Activity for LMAT
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Jonathan modified a wiki page
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Hi Matt, sorry for the severe delay, I think there finally may be a resolution to the current compile issues. I just mentioned this in another post: https://sourceforge.net/p/lmat/discussion/general/thread/d1185a12/. Please try the cmake build version: https://github.com/LivGen/LMAT I'm hoping it will resolve this issue. Note this is version 1.2.4, which is the one I recommend using, thanks. --Jonathan
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Hello Mathieue, sorry for not responding earlier, it took some time for me to recognize a likely solution here. We are moving the development over to github and using cmake for the build process. This version should compile on newer linux distributions. This is version 1.2.4 of LMAT and the one I'd recommend starting with. Please clone the repo here: https://github.com/LivGen/LMAT and feedback on whether this solves your problem (or doesn't) is welcome. I will try to update the sourceforge page soon...
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Matt Feltz posted a comment on discussion General Discussion
Hello, I am trying to install LMAT on a standalone Centos7 server in a shared directory. I believe I have all dependencies installed, I have downloaded the runtime inputs and placed them in the runtime_inputs folder, and I have set the LMAT_DIR variable to the LMAT directory. During the make I get several warnings that variables are uninitialized, then finally the make fails with: /src/kmerdb/lib/libmetag.a(Utils.o): In function std::basic_istream<char, std::char_traits<char> >& std::getline<char,...
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Mat posted a comment on discussion General Discussion
Hi, When running make, I get this: SortedDb.cpp: At global scope: SortedDb.cpp:89:338: error: redeclaration of ‘void metag::SortedDb<tid_T>::add_data(const char, size_t, bool, bitreduce_map_t, my_map&, int, bool, FILE, FILE, uint32_t, uint32_t)’ may not have default arguments [-fpermissive] void SortedDb<tid_T>::add_data(const char filename, size_t stopper = 0, bool use_tax_histo_format = true, bitreduce_map_t p_br_map = NULL , my_map &species_map = NULL, int tid_cutoff = 0, bool strainspecies =...
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Thanks, the first command fetched everything I needed.
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Hi Mathieu, Running this in the runtime_inputs directory should downloaded the neded...
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Hello, I am currently trying to asses a set using kML+Human.v4-14.20.g10.db. I am...
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Each read is assigned a match score measuring how closely the read matches to the...
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Biren Dave posted a comment on discussion General Discussion
For example: 105.676 78 1235458 no rank,Stenotrophomonas maltophilia AU12-09 20.136...
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Hello, After running LMAT, I get a fastsummary file with four columns. What do the...
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I was able to solve this issue, simply by adding "bash" before the command: bash...
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I was able to solve this issue, simply by adding "bash" before the command: bash...
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I was able to solve this issue, simply by adding "bash" before the command: bash...
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Hi Jonathan, I tried this, but I'm getting this error: ./get_db.sh: 96: [: 04072014:...
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Hi Biren, The current specification should be: 04072014 for example: get_db.sh --dtype=inputs...
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Reading lmat-doc.txt: for the ./get_db.sh --dtype=inputs --name=<name-of-input> --outdir=<LMAT-root-dir>/runtime_inputs...
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Sasha modified a comment on discussion General Discussion
Hi, Linux is required to run LMAT. We don't support OSX at this time. Sorry for the...
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Hi, Linux is required to run LMAT. We don't support OSX at this time. Sorry. Best...
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Hi Ara, thanks for the information. It maybe that the shell script syntax is slightly...
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Ara posted a comment on discussion General Discussion
Hello all, I am having trouble getting LMAT to run under OS X with Xcode 7.2 installed....
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What's New
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Example LMAT Run
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shahrok modified a comment on discussion General Discussion
Hi Jonathan, To make a db on lmat from Bacterial Refseq, I downloaded these two files:...
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Hi Jonathan, To make a db on lmat from Bacterial Refseq, I downloaded these two files:...
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Fiona Whelan posted a comment on discussion General Discussion
That did it! Thanks again!
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Hi Yvonne, Please comment out or remove that line. Originally, we experimented with...
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Yvonne posted a comment on discussion General Discussion
Hi, I ran into a problem during the installation of LMAT-1.2.6 by running "make"...
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Hi Fiona, This may be an unfortunate consequence of the default settings. I believe...
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Hi Jonathan, I was hoping I could ask a quick follow up question. I've been using...
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Hi Jonathan, I was hoping I could ask a quick follow up question. I've been using...
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Hi Jonathan, I was hoping I could ask a quick follow up question. I've been using...
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Hi Jonathan, I was hoping I could ask a quick follow up question. I've been using...
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Thanks, Jonathan. I must have missed these in the lmat-doc.txt - sorry. Thanks for...
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Hello Fiona, thanks for the question. There are two scripts in the bin directory...
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Good afternoon, Thank you so much for actively maintaining such a great tool. I've...
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Hello Minguy Gan, Thank you for the question. I understand the database size is an...
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gmy posted a comment on discussion General Discussion
Hi, I want to do taxonomic assignment of our metagenomics data. But we only consider...
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What's New
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Enrique Zozaya Valdés posted a comment on discussion General Discussion
Yeah I can do that. Thanks a lot for that and all your help. I'll work with this....
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Sorry for the misunderstanding. There isn't a ready made script to do that, although...
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Ok thanks for that, but that's not exactly what I'm after. Maybe I didn't explain...
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Each read is assigned to the lowest rank possible. By default run_rl.sh should create...
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Hi Jonathan, Thanks again for your reply. I just installed LMAT and ran it with the...
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Hi Enrique, Yes, it's a log-odds type score: log(X/Y) where Y is the null value,...
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Hi Jonathan, Many thanks for your quick and informative reply.So I think I'll give...
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Hello Enrique, LMAT should handle longer contigs - we've tested on PacBio reads with...
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Hi, I have a host-associated Illumina metagenome assembly and I need a tool to separate...
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What's New
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LMAT released /LMAT-1.2.6.tgz
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Home
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What's New
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Apologies to anyone who downloaded the LMAT-1.2.5.tgz release before March 19 2015...
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What's New
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Hi Jose, Thanks for downloading LMAT and providing so much feedback. We appreciate...
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Jose posted a comment on discussion General Discussion
First of all, I would like to congratulate the LLNL Bioinformatics team for LMAT....
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Example LMAT Run
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Example LMAT Run
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Example LMAT Run
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Home
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Example LMAT Run
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Example LMAT Run
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Example LMAT Run
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Example LMAT Run
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Home
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Home
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What's New
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The ftp server is back online!
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Due to a hardware failure the LMAT ftp server where all of the LMAT databases are...
