Closed najouamghazli closed 5 years ago
Hello Najoua
I think that both problem are linked is the version of R you have (not shure for root_tree.R).
You should still have a file ~/FROGSTest/13-tree-pynast.log. I think you already looked at it. In this file you will find the command launched by tree.py:
The final command root_tree.R should be test by using this syntaxe (as indicated in the log file): Rscript root_tree.R ....
Could you follow the log file and tell me which command fails ?
When you executed the RScript command of the r_composition.py, you obtain an error : Error: This is R 3.2.2, package 'phyloseq' needs >= 3.4.0
In FROGS we start working with this version of R, and I never test an older version. As it said and as we recommend, you need to upgrade your R version. This will may be solve your problem in tree if it the root_tree.R which fails.
Let me know!
Hello Maria,
thank you for your fast response.
For the first problem, the last command that were launched is:
# reconstruction a phylogenetic tree (FastTree version : found)
Command:
FastTree -nt -gtr /home/najoua/FROGSTest/1542967507.28_3050_pynast_aligned.fasta > /home/najoua/FROGSTest/1542967507.28_3050_fasttree.nwk 2> /home/najoua/FROGSTest/1542967507.28_3050_fasttree.stderr
Execution:
start: 23 Nov 2018 11:05:17
And there is no command that used the syntax: Rscript root_tree.R
As for the second problem, I don't seem to understand ! Because I'm already using R 3.4.4 and installed the phyloseq package under this version
najoua@Bioinfo:~$ R --version
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under the terms of the
GNU General Public License versions 2 or 3.
For more information about these matters see
http://www.gnu.org/licenses/.
Thank you,
Najoua
Ok, so it's two different problem.
Could you test manually the pynast command line followed by the fasttree command line ? It seem's that th problem is during the fasttree step but what is the Error ?
Concerning R, what do you have in the ~/FROGSTest/15-phylo_composition.log ? You may have some lines like this :
# Run 1 code Rmarkdown (Rscript version : [1] "R version 3.4.0 (2017-04-21)"
[1] "Rmarkdown version: 1.5"
[1] "Phyloseq version: 1.20.0")
Do not take car about the version, my point is to check which version of R is used for you.
Okay so here's the result of the command:
najoua@Bioinfo:~$ /home/najoua/FROGS-3.0.0//app/tree.py --nb-cpus 2 --input-otu /home/najoua/FROGS-3.0.0//test/data/to_test_pynast.fasta --biomfile /home/najoua/FROGS-3.0.0//test/data/to_test_pynast.biom --template-pynast /home/najoua/FROGS-3.0.0//test/data/otus_pynast.fasta --out-tree /home/najoua/FROGSErrors//13-tree-pynast.nwk --html /home/najoua/FROGSErrors//13-tree-pynast.html --log-file /home/najoua/FROGSErrors//13-tree-pynast.log
Traceback (most recent call last):
File "/home/najoua/FROGS-3.0.0//app/tree.py", line 330, in <module>
FastTree(align, fasttree, fasttree_stderr).submit( args.log_file )
File "/home/najoua/FROGS-3.0.0/lib/frogsUtils.py", line 141, in submit
subprocess.check_output( self.get_cmd(), shell=True )
File "/usr/lib/python2.7/subprocess.py", line 223, in check_output
raise CalledProcessError(retcode, cmd, output=output)
subprocess.CalledProcessError: Command 'FastTree -nt -gtr /home/najoua/FROGSErrors/1542985853.55_5149_pynast_aligned.fasta > /home/najoua/FROGSErrors/1542985853.55_5149_fasttree.nwk 2> /home/najoua/FROGSErrors/1542985853.55_5149_fasttree.stderr' returned non-zero exit status 127
And for the R problem, I don't even have the file ~/FROGSTest/15-phylo_composition.log
The last file that were generated is 13-tree-pynast.log
What I was asking was the results of :
FastTree -nt -gtr /home/najoua/FROGSErrors/1542985853.55_5149_pynast_aligned.fasta > /home/najoua/FROGSErrors/1542985853.55_5149_fasttree.nwk 2> /home/najoua/FROGSErrors/1542985853.55_5149_fasttree.stderr
If you do not have the input file anymore you may launch the tree.py command line with the --debug option
/home/najoua/FROGS-3.0.0//app/tree.py --nb-cpus 2 --input-otu /home/najoua/FROGS-3.0.0//test/data/to_test_pynast.fasta --biomfile /home/najoua/FROGS-3.0.0//test/data/to_test_pynast.biom --template-pynast /home/najoua/FROGS-3.0.0//test/data/otus_pynast.fasta --out-tree /home/najoua/FROGSErrors//13-tree-pynast.nwk --html /home/najoua/FROGSErrors//13-tree-pynast.html --log-file /home/najoua/FROGSErrors//13-tree-pynast.log --debug
and then the fasttree command line on those outputfiles
For the R problem where did you get the Rscript command line ?
is Fasttree in you PATH ? is it not in the libexec directory ?
for R, you have a Rscript file (probably link) in the FROGS/libexec directory. make shure that this Rscript is linked to th R 3.4.4 version
I just soft linked R 3.4.4 to the Rscript in the libexec directory, and added Fasttree to the PATH (it already exist in the libexec directory)
but nothing changed.
najoua@Bioinfo:~$ echo $PATH
/home/najoua/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin:/usr/bin/fasttree:/usr/bin/libexec
najoua@Bioinfo:~/FROGS-3.0.0/test$ ls -l /usr/bin/libexec/
total 1480
-rwxr-xr-x 1 root root 12133 nov. 23 10:04 addAffiliation2biom.py
-rwxr-xr-x 1 root root 11229 nov. 23 10:04 aggregate_affiliated_otus.py
-rwxr-xr-x 1 root root 10702 nov. 23 10:04 biom2tsv.py
-rwxr-xr-x 1 root root 3594 nov. 23 10:04 biomFastaUpdate.py
-rwxr-xr-x 1 root root 26717 nov. 23 10:04 biomTools.py
-rwxr-xr-x 1 root root 195064 nov. 23 10:04 blastn
lrwxrwxrwx 1 root root 36 nov. 23 10:04 classifier.jar -> /home/najoua/RDPTools/classifier.jar
-rwxr-xr-x 1 root root 14321 nov. 23 10:04 combine_and_split.py
-rwxr-xr-x 1 root root 19874 nov. 23 10:04 derepSamples.py
-rwxr-xr-x 1 root root 4177 nov. 23 10:04 extractSwarmsFasta.py
-rwxr-xr-x 1 root root 198584 nov. 26 10:02 fasttree
-rwxr-xr-x 1 root root 10617 nov. 23 10:04 filterSeq.py
-rwxr-xr-x 1 root root 73472 nov. 23 10:04 flash
-rwxr-xr-x 1 root root 124229 nov. 23 10:04 ITSx
-rwxr-xr-x 1 root root 4393 nov. 23 10:04 multiAffiFromBiom.py
-rwxr-xr-x 1 root root 8728 nov. 23 10:04 needleall_on_bestBlast.py
-rwxr-xr-x 1 root root 6078 nov. 23 10:04 needleallSam_to_tsv.py
-rwxr-xr-x 1 root root 28745 nov. 23 10:04 parallelChimera.py
-rwxr-xr-x 1 root root 21873 nov. 23 10:04 parallelITSx.py
-rwxr-xr-x 1 root root 11012 nov. 23 10:04 remove454Adapt.py
-rwxr-xr-x 1 root root 12833 nov. 23 10:04 removeConta.py
-rwxr-xr-x 1 root root 1401 nov. 23 10:04 root_tree.R
lrwxrwxrwx 1 root root 10 nov. 26 10:16 Rscript -> /usr/bin/R
-rwxr-xr-x 1 root root 8604 nov. 23 10:04 select_inclusive_amplicon.py
-rwxr-xr-x 1 root root 18685 nov. 23 10:04 silva2retrainRDP.py
-rwxr-xr-x 1 root root 6525 nov. 23 10:04 sortAbundancies.py
-rwxr-xr-x 1 root root 26709 nov. 23 10:04 splitbc.pl
-rwxr-xr-x 1 root root 575352 nov. 23 10:04 swarm
-rwxr-xr-x 1 root root 5613 nov. 23 10:04 swarm2biom.py
-rwxr-xr-x 1 root root 14825 nov. 23 10:04 tsv2biom.py
najoua@Bioinfo:~/FROGS-3.0.0/test$ /usr/bin/libexec/Rscript --version
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under the terms of the
GNU General Public License versions 2 or 3.
For more information about these matters see
http://www.gnu.org/licenses/.
When I run the first command, here what it gives:
najoua@Bioinfo:~$ /home/najoua/FROGS-3.0.0//app/tree.py --nb-cpus 2 --input-otu /home/najoua/FROGS-3.0.0//test/data/to_test_pynast.fasta --biomfile /home/najoua/FROGS-3.0.0//test/data/to_test_pynast.biom --template-pynast /home/najoua/FROGS-3.0.0//test/data/otus_pynast.fasta --out-tree /home/najoua/FROGSErrors//13-tree-pynast.nwk --html /home/najoua/FROGSErrors//13-tree-pynast.html --log-file /home/najoua/FROGSErrors//13-tree-pynast.log --debug
Traceback (most recent call last):
File "/home/najoua/FROGS-3.0.0//app/tree.py", line 330, in <module>
FastTree(align, fasttree, fasttree_stderr).submit( args.log_file )
File "/home/najoua/FROGS-3.0.0/lib/frogsUtils.py", line 141, in submit
subprocess.check_output( self.get_cmd(), shell=True )
File "/usr/lib/python2.7/subprocess.py", line 223, in check_output
raise CalledProcessError(retcode, cmd, output=output)
subprocess.CalledProcessError: Command 'FastTree -nt -gtr /home/najoua/FROGSErrors/1543225355.19_4932_pynast_aligned.fasta > /home/najoua/FROGSErrors/1543225355.19_4932_fasttree.nwk 2> /home/najoua/FROGSErrors/1543225355.19_4932_fasttree.stderr' returned non-zero exit status 127
Merci beaucoup
Hi najouamghazli
What is in your /home/najoua/FROGSErrors/1543225355.19_4932_fasttree.stderr ?
a+
Here is what in the file /home/najoua/FROGSErrors/1543225355.19_4932_fasttree.stderr
/bin/sh: 1: FastTree: not found
So it said that FastTree is not in your path.
fasttree is not named correctly in your libexec directory!
Exactely. I renamed it and I'm running the test again right now, I'll tell you if everthing went okay ... or else if there's an error (I don't hope so)
Thank you so much for your help.
Hello!
I'm encountering the same problem as #28
najoua@Bioinfo:~/FROGS-3.0.0/test$ bash test.sh ~/FROGS-3.0.0/ 2 4 ~/FROGSTest/
najoua@Bioinfo:~$ pynast --input_fp FROGSTest//04-filters.fasta --template_fp /home/najoua/FROGS-3.0.0//test/data/otus_pynast.fasta --min_len 349 --fasta_out FROGSTest/04-filters_pynast_aligned.fasta --failure_fp FROGSTest/04-filters_pynast_fail.fasta --log_fp FROGSTest/04-filters_pynast_log.txt
All of this seems right, but then I can't find the "root_tree.R"
I've tried to reinstall phyloseq package
But the same problem arises again
Can anyone help me solve this ?
Best,
Najoua