askarbek-orakov / asar Goto Github PK

I'm attempting to use the preset dataset that comes with the files to check and learn how to use this tool. The app seems to have some error that I can't figure out why it is happening. The command window in Rstudio displays the following information

Warning: Error in if: the condition has length > 1

Hi Askarbek,

I'm very new on the metagenomics and trying to use your pipeline ASAR using my illumina MiSeq sequencing data.

I got the .fseed, .ko and .seed file from MG-RAST using terminal with our lab super computer server (as i have a mac, and slurm sbatch, srun command doesn't work with my mac) and i put all obtained data in the bash folder (where all scripts are), and i ckecked the data using checkdownload.R on the R console, it worked but there was an error to get the .Rdata.
I re-run the createPathView.R script on R console to find the error...

sh: ghead: command not found
Error in fread(paste0("ghead -n -1 ", paste0(path, fname)), sep = "\t", :
File is empty: /var/folders/1n/_c3klvwx37b5k897sgcrtr840000gp/T//RtmpgTmRgM/file9445e83c2c3

As you said on your page, if there is an error with lack of “ghead” command in the system, it should be changed with “head”. So i changed ahead to head but same error is on my R studio.

head: illegal line count -- -1
Error in fread(paste0("head -n -1 ", paste0(path, fname)), sep = "\t", :
File is empty: /var/folders/1n/_c3klvwx37b5k897sgcrtr840000gp/T//RtmpgTmRgM/file9443bf77b8b

And there was also File empty error which looks like, there is some problem of path...
For the location of a file, just write the path in the function(path ="Path/to/direcotry/") or everywhere ? like :

load.fdata.from.file <- function(path = "Path/to/direcotry/") {
flist<-dir(path = "Path/to/direcotry/", pattern = "*.3.fseed$")
cat(paste(flist,collapse = "\n"))
fannot<-lapply(flist,function(.x){fread(paste0('head -n -1 ./', .x),sep='\t',header = TRUE)})
return(fannot)

Thanks for your help :)
Mia

When executing prepareProject.sh it created an mpg86515.meta.csv file (only 282 bytes) and a prepareProject.tex of only 43 KB. No project. was created.
This is the output below. FYI: I am hiding my web key name as wells my computer name (xxx)
Have you seen this issue before and what needs to be done to fix it?

Kind regards

Marcos-MBP:bash xxx$ ./prepareProject.sh mgp86515
MGRAST download preparation script.\n Usage:\n prepareProject.sh webkey projectID\n

mgp86515
j mgp86515

processing file: prepareProject.Rmd
|... | 5%
inline R code fragments

|...... | 10%
label: loadPackages (with options)
List of 2
$ include: logi FALSE
$ cache : logi FALSE

|......... | 14%
ordinary text without R code

|............ | 19%
label: setup (with options)
List of 2
$ include: logi FALSE
$ cache : logi FALSE

|............... | 24%
ordinary text without R code

|................... | 29%
label: functions (with options)
List of 1
$ include: logi FALSE

|...................... | 33%
ordinary text without R code

|......................... | 38%
label: get.the.project (with options)
List of 1
$ echo: logi FALSE

|............................ | 43%
ordinary text without R code

|............................... | 48%
label: project.description (with options)
List of 2
$ echo : logi FALSE
$ results: chr "asis"

|.................................. | 52%
ordinary text without R code

|..................................... | 57%
label: list.metagenomes (with options)
List of 1
$ echo: logi FALSE

|........................................ | 62%
ordinary text without R code

|........................................... | 67%
label: ask.4.biome
|.............................................. | 71%
ordinary text without R code

|.................................................. | 76%
label: make.sango.scripts (with options)
List of 1
$ echo: logi FALSE

|..................................................... | 81%
inline R code fragments

|........................................................ | 86%
label: docVersion (with options)
List of 3
$ echo : logi FALSE
$ results: chr "asis"
$ cache : logi FALSE

|........................................................... | 90%
ordinary text without R code

|.............................................................. | 95%
label: sessionInfo (with options)
List of 4
$ echo : logi FALSE
$ results: chr "asis"
$ class : chr "text"
$ warning: logi FALSE

|.................................................................| 100%
ordinary text without R code

output file: prepareProject.knit.md

/usr/local/bin/pandoc +RTS -K512m -RTS prepareProject.utf8.md --to latex --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output prepareProject.tex --template /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rmarkdown/rmd/latex/default-1.17.0.2.tex --number-sections --highlight-style tango --pdf-engine pdflatex --variable graphics=yes --variable 'geometry:margin=1in' --variable 'compact-title:yes'
Error: Failed to compile prepareProject.tex.
In addition: Warning messages:
1: In pander.default(devtools::session_info()) :
No pander.method for "session_info", reverting to default.
2: In pander.default(x[[i]], indent = indent + 1) :
No pander.method for "platform_info", reverting to default.
3: In system2(..., stdout = FALSE, stderr = FALSE) :
error in running command
Execution halted
Marcos-MBP:bash xxx$

Apologies if this is answered somewhere else, but is there a way to use MGRAST profiles that have already been downloaded locally?

I am relatively new to using batch scripts. Is there a way to install a 'simple' version of slurm to allow sbatch and srun commands to be executable using bash, not on a HPC node?

Hi,
I'm just wondering if we can use this tool for data that was annotated outside of MG-RAST?

Thanks!