Error when running Sartools Deseq2 through galaxy

[inestiouiri]

Hi all , I'm running sartools deseq2 on my local galaxy instance and here is what i got. Help me please

[hvaret]

Dear @inestiouiri, I am not a Galaxy specialist, could you please post the content of the *.log file generated by SARTools and containing the output of the R console? Thanks, Hugo

[inestiouiri]

Dear @hvaret, Log file gives exactly the same thing please take a look.

[hvaret]

OK thanks, unfortunately I can't figure out what happened. @loraine-gueguen, do you know where the error could come from? Thanks! Hugo

[inestiouiri]

and when i execute the Rscript command from the terminal

i got that

logsartools.txt logsartools.txt

[hvaret]

OK it is strange because SARTools seems to be correctly loaded but then the execution is stopped.

[loraine-gueguen]

Can you please have a look at the R log dataset generated as output as said Hugo, not on the errors, but on the content of the file ("view data" with the small eye on the Galaxy dataset) ?

[inestiouiri]

Dear @loraine-gueguen,

It gives that

[1] "rawDir must be a character vector of length 1 specifying an accessible directory"

[loraine-gueguen]

ok. Can you please give me the format (or datatype) displayed in Galaxy of your dataset given as sartools input for 'Zip file containing raw counts files' (should be no_unzip.zip) ?

[inestiouiri]

Dear @loraine-gueguen,

I used test data of sartools and yes it's a no_zip.zip file and for target file i used the target.txt.

[loraine-gueguen]

Make sure you have read rights on the directory given as argument for rawDir (and on all the files inside) and then please try to run the Rscript command again from a terminal after removing the stdout redirection > /usr/.../*.dat What appears on stdout ?

[inestiouiri]

Deat @loraine-gueguen,

i still have the same problem. :( and the Rscript command still load all packages and give out. "Welcome to SARTools version 1.3.2. R template scripts are available on GitHub." When we read the log we find that the tool is looking for files under /usr/local/galaxy/database/job_working_directory/001/1275 and when we go to see what we have we find under 001 a different directory which is /usr/local/galaxy/database/job_working_directory/001/1265. :(

[loraine-gueguen]

Don't use the Galaxy tree: copy the input files (target and rawdir) in a new working directory, run the Rscript and see what happens.

[inestiouiri]

Welcome to SARTools version 1.3.2.
R template scripts are available on GitHub.
----------------------------------------------

[1] "All the parameters are correct" Target file: label files group WT1 WT1 WT1.htseq.out WT WT2 WT2 WT2.htseq.out WT KO1 KO1 KO1.htseq.out KO KO2 KO2 KO2.htseq.out KO Loading files: WT1.htseq.out: 8222 rows and 183 null count(s) WT2.htseq.out: 8222 rows and 193 null count(s) KO1.htseq.out: 8222 rows and 210 null count(s) KO2.htseq.out: 8222 rows and 193 null count(s)

Features removed: alignment_not_unique ambiguous no_feature not_aligned too_low_aQual

Top of the counts matrix: WT1 WT2 KO1 KO2 feat0001 2728 1636 668 2378 feat0002 3169 1892 376 1228 feat0003 2784 1626 622 2117 feat0004 6311 4283 374 1470 feat0005 12769 9132 718 3199 feat0006 3953 2867 666 2579

Bottom of the counts matrix: WT1 WT2 KO1 KO2 feat8212 0 0 0 0 feat8213 1 0 0 1 feat8214 0 2 0 1 feat8215 15 14 5 5 feat8216 45 49 13 27 feat8217 1 0 0 0 Error in title(...) : X11 font -adobe-helvetica-%s-%s---%d-------*, face 5 at size 12 could not be loaded Calls: descriptionPlots ... plot.density -> plot.default -> localTitle -> title Execution halted
:o

[hvaret]

I think the problem now comes from the machine you're hosting Galaxy. I think a Linux library/package is missing.

[loraine-gueguen]

I think so too.

[inestiouiri]

Dear @loraine-gueguen and @hvaret,

Ok.Thank you so much guys for you quick answers. :)