janepipistrelle / bacterial_gwas_tutorial Goto Github PK

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