FROGS Tree Reconstruction of phylogenetic tree issue

[mariemh23]

Hello,

I try to run Frogs tree. I put the fasta file and the biom abundance file (from filter step 4 of FROGS tutorial : http://sepsis-omics.github.io/tutorials/modules/frogs/#output_3 ). However, I got this erreur :

File "/usr/local/galaxy/tools/FROGS_2/app/tree.py", line 147, in get_version return Cmd.get_version(self, 'stdout').split()[-1].strip() IndexError: list index out of range

any help? thx

[mariabernard]

Hello,

could you share these files ? and Could you indicate me the command line you use ?

Regards

[mariemh23]

Dear @mariabernard This is my command line : python2.7 /usr/local/galaxy/tools/FROGS_2/app/tree.py --input-otu /scratch/database/files/023/dataset_23055.dat --biomfile /scratch/database/files/023/dataset_23056.dat --nb-cpus 1 --out-tree /scratch/database/files/023/dataset_23345.dat --html /scratch/database/files/023/dataset_23346.dat

and please find attached input files

Filter_data.gz

thx

[mariabernard]

Filter_data.gz is corrupted. I see the begining of the abundance biom file, but its not completed, and I need the fasta file also

[mariemh23]

Sorry... and now? Filter_galaxy.gz

[mariabernard]

I successfully construct the tree python ~/workspace/git/FROGS/FROGS_master/app/tree.py -i Filters__sequences.fasta -b FROGS_Filters__abundance.biom1

Here are the results: http://genoweb.toulouse.inra.fr/~mbernard/mariemh23_github/

are you sure about your input in Galaxy ?

[mariemh23]

Thanks for your help .

I tried the same line command as you on our server : /usr/local/galaxy/tools/FROGS_2/app/tree.py --input-otu Filter_galaxy2/Filterssequences.fasta --biomfile Filter_galaxy2/FROGS_Filtersabundance.biom1

. I always get the same mistake. Application Software :/usr/local/galaxy/tools/FROGS_2/app/tree.py (version : 1.0.0) Command : /usr/local/galaxy/tools/FROGS_2/app/tree.py --input-otu Filter_galaxy2/Filterssequences.fasta --biomfile Filter_galaxy2/FROGS_Filtersabundance.biom1

Number of input OTUs sequences: 1702

Mafft multiple alignment. (mafft version : v7.205)

Command: mafft --auto --thread 1 Filter_galaxy2/Filterssequences.fasta > Filterssequences_mafft_aligned.fasta 2> /dev/null

Execution: start: 23 Apr 2018 12:11:27 end: 23 Apr 2018 12:11:36

reconstruction a phylogenetic tree (FastTree version : 2.1.10)

Command: FastTree -nt -gtr Filterssequences_mafft_aligned.fasta > 1524481887.66_88772_Filterssequences.fasttree 2> /dev/null

Execution: start: 23 Apr 2018 12:11:36 end: 23 Apr 2018 12:12:10

Traceback (most recent call last): File "/usr/local/galaxy/tools/FROGS_2/app/tree.py", line 330, in RootTree(fasttree, args.out_tree).submit(args.log_file) File "/usr/local/galaxy/tools/FROGS_2/lib/frogsUtils.py", line 135, in submit FH_log.write( '# ' + self.description + ' (' + os.path.basename(self.program) + ' version : ' + self.get_version() + ')\n' ) File "/usr/local/galaxy/tools/FROGS_2/app/tree.py", line 147, in get_version return Cmd.get_version(self, 'stdout').split()[-1].strip() IndexError: list index out of range

Where do you think the problem resides?

[mariabernard]

If you compare with my log.txt file:

• mafft and fasttree run ok
• root_tree.R not

could you test this:

export PATH=/usr/local/galaxy/tools/FROGS_2/libexec:$PATH
root_tree.R -v

[mariemh23]

Dear Maria,

it seems that the function is not installed in my serveur ? Is it an R package? If so, which one? root_tree.R: command not found

[mariabernard]

Hello,

It's an R script that we developped. It should be there : /libexec/root_tree.R . Do you have it ? Does it have execution rigths?

[mariemh23]

Hi,

we installed the script correctly and checked the execution rights. I tried again " root_tree.R -v " and I got this

• caught segfault * address 0x6, cause 'memory not mapped'

Traceback: 1: dyn.load(file, DLLpath = DLLpath, ...) 2: library.dynam(lib, package, package.lib) 3: loadNamespace(package, lib.loc) 4: doTryCatch(return(expr), name, parentenv, handler) 5: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 6: tryCatchList(expr, classes, parentenv, handlers) 7: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L msg <- conditionMessage(e) sm <- strsplit(msg, "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && identical(getOption("show.error.messages"), TRUE)) { cat(msg, file = stderr()) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))}) 8: try({ attr(package, "LibPath") <- which.lib.loc ns <- loadNamespace(package, lib.loc) env <- attachNamespace(ns, pos = pos, deps)}) 9: library(ape) An irrecoverable exception occurred. R is aborting now ... Segmentation fault

[mariabernard]

What is you version of R ? We assure that the scripts work with the version 3.4.0 This script import two packages ape and phangorn (cf Readme). (NB: ape is not precised in the readme as it is a dependancy of Phyloseq. )

Do you have these pakages installed ?

R
library(ape)
library(phangorn)