janepipistrelle / bacterial_gwas_tutorial Goto Github PK
View Code? Open in Web Editor NEWTutorial for bacterial GWAS pipline and bugwas, created for Bodega Bay 2016 NGS workshop
License: Creative Commons Zero v1.0 Universal
Tutorial for bacterial GWAS pipline and bugwas, created for Bodega Bay 2016 NGS workshop
License: Creative Commons Zero v1.0 Universal
Hi Jane,
This is a great tutorial you have put together. Thank you!
I run;
Rscript /usr/local/biotools/bacterialGWAS/kmerGWAS/kmerAnalysis.R -dataFile
data/fus300.kmerfiles.txt -prefix fus300
-removeKmerTxt FALSE -minCov 5 -externalSoftware data/dependencies.txt
stdout:
Read min-coverage = 5
Read 13622449 items
null device
1
FALSE
But when I run the following command. I have the error;
Error in file(file, "rt") : cannot open the connection
Calls: read.table -> file
In addition: Warning message:
In file(file, "rt") :
cannot open file './output/fus300_kmer_lmmout.assoc.txt': No such file or directory
Execution halted
But I can't find where this file is generated in the code.
What am I missing? please advise.
I also have a few a suggestions:
Considering that in most cases, bioinformaticians begin with raw sequencing data (fastqs), It would be great if you at least share the upstream steps e.g. the details for generating the tree such as model and why you use it? such that someone with raw data can arrive at the starting point for this tutorial or share a link to such a guide for upstream processing.
it would also be great to share the expected outputs if the command completed successfully. As you can see in my case, I'm having a challenging determining if the command has run successfully or not.
Finally, adding version numbers for R and R-packages would be super helpful as things begin to break as these changes. Perhaps the output of sessionInfo() in a working environment would be great.
Thanks
Hi,
I am currently running through the tutorial in the hope of performing gwas with my own data. The tutorial has been very useful (thank you!)
On the error correction step, using kmerLMM.R I am coming across a segmentation fault, followed by the program not being able to find the './output/fus300_kmer_lmmout.assoc.txt' file.
Reading Files ...
Segmentation fault
Error in file(file, "rt") : cannot open the connection
Calls: read.table -> file
In addition: Warning message:
In file(file, "rt") :
cannot open file './output/fus300_kmer_lmmout.assoc.txt': No such file or directory
Execution halted
I wondered if you could point me towards what is going wrong.
Many thanks
Michelle
A declarative, efficient, and flexible JavaScript library for building user interfaces.
๐ Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. ๐๐๐
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google โค๏ธ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.