-
Notifications
You must be signed in to change notification settings - Fork 8
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
PhylotaR setup issue #39
Comments
Hi Matteo, It seems there is an error when trying to determine the version of your installed version of the NCBI BLAST+ tools. It is hard for me to examine exactly where things are going wrong as I don't have access to your computer. Could you run the following script? It basically recreates what cmd_path <- file.path('C:/Program Files/ncbi-blast-2.7.1+/bin', 'blastn')
res <- phylotaR:::cmdln(cmd = cmd_path, args = '-version')
# Is the status TRUE?
(res[['status']] == 0)
# What are the BLASTN details?
stdout <- rawToChar(res[['stdout']])
(stdout <- strsplit(x = stdout, split = '\n')[[1]])
# Can we extract the version number?
vrsn <- gsub('[a-zA-Z:+]', '', stdout[[1]])
vrsn <- gsub('\\s', '', vrsn)
(vrsn <- as.numeric(strsplit(vrsn, '\\.')[[1]]))
# Version should be 2 +, expect TRUE
(vrsn[1] >= 2 & vrsn[2] >= 0) For reference, here is the above code working for my machine.
|
Thank you for the answer! I ran the code and I ge this:
|
OK. That all looks fine. I expected that to fail. Can you repeat the code I sent you but with cmd_path <- file.path('C:/Program Files/ncbi-blast-2.7.1+/bin',, 'makeblastdb')
res <- phylotaR:::cmdln(cmd = cmd_path, args = '-version')
# Is the status TRUE?
(res[['status']] == 0)
# What are the details?
stdout <- rawToChar(res[['stdout']])
(stdout <- strsplit(x = stdout, split = '\n')[[1]])
# Can we extract the version number?
vrsn <- gsub('[a-zA-Z:+]', '', stdout[[1]])
vrsn <- gsub('\\s', '', vrsn)
(vrsn <- as.numeric(strsplit(vrsn, '\\.')[[1]]))
# Version should be 2 +, expect TRUE
(vrsn[1] >= 2 & vrsn[2] >= 0) Also, can you try running this? It should return a list of the NCBI paths. Given your code error it should fail. cmd_path <- 'C:/Program Files/ncbi-blast-2.7.1+/bin'
(phylotaR:::blast_setup(d = cmd_path, v = TRUE, wd = getwd())) |
This is what I get:
|
Hi Matteo, OK. So it looks like we're getting an unexpected "~1:" in the makeblastdb version description. I've made a fix to hopefully correct the problem for you. Can you try installing the development version and running your pipeline code again? To install the latest development version on GitHub: library(devtools)
install_github('ropensci/phylotaR') Dom |
Hi Dom, However another issue came out: During the blast phase an error occured: -Unexpected Error : blastn failed to run. Check BLAST log files. According to the blast log file: -BLAST query/options error: '"6' is not a valid output format Best, Matteo |
Hi Matteo, Sorry for the persistent problems. I've created some new checker functions during the setup step. If you update phylotaR to the latest on GitHub and try running your pipeline again, does it still work? And does the error crop up again? It should get caught earlier. |
Hi, i installed phylotaR yesterday and also received the same error as pittaro: phylotaR: Implementation of PhyLoTa in R [v1.0.0]Checking for valid NCBI BLAST+ Tools ...
|
Hi, |
I confirm @agamisch issue. Trying to reproduce Aotus example I got the following error: |
Hi @basil-yakimov, Are you using the latest version of phylotaR, downloaded from GitHub? Try running: remotes::install_github('ropensci/phylotaR') I recently fixed issues relating to that particular error. Otherwise, if the error is still occurring I will need more information about your system and set-up. Thanks! |
I am using version from CRAN. Here is a report after the attempt to install from github:
Then I updated my R from 3.5.3 to 3.6.1. Got the same error:
|
Previously restez was taken down from CRAN, but it is now available again (https://cran.r-project.org/web/packages/restez/index.html). Installing |
Thanks to @joelnitta for pointing out the update of restez. I am closing this now, as the test is passed in current version: $ radian
R version 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Platform: x86_64-pc-linux-gnu (64-bit)
r$> library(phylotaR)
wd<-getwd()
r$> txid<-9504
r$> setup(wd = wd, txid = txid, ncbi_dr = "/workspaces//blast", v = TRUE)
-----------------------------------------------------
phylotaR: Implementation of PhyLoTa in R [v1.2.0.999]
-----------------------------------------------------
Checking for valid NCBI BLAST+ Tools ...
Failed to run: [/workspaces/blast/makeblastdb]. Reason:
[Error : Failed to execute '/workspaces/blast/makeblastdb' (No such file or directory)
]Failed to run: [/workspaces/blast/blastn]. Reason:
[Error : Failed to execute '/workspaces/blast/blastn' (No such file or directory)
]Error:Unable to find correct versions of NCBI BLAST+ tools
Error in blast_setup(d = ncbi_dr, v = v, wd = wd, otsdr = outsider) :
Unable to find correct versions of NCBI BLAST+ tools
r$> setup(wd = wd, txid = txid, ncbi_dr = "/workspaces//blast/bin", v = TRUE)
-----------------------------------------------------
phylotaR: Implementation of PhyLoTa in R [v1.2.0.999]
-----------------------------------------------------
Checking for valid NCBI BLAST+ Tools ...
Found: [/workspaces/blast/bin/makeblastdb]
Found: [/workspaces/blast/bin/blastn]
. . Running makeblastdb
Setting up pipeline with the following parameters:
. blstn [/workspaces/blast/bin/blastn]
. btchsz [100]
. date [2022-09-18]
. db_only [FALSE]
. mdlthrs [3000]
. mkblstdb [/workspaces/blast/bin/makeblastdb]
. mncvrg [51]
. mnsql [250]
. multiple_ids [FALSE]
. mxevl [1e-10]
. mxnds [1e+05]
. mxrtry [100]
. mxsql [2000]
. mxsqs [50000]
. ncps [1]
. outfmt [6 qseqid sseqid pident length evalue qcovs qcovhsp]
. outsider [FALSE]
. srch_trm [NOT predicted[TI] NOT "whole genome shotgun"[TI] NOT unverified[TI] NOT "synthetic construct"[Organism] NOT refseq[filter] NOT TSA[Keyword]]
. txid [9504]
. v [TRUE]
. wd [/workspaces/phylotaR]
. wt_tms [1, 3, 6 ...]
----------------------------------------------------- |
Great! Please let me know if you encounter any problems with restez. |
Hi,
I'm trying to run phylotaR in R 3.4.4 with the following code:
devtools::install_github('ropensci/phylotaR')
library(phylotaR)
wd<-getwd()
ncbi_dr<-"C:/Program Files/ncbi-blast-2.7.1+/bin"
txid<-9504
setup(wd = wd, txid = txid, ncbi_dr = ncbi_dr, v = TRUE)
then I get:
phylotaR: Implementation of PhyLoTa in R [v1.0.0]
Checking for valid NCBI BLAST+ Tools ...
Error in if (tst) { : missing value where TRUE/FALSE needed
Inoltre: Warning message:
In blast_setup(d = ncbi_dr, v = v, wd = wd) :
NAs introduced by coercion
Do you have any suggestion? I could not find a solution for this problem
Best,
Matteo
The text was updated successfully, but these errors were encountered: