"sh: usearch: command not found Error: It seems like you don't have USEARCH installed"

[CristianRiccio]

Hi,

When I run this command:

LTRpred(genome.file = system.file("Hsapiens_ChrY.fa", package = "LTRpred"))

I get the following error:

sh: usearch: command not found
Error: It seems like you don't have USEARCH installed locally on your machine or the PATH variable to the USEARCH program is not set correctly. Please consult the Installation vignette or http://drive5.com/usearch/download.html for details on how to install USEARCH.

But I have installed USEARCH. I even used it on random fasta files:

usearch -cluster_fast c_elegans.PRJNA13758.WS263.genomic.fa -id 0.9 -centroids c_elegans.PRJNA13758.WS263.genomic.fa

and it ran (albeit with a memory error). I have added the folder in which usearch is located to my PATH variable and added the whole path to USEARCH to my PATH variable. Note that I have renamed the executable to usearch.

I work on Mac OSX and I have installed version 10.0.240 of USEARCH.

[HajkD]

Hi @CristianRiccio

Could you please send me the output of your R console when you run the command:

system("usearch -version")

In my case, I get usearch v8.1.1861_i86osx32 which means that usearch is installed/linked at /usr/local/bin/.

After you sent me your output I am happy to try helping you troubleshoot :)

Cheers, Hajk

[CristianRiccio]

In Rstudio:

system("usearch -version")
sh: usearch: command not found

In the Terminal (on MacOS X):

usearch -version
usearch v10.0.240_i86osx32

In R running in the Terminal:

system("usearch -version")
usearch v10.0.240_i86osx32

In R opened in the Terminal:

library(LTRpred)
Warning message:
package ‘LTRpred’ was built under R version 3.4.4
LTRpred(genome.file = system.file("Hsapiens_ChrY.fa", package = "LTRpred"))

 *** caught segfault ***
address 0x18, cause 'memory not mapped'

Traceback:
 1: dyn.load(file, DLLpath = DLLpath, ...)
 2: library.dynam(lib, package, package.lib)
 3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
 4: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),     versionCheck = vI[[i]]), from = package)
 5: loadNamespace(name)
 6: doTryCatch(return(expr), name, parentenv, handler)
 7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 8: tryCatchList(expr, classes, parentenv, handlers)
 9: tryCatch(loadNamespace(name), error = function(e) stop(e))
10: getNamespace(ns)
11: asNamespace(ns)
12: getExportedValue(pkg, name)
13: stringr::str_detect
14: test_installation_gt()
15: LTRpred(genome.file = system.file("Hsapiens_ChrY.fa", package = "LTRpred"))

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace

In Rstudio:

LTRpred(genome.file = system.file("Hsapiens_ChrY.fa", package = "LTRpred"))
sh: usearch: command not found
Error: It seems like you don't have USEARCH installed locally on your machine or the PATH variable to the USEARCH program is not set correctly. Please consult the Installation vignette or http://drive5.com/usearch/download.html for details on how to install USEARCH.

My R version is 3.4.4 in Rstudio and 3.4.1 in R opened in the Terminal. I didn't know Rstudio could use another version of R than the Terminal. So, I installed the latest version: 3.5.1. I tried the LTRpred() function again and this time, I got:

LTRpred(genome.file = system.file("Hsapiens_ChrY.fa", package = "LTRpred"))
sh: vsearch: command not found
Error: It seems like you don't have VSEARCH installed locally on your machine or the PATH variable to the VSEARCH program is not set correctly. Please consult the Installation vignette or https://github.com/torognes/vsearch ufor details on how to install VSEARCH.

I will go ahead and install VSEARCH and let you know how it goes.

[CristianRiccio]

I installed vsearch with conda and the LTRpred() function worked! It's now running on my genome file. I'll read your documentation but I'll probably be back for more questions. Thanks.

[HajkD]

I am happy to hear that it works now.

Cheers, Hajk