GMATA software for Genomic SSR marker Activity
Genome-wide Microsatellite Analyzing Toward Application: GMATA
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Activity for GMATA software for Genomic SSR marker
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KEERTHY VIJAYAN posted a comment on discussion General Discussion
While using the GMATA in windows I am getting this error. Even though I installed Perl, Java and R to my system it is showing this error message. Suddenly the program finished window appears but it is showing the working directory doesnot contain sequence file. also when I tried in another computer, it always shows path contains space and the file is not opening. eventhough, I removed all the spaces it shows the same error. Please help me!
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wss posted a comment on discussion General Discussion
Hi, I installed GMATA software on the Mac platform. There appeared some problems when I performed marker designing with the GMATA Graphic mode. The output file.fa.ssr.mk only had the information of column name, the concrete information such as primer sequence, primer position, and product size were all lost. I had installed primer3 on my Mac. Does anybody have the same problem? Is there any solution can solve this problem? Thanks in advance.
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Ren Parch posted a comment on discussion General Discussion
Hi, have you figured it out? I had the same problem
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Hello, I have installed R, Perl and Java but I cannot generate the graphics of statistical plot. I read one of your comments. but I didn't seem to get it right. Could you please help me. Thank you
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Ravi posted a comment on a blog post
I used GUI based GMATA for SSR identification. I found each result of the rice bean assembly data except the statistical plotting. It is showing output as, "file path C:\Users\anuj\Downloads\GMATA-master and output file: 12 figures ending with .jpg" I tried to find the output file but couldn't find it anywhere in my system. Please tell me where this file is stored.
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Xuewen Wang modified a wiki page
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GMATA software for Genomic SSR marker released /latest_version/GMATA-master_v2.3.zip
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HIFZUR RAHMAN posted a comment on discussion General Discussion
Dear sir, I installed GMATA as per intallation guide on windows 10 platform . I have installed Active Perl 5.28 and R4.0.2 as well as Java setup 8u261. and Downloaded "binv21rel" zip file. Unzipped it in a folder named "GMATA" and the downloaded GMATA jar file in GMATA folder. Then tried to run but just command prompt window in blinking for just fraction of second and disappearing. Please help me how to sort it out and run the program.
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imane rcd posted a comment on discussion General Discussion
Hello I'am facting the some problem too, unfortunately it dosen't work even if i use the commande line ,i get this message "Can't open perl script "gmata.pl": No such file or directory". thank you
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Omar Ruíz-Rivero posted a comment on discussion General Discussion
Hi there, I have run GMATA in Windows 7, but after perfom the SSR analysis and use the sat2 file for carry on the Statistical plotting, I do not get the pie chart of the grouped motiv distrubution . I would appreciate very much if you could help me on this matter. I am working with a draft genome sequence (genome assembled into scaffolds), therefore I do not know the orientation of DNA neither the distrubution of scaffolds in the chromosomes. Cheers, Omar
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The GMATA will be running well at Linux system. I tested it and works. An alternataive way is to run the command line for GMATA at any other systems: perl gmata.pl -c configureFile -i yourseqfile
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The GMATA will be run well at Linux system. I tested it and works.
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Poornima, Your running looks good. You can find you results in E drive where the output will be in the same directory as your input file. It is better to download the latest R, not the Rstudio.
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Poornima K Narayana posted a comment on discussion General Discussion
Hello everyone, I am stuck up at the first step of GMATA. I have downloaded Rstudio, perl 5 and Java. I have the binv21rel file in the folder where GMATA.jar is downloaded. The program starts running but gives "Program is finished" on screen. Running statement: -r 5 -m 2 -x 10 -s 0 -i E:\Test.fa File path: C:\WINDOWS\system32 Program starts running... All my files are in E drive. I hope my question is understood
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Sangita posted a comment on discussion General Discussion
Dear Dr Xuewen Wang, I have successfully installed the GMATA software. The software is working brilliantly upto GBrowse viewing, but when I run Marker desgning, the program runs and show results with 3 output files. But the output files are not available/ visible in the respective folder. Kindly suggest.
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kartikay prasad posted a comment on discussion General Discussion
i am facing the same issue which madhavi is facing, if anyone have any soloution for this problem pls do tell us. I am using linux operating system. Thanks in advance
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madhavi posted a comment on discussion General Discussion
Hello GMATA is not working for me? i am using ubuntu16 version? can anyone help me with it. i ahve attached the screenshot below.Thank you
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donglai posted a comment on discussion General Discussion
thanks very much ,i 'll try it . best wishes!
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Your R installation is not completed. The possible problem is that your system blocked the addition of R path to your enviromental pathway during R installation. You have to add the R path to your system enviromental variable manully. Once the path is correct, you can type "cmd" in run to start a command interface. Then type "Rscript" in the command line. If you can see a discription of R , versionxxxx, it is successful. Then You can continue GMATA.
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How to use I have created a detailed point by point tutorial to show how to install GMATA in file GMATA_installation.PDF . You can download this file at https://sourceforge.net/projects/gmata/files/
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You have to install the e-PCR dependent in Linux. You can dwonload from GMATA source code page: https://sourceforge.net/projects/gmata/files/
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Your R installation is not completed. The possible problem is that your system blocked the addition of R path to your enviromental pathway during R installation. You have to add the R path to your system enviromental variable manully. Once the path is correct, you can type "cmd" in run to start a command interface. Then type "Rscript" in the command line. If you can see a discription of R , versionxxxx, it is successful. Then You can continue GMATA.
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Dear Dr Xuewen Wang I installed it in my computer running under windows 10 system, I can executable SSR identification,but when run SSR statistical plotting, can't find output graphics. I have R(3.4), Java and Perl 5 already in my computer as recommended in the user manual With best regards
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It seems that your R language installation is not correct, or the Enviromental path to R is not set.
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Chen Yincheng posted a comment on discussion General Discussion
Dear Xuewen Thank you for you suggestion in the previous e-mail. now i can successfully execute the GMATA.jar but can not generate the plots, the running information show : Program starts running... Plotting statistical graphics. Output files: 12 figures ending with .jpg but i could not find any graphics file in working directory or the directory which had target fasta file, and i want to try plotting by myself, and the PDF file," Rplot.pdf " in binv21rel file folder can not to open by, can you suggest...
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The issue was caused by the wrong directory of your path or missing module of e-PCR. You system will need a dependent of e-PCR or you can set up the correct path to e-PCR in the graphic interface. You download the e-PCR module for Linux and MacOS from GMATA software download page in the sourceforge. You may not need to do anything in windows platform. You can followed the detailed instructions above.
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The issue was caused by the wrong directory of your path or missing module of e-PCR. You system will need a dependent of e-PCR or you can set up the correct path to e-PCR in the graphic interface. You download the e-PCR module for Linux and MacOS from GMATA software download page in the sourceforge. You may not need to do anything in windows platform. You can followed the detailed instructions below.
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shengweima modified a comment on discussion General Discussion
There is an error in linux system. perl elctPCR.pl -i /data2/masw_data/SSR/IWGSCv1.fa -mk /data2/masw_data/SSR/IWGSCv1.fa.ssr.mk.sts -pf u To do marker ePCR, marker allels counting. parameters: w=12 f=1 pf=u m=3000 n=0 g=0 d=100-1000 p=-, Output files: /data2/masw_data/SSR/IWGSCv1.fa.eMap /data2/masw_data/SSR/IWGSCv1.fa.eMap.amp /data2/masw_data/SSR/IWGSCv1.fa.eMap.frg results yielded at Tue Apr 18 21:24:34 2017 Can't exec "e-PCR": No such file or directory at elctPCR.pl line 37. system call failed:...
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Any question and help are welcome at this topic Here (2017-04-24) I updated instruction for installation at Linux and Mac OS . 1) Primer3 dependent The dependent for Primer3 can be downloaded from https://sourceforge.net/projects/primer3/files/primer3/ to make sure the downloaded version for in and out format is : -io_version=3 you can try the version ID from command line 2) e-PCR dependent e-PCR is needed for emapping in Linux and Mac OS. I backed up e-PCR here at download page for GMATA software...
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Any question and help are welcome at this topic Here (2017-04-24) I updated instruction for installation at Linux and Mac OS . 1) Primer3 dependent The dependent for Primer3 can be downloaded from https://sourceforge.net/projects/primer3/files/primer3/ to make sure the downloaded version for in and out format is : -io_version=3 you can try the version ID from command line 2) e-PCR dependent e-PCR is needed for emapping in Linux and Mac OS. I backed up e-PCR here at download page for GMATA software...
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Here I updated instruction for installation at Linux and Mac OS . 1) Primer3 dependent The dependent for Primer3 can be downloaded from https://sourceforge.net/projects/primer3/files/primer3/ to make sure the downloaded version for in and out format is : -io_version=3 you can try the version ID from command line 2) e-PCR dependent e-PCR is needed for emapping in Linux and Mac OS. I backed up e-PCR here at download page for GMATA software website. to download the version for e-PCR module,So you can...
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您好！下载的binv21rel.zip里边没有在linux运行的e-PCR啊？ perl elctPCR.pl -i /data2/masw_data/SSR/IWGSCv1.fa -mk /data2/masw_data/SSR/IWGSCv1.fa.ssr.mk.sts -pf u To do marker ePCR, marker allels counting. parameters: w=12 f=1 pf=u m=3000 n=0 g=0 d=100-1000 p=-, Output files: /data2/masw_data/SSR/IWGSCv1.fa.eMap /data2/masw_data/SSR/IWGSCv1.fa.eMap.amp /data2/masw_data/SSR/IWGSCv1.fa.eMap.frg results yielded at Tue Apr 18 21:24:34 2017 Can't exec "e-PCR": No such file or directory at elctPCR.pl line 37. system call...
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Dossa, The emapping fucntion of GMATA allows multiple DNA sequences . You can put...
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Komivi DOSSA posted a comment on discussion General Discussion
Dear Dr Xuewen Wang, it will be great if the e-mapping feature could allow 2 or more...
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Komivi, Great to know software GMATA is working in your Windows 10 now. Xuewen
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Dear Dr Xuewen Wang, thanks for these explanations. It is running well now under...
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Dear Dr Xuewen Wang, thanks for this explanations. It is running well now under windows10....
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Glad to know that you made GMATA work for you now. Xuewen 2016-09-08 01:32:38，madhusudhana...
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Komiv, Glad to answer your question here. You don't need to unzip the file “GMATA.jar”....
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Komiv, Glad to answer your question here. You don't need to unzip the file “GMATA.jar”....
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Dear Dr Xuewen Wang, thanks for this useful software package you recently released....
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