Error in my.system(cmd) : res == 0 is not TRUE

[kinerett]

please help... i used the original files that come with the code, but when i use cneFinalListDanRer10Hg38 <- lapply(cneMergedListDanRer10Hg38, blatCNE)

it returns: Error in my.system(cmd) : res == 0 is not TRUE

why is that? how can i solve this? tnx

[ge11232002]

Do you have BLAT installed on your system?

[kinerett]

No i didnt... i understod it latter... i instaled blat but had a problem with the huge memory missing error... do you have a code to use with the other aligning methods you mentioned? I saw they can be installed in r through bioconductor... ( im not a programer if its not clear 😊 just a desparet genetics student) thank you very much!

בתאריך יום שבת, 29 בדצמבר 2018, מאת Ge Tan notifications@github.com:

Do you have BLAT installed on your system?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/ge11232002/CNEr/issues/21#issuecomment-450512139, or mute the thread https://github.com/notifications/unsubscribe-auth/AsD2qKvlKDY-yu8ZITBiL2uDb3GRrDTDks5u97fHgaJpZM4ZjE_Z .

--

Kineret Taler Dr Adi Inbal's lab Department of Medical Neurobiology Institute for Medical Research – Israel-Canada The Hebrew University of Jerusalem Jerusalem 9112002, Israel Kineret.Taler@mail.huji.ac.il 0546356947

[ge11232002]

What's the specs of your machine? The example data should only needs small amount of memory. Other aligning methods are not implemented yet.

[devenderarora]

Dear Author, I am also facing the same issue.May I know if there is any fix for this error. I have installed BLAST and working on server with decent configuration. Although same function is running when just executed like: lavToPsl, axtChain, chainMergeSort, chainPreNet, chainNet, netSyntenic, netToAxt, axtSort

[ge11232002]

You installed BLAST or BLAT?

[devenderarora]

Typo error.. :D I installed both BLAT and ucsc-BLAT via anaconda.

[ge11232002]

It's hard for me to tell what exactly happened. When you run BLAT step in R, it simply calles the external BLAT program. Try to run the exact command on a shell and see what the error is. The exact commmand is shown as message in R.

[devenderarora]

In shell the command runs smoothly. I did able to get chain and net files but with little tweaks but still not able to figure out this R error.

[ge11232002]

Probably the BLAT installed by Anaconda is searchable in your R environment. Try

system("blat")

If it gives you the error of "sh: blat: command not found", you can use R package reticulate to load your conda environment.

[Miracle-Yao]

Hi @ge11232002 Thank you so much for providing such great software! But when I run it, there are some problems.

……
> lavs <- list.files(path="/data/CNEr/mm10vsgg6", pattern="\\.lav$")
> system("blat")
blat - Standalone BLAT v. 35 fast sequence search command line tool
usage:
   blat database query [-ooc=11.ooc] output.psl
where:
   database and query are each either a .fa , .nib or .2bit file,
   or a list these files one file name per line.
……
> psls <- lavToPsl(lavs, removeLav=FALSE, binary="lavToPsl")
Run lavToPsl...
sh: lavToPsl: command not found
Warning message:
In system2(command = binary, args = arguments) : error in running command

The prompt says there is no such command. I have installed BLAT as discussed above, and also used system("blat"). My BLAT is installed with conda.What do I need to do next? And I want to know how to load the conda environment with R package reticulate.

Looking forward to your reply! Best wishes! DC

[Miracle-Yao]

Hi,everyone

Sorry, I found that the error was caused by not installing UCSC Kent tools. I've tried to run the whole process, but I've found a puzzlement called "The scanning window size must be equal or larger than identity!" If so, then how to identify CNEs with 70% identity over 30bp.

Best wishes! DC