.268940380109346 20.577974485810987 20-24 24.068976263439463 28.431932685815198 26.956837895392926 20.542253155352412 25-29 24.218102734051367 28.77485501242751 26.62593206296603 20.381110190555095 30-34 24.036868268434134 27.72887323943662 27.407829328914662 20.826429163214584 35-39 24.377954391979635 28.221910550101292 26.59602098592281 20.80411407199626 40-44 24.928381686546174 27.845200270847442 26.579509349445285 20.6469086931611 45-49 24.33757563112873 27.628833715835594 27.341957020655123 20.691633632380555 50-54 23.963133640552993 28.524827836172527 26.70222130171387 20.809817221560607 55-59 24.704663212435232 28.238341968911918 27.10880829015544 19.94818652849741 60-64 24.229372080954853 28.42241826673586 27.20290607161391 20.14530358069538 65-69 24.215432418436045 28.239254272397723 27.845675815639563 19.69963749352667 70-74 24.236336475557614 28.02761036418894 27.254932261886367 20.481120898367074 75-79 23.818583843266314 27.63408237774464 28.323134673728596 20.22419910526045 80-84 23.890063424947147 27.695560253699792 28.45356571958954 19.960810601763523 85-89 24.38027357056758 27.938787275300037 27.157905770137837 20.523033383994548 90-94 24.51238798102267 27.69109119662625 27.770163415919875 20.02635740643121 95-99 24.198144981605267 27.700917145966113 27.877092077309705 20.22384579511892 100-104 24.035133040557994 28.504262464479464 27.403771635236374 20.05683285972617 105-109 23.51782752902156 27.52902155887231 28.581053067993366 20.37209784411277 110-114 24.661654135338345 28.011407829919627 27.461757842883074 19.865180191858958 115-119 24.341325083784483 28.290796597061096 27.9969064191802 19.370971899974222 120-124 24.643553184942046 27.47461278079803 27.87465381064725 20.00718022361268 125-129 24.11137132448608 28.092635961488423 27.926099401509237 19.86989331251626 130-134 25.21669341894061 27.68860353130016 27.463884430176567 19.630818619582666 135-139 25.62855268911237 27.924136423261913 26.841932662877134 19.60537822474858 140-144 25.83901924890442 27.536473068175514 27.303489210628502 19.321018472291563 145-149 25.36088006439496 28.44647169305071 26.981486450228065 19.211161792326266 150-151 25.526901426888337 29.20539337609635 26.443251734520224 18.824453462495093 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 83.0 1 50.0 2 10.5 3 5.5 4 5.0 5 3.0 6 3.0 7 3.0 8 3.0 9 2.0 10 2.0 11 3.0 12 1.5 13 1.5 14 2.0 15 1.0 16 2.0 17 1.5 18 0.5 19 1.5 20 2.0 21 1.5 22 1.5 23 1.5 24 1.0 25 1.5 26 2.0 27 5.0 28 7.0 29 6.0 30 9.5 31 12.0 32 16.5 33 21.5 34 36.0 35 47.0 36 57.5 37 77.5 38 105.0 39 148.0 40 187.0 41 218.0 42 242.5 43 265.5 44 287.5 45 291.5 46 291.0 47 275.0 48 231.5 49 196.0 50 175.5 51 159.5 52 123.5 53 90.5 54 69.5 55 56.0 56 41.5 57 21.0 58 18.5 59 14.5 60 10.5 61 11.0 62 6.5 63 3.5 64 1.5 65 1.0 66 1.0 67 2.0 68 2.0 69 1.5 70 1.5 71 0.0 72 0.0 73 0.0 74 0.0 75 0.0 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content warn #Base N-Count 1 2.725 2 1.55 3 2.275 4 3.15 5 3.6249999999999996 6 3.5249999999999995 7 3.5999999999999996 8 3.5249999999999995 9 3.125 10-14 3.65 15-19 3.975 20-24 3.7350000000000003 25-29 3.44 30-34 3.44 35-39 3.7449999999999997 40-44 4.005 45-49 4.14 50-54 3.435 55-59 3.5000000000000004 60-64 3.65 65-69 3.45 70-74 2.935 75-79 2.765 80-84 3.0349999999999997 85-89 4.595 90-94 5.1499999999999995 95-99 3.505 100-104 3.225 105-109 3.52 110-114 3.5749999999999997 115-119 3.025 120-124 2.5100000000000002 125-129 3.925 130-134 6.550000000000001 135-139 8.52 140-144 9.865 145-149 6.825 150-151 4.5125 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 95.7 #Duplication Level Percentage of deduplicated Percentage of total 1 98.09299895506793 93.875 2 1.6980146290491118 3.25 3 0.07836990595611285 0.22499999999999998 4 0.0 0.0 5 0.0 0.0 6 0.026123301985370953 0.15 7 0.0 0.0 8 0.0 0.0 9 0.026123301985370953 0.22499999999999998 >10 0.052246603970741906 0.7250000000000001 >50 0.026123301985370953 1.55 >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 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 62 1.55 No Hit GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG 18 0.44999999999999996 Illumina Single End PCR Primer 1 (100% over 50bp) NTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 11 0.27499999999999997 No Hit NANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 9 0.22499999999999998 No Hit NGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 6 0.15 No Hit >>END_MODULE >>Adapter Content warn #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 0.0 0.0 0.0 0.0 0.0 62-63 0.0125 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 0.05 0.0 0.0 0.0 0.0 72-73 0.0625 0.0 0.0 0.0 0.0 74-75 0.075 0.0 0.0 0.0 0.0 76-77 0.075 0.0 0.0 0.0 0.0 78-79 0.075 0.0 0.0 0.0 0.0 80-81 0.1 0.0 0.0 0.0 0.0 82-83 0.1875 0.0 0.0 0.0 0.0 84-85 0.2375 0.0 0.0 0.0 0.0 86-87 0.3375 0.0 0.0 0.0 0.0 88-89 0.4625 0.0 0.0 0.0 0.0 90-91 0.5625 0.0 0.0 0.0 0.0 92-93 0.675 0.0 0.0 0.0 0.0 94-95 0.8 0.0 0.0 0.0 0.0 96-97 0.95 0.0 0.0 0.0 0.0 98-99 1.125 0.0 0.0 0.0 0.0 100-101 1.2999999999999998 0.0 0.0 0.0 0.0 102-103 1.4249999999999998 0.0 0.0 0.0 0.0 104-105 1.5375 0.0 0.0 0.0 0.0 106-107 1.7125 0.0 0.0 0.0 0.0 108-109 2.0125 0.0 0.0 0.0 0.0 110-111 2.2875 0.0 0.0 0.0 0.0 112-113 2.4749999999999996 0.0 0.0 0.0 0.0 114-115 2.8 0.0 0.0 0.0 0.0 116-117 3.1875 0.0 0.0 0.0 0.0 118-119 3.5875000000000004 0.0 0.0 0.0 0.0 120-121 4.0625 0.0 0.0 0.0 0.0 122-123 4.625 0.0 0.0 0.0 0.0 124-125 4.9625 0.0 0.0 0.0 0.0 126-127 5.475 0.0 0.0 0.0 0.0 128-129 5.9125 0.0 0.0 0.0 0.0 130-131 6.362500000000001 0.0 0.0 0.0 0.0 132-133 6.8375 0.0 0.0 0.0 0.0 134-135 7.324999999999999 0.0 0.0 0.0 0.0 136-137 7.925000000000001 0.0 0.0 0.0 0.0 138-139 8.45 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 719224 spots for SRR7170006.sra Written 719224 spots for SRR7170006.sra Read 719224 spots for SRR7170006.sra Written 719224 spots for SRR7170006.sra Read 719224 spots for SRR7170006.sra Written 719224 spots for SRR7170006.sra Read 719224 spots for SRR7170006.sra Written 719224 spots for SRR7170006.sra Read 719224 spots for SRR7170006.sra Written 719224 spots for SRR7170006.sra Read 719224 spots for SRR7170006.sra Written 719224 spots for SRR7170006.sra Read 719224 spots for SRR7170006.sra Written 719224 spots for SRR7170006.sra Read 719224 spots for SRR7170006.sra Written 719224 spots for SRR7170006.sra Read 719241 spots for SRR7170006.sra Written 719241 spots for SRR7170006.sra Read 719224 spots for SRR7170006.sra Written 719224 spots for SRR7170006.sra Read 719224 spots for SRR7170006.sra Written 719224 spots for SRR7170006.sra Read 719224 spots for SRR7170006.sra Written 719224 spots for SRR7170006.sra Read 719224 spots for SRR7170006.sra Written 719224 spots for SRR7170006.sra Read 719224 spots for SRR7170006.sra Written 719224 spots for SRR7170006.sra Read 719224 spots for SRR7170006.sra Written 719224 spots for SRR7170006.sra Read 719224 spots for SRR7170006.sra Written 719224 spots for SRR7170006.sra Read 719224 spots for SRR7170006.sra Written 719224 spots for SRR7170006.sra Read 719224 spots for SRR7170006.sra Written 719224 spots for SRR7170006.sra Read 719224 spots for SRR7170006.sra Written 719224 spots for SRR7170006.sra Read 719224 spots for SRR7170006.sra Written 719224 spots for SRR7170006.sra SRR ids: ['SRR7170006.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_33lypqme SRR7170006.sra spots: 14384497 blocks: [[1, 719224], [719225, 1438448], [1438449, 2157672], [2157673, 2876896], [2876897, 3596120], [3596121, 4315344], [4315345, 5034568], [5034569, 5753792], [5753793, 6473016], [6473017, 7192240], [7192241, 7911464], [7911465, 8630688], [8630689, 9349912], [9349913, 10069136], [10069137, 10788360], [10788361, 11507584], [11507585, 12226808], [12226809, 12946032], [12946033, 13665256], [13665257, 14384497]] SRR7170006 file size 4852733 SRR7170006 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 SRR7170006 SRR7170006_1.fastq SRR7170006_2.fastq Input file: SRR7170006_1.fastq Paired file: SRR7170006_2.fastq trimmed: SRR7170006-trimmed-pair1.fastq, SRR7170006-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 Wed Feb 12 10:33:30 2025 >> started Wed Feb 12 10:33:46 2025 >> done (15.719s) 14384497 read pairs processed; of these: 21794 ( 0.15%) short read pairs filtered out after trimming by size control 99405 ( 0.69%) empty read pairs filtered out after trimming by size control 14263298 (99.16%) read pairs available; of these: 6569545 (46.06%) trimmed read pairs available after processing 7693753 (53.94%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 4 0.00% 19 5 0.00% 20 13 0.00% 21 4 0.00% 22 13 0.00% 23 10 0.00% 24 5 0.00% 25 15 0.00% 26 11 0.00% 27 8 0.00% 28 15 0.00% 29 8 0.00% 30 18 0.00% 31 8 0.00% 32 13 0.00% 33 19 0.00% 34 12 0.00% 35 18 0.00% 36 25 0.00% 37 27 0.00% 38 37 0.00% 39 24 0.00% 40 29 0.00% 41 39 0.00% 42 56 0.00% 43 36 0.00% 44 54 0.00% 45 61 0.00% 46 90 0.00% 47 86 0.00% 48 104 0.00% 49 112 0.00% 50 112 0.00% 51 144 0.00% 52 142 0.00% 53 164 0.00% 54 153 0.00% 55 190 0.00% 56 185 0.00% 57 221 0.00% 58 232 0.00% 59 276 0.00% 60 309 0.00% 61 341 0.00% 62 370 0.00% 63 438 0.00% 64 476 0.00% 65 580 0.00% 66 737 0.01% 67 958 0.01% 68 1272 0.01% 69 2071 0.01% 70 3317 0.02% 71 2057 0.01% 72 1548 0.01% 73 1574 0.01% 74 1738 0.01% 75 1913 0.01% 76 1846 0.01% 77 2161 0.02% 78 2305 0.02% 79 2680 0.02% 80 2861 0.02% 81 3315 0.02% 82 3719 0.03% 83 4347 0.03% 84 5715 0.04% 85 6870 0.05% 86 7177 0.05% 87 7961 0.06% 88 8988 0.06% 89 9654 0.07% 90 9945 0.07% 91 10345 0.07% 92 11118 0.08% 93 11792 0.08% 94 12580 0.09% 95 13984 0.10% 96 15029 0.11% 97 15621 0.11% 98 16557 0.12% 99 16752 0.12% 100 18025 0.13% 101 18683 0.13% 102 20304 0.14% 103 21122 0.15% 104 22452 0.16% 105 23552 0.17% 106 25029 0.18% 107 25800 0.18% 108 27264 0.19% 109 28208 0.20% 110 28953 0.20% 111 29730 0.21% 112 30672 0.22% 113 32499 0.23% 114 33023 0.23% 115 35105 0.25% 116 36123 0.25% 117 37583 0.26% 118 38528 0.27% 119 39437 0.28% 120 40366 0.28% 121 41391 0.29% 122 42422 0.30% 123 43826 0.31% 124 45476 0.32% 125 46563 0.33% 126 48570 0.34% 127 49698 0.35% 128 51139 0.36% 129 52748 0.37% 130 54405 0.38% 131 55584 0.39% 132 57392 0.40% 133 59654 0.42% 134 60905 0.43% 135 64122 0.45% 136 67197 0.47% 137 71383 0.50% 138 75547 0.53% 139 80764 0.57% 140 84481 0.59% 141 89384 0.63% 142 93940 0.66% 143 101298 0.71% 144 115243 0.81% 145 124927 0.88% 146 146276 1.03% 147 189368 1.33% 148 286394 2.01% 149 514268 3.61% 150 2916903 20.45% 151 7693753 53.94% 14263298 reads passed initial QC criterion=sequence-density sequence-density=0.25 sequence-density-rank=1 fanout-score=2.44 fanout-score-rank=32 prefix-density=0.27 prefix-fanout=2.3 sequence=CCAACATACCAGTGCACAAACGCACGCTTGGCATACATGAGATCAAACTTGTGGTCAATGCGAGAGAAGACTTCTGCAACACTTGTGGAATTGGAAATCATGCAAACAGCCCTCTGAACCTTAGCAAGGTCGCCTCCTGGAACAACAGTTGGTGGCTGGTAGTTGATGCCACACTTGAACCCAGTTGGGCACCA criterion=fanout-score sequence-density=0.01 sequence-density-rank=42 fanout-score=103.61 fanout-score-rank=1 prefix-density=0.09 prefix-fanout=9.7 sequence=ATATTCATCATAACTCAATTACATTATTCTCACCCAGAACATCTCTTCCAGCAATAGATACAAACCATGGCAATTAACTAGAGCAGAACATCATTTCACAAGGTTTATAAGGAAAGAGACCTCCTTGACTTGGACAAACACTCGTCTATAAGAAACACCCAAATTTCCAACTATTCGGCTGTTTGTTTCATTAATAACTGGAGAGCAGGAGATGCCAGTGCCTCAGACAAACTGATCAAGGTACTCTTCCACGGTGGTATATTTGACATCTGGATATAGCTCAGAGGCCTCAAGGCCCCATGATGGGTCAATCTCAAAGTTGGTCATGTCACCATTAACGAGGGCTGAGTGGTTGATTGACAGAACAATATTAATCGGAATCGGAGACTCTTGGATGTCCTTCAGAAGTTTCTCTTCAGGAACAAAGGTTTTTTCGAGGGTTTTGCCAATCTTTTTCTCCCATAGATCAATAAGCTCATTGAATGAGTAGGTGTTTTTAGGAGGCTTGATT criterion=sequence-density sequence-density=0.26 sequence-density-rank=1 fanout-score=5.11 fanout-score-rank=18 prefix-density=0.40 prefix-fanout=3.4 sequence=GCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATG criterion=fanout-score sequence-density=0.12 sequence-density-rank=28 fanout-score=52.88 fanout-score-rank=1 prefix-density=0.50 prefix-fanout=12.5 sequence=TGTTGGTGGTGGGACTGGAGCTGTCGTTAACACCATCGTCTCTAAATACCCTTCAATTAAGGGCATTAACTTTGATCTGCCCCACGTCATTGAGGATGCCCCATCTTATCCCGGTGTGGAGCATGTTGGTGGGGACATGTTTGTTAGCGTGCCCAAAGCAGATGCCGTTTTCATGAAGTGGATATGCCATGATTGGAGCGACGCACACTGCTTAAAATTCTTGAAGAATTGCTATGACGCCTTGCCGGAAAACGGCAAGGTGATACTTGTTGAGTGCATTCTTCCCGTGGCTCCTGACACAAGCCTTGCCACCAAGGGAGTCGTGCACATTGATGTTATCATGCTGGCGCACAACCCCGGTGGGAAAGAGAGGACCGAAAAGGAATTTGAGGGCTTAGCAAAGGGAGCTGGCTTTCAAGGTTTTGAAGTAATGTGCTGTGCATTCAACACACATGTCATTGAATTCCGCAAGAACTAA SRR7170006 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 12 10:34:29 Started mapping on | Feb 12 10:34:29 Finished on | Feb 12 10:36:02 Mapping speed, Million of reads per hour | 552.13 Number of input reads | 14263298 Average input read length | 292 UNIQUE READS: Uniquely mapped reads number | 13431512 Uniquely mapped reads % | 94.17% Average mapped length | 291.77 Number of splices: Total | 11088511 Number of splices: Annotated (sjdb) | 10880359 Number of splices: GT/AG | 10936022 Number of splices: GC/AG | 117500 Number of splices: AT/AC | 8818 Number of splices: Non-canonical | 26171 Mismatch rate per base, % | 0.43% Deletion rate per base | 0.03% Deletion average length | 2.75 Insertion rate per base | 0.02% Insertion average length | 2.31 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 241841 % of reads mapped to multiple loci | 1.70% Number of reads mapped to too many loci | 23711 % of reads mapped to too many loci | 0.17% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.91% % of reads unmapped: other | 0.06% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 608974 608974 608974 N_multimapping 241841 241841 241841 N_noFeature 286189 13209917 373232 N_ambiguous 190895 730 55905 UnstrandedReadsAssigned:12954428 PositiveStrandReadsAssigned:220865 NegativeStrandReadsAssigned:13002375 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=149 echo kmer=145 SRR7170006 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: SRR7170006-trimmed-pair1.fastq SRR7170006-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 14,263,298 reads, 12,971,390 reads pseudoaligned [quant] estimated average fragment length: 222.846 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,176 rounds 52401 SRR7170006.ke.tsv 34699 SRR7170006.se.tsv 87100 total ==> SRR7170006.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1796.15 228 9.24707 Potri.005G024800.1.v4.1 1035 813.154 18 1.61255 Potri.004G059700.1.v4.1 961 739.167 7 0.689872 Potri.007G009000.2.v4.1 1416 1194.15 0 0 Potri.003G141000.2.v4.1 2943 2721.15 198 5.3006 Potri.016G087400.1.v4.1 270 87.3675 1609 1341.59 Potri.015G069301.1.v4.1 564 344.788 0 0 Potri.010G195200.1.v4.1 1773 1551.15 1 0.0469632 Potri.012G127500.1.v4.1 977 755.167 2389 230.455 ==> SRR7170006.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 1341 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 273 Potri.001G212900.v4.1 1 Potri.001G182400.v4.1 26 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 0 SRR7170006 completed mapping pipeline successfully