Unable to install Kmergenie

Question

[yanan.sun2]

Dear all, I tried to install and run KmerGenie. I downloaded the kmergeni-1.6892.tar.gz, unzipped it and did make under the folder. But it didn't work. It shows like the following when I try to run it:

[qiu@QIUSERV Kmergenie]$ ./kmergenie 45420_R2.fastq.gz
running histogram estimation
Linear estimation: ~2233 M distinct 56-mers are in the reads
K-mer sampling: 1/426
| processing                                                                                                                                                                      |
[going to estimate histograms for values of k: 91 81 71 61 51 41 31 21
--------------------------------------------------------------------------------                                                                             ---------------------Total time Wallclock  1025.82 s
fitting model to histograms to estimate best k

Caught exception in fit_histogram worker thread (histfile = histograms-k31.histo                                                                             ):
Traceback (most recent call last):
  File "/home/qiu/Data/polychaete_mito/K25/Kmergenie/scripts/decide", line 62, I                                                                             n fit_histogram
    rc, stdout, stderr = run(command)
  File "/home/qiu/Data/polychaete_mito/K25/Kmergenie/scripts/decide", line 43, I                                                                             n run
    process = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subproces                                                                             s.PIPE)
  File "/usr/local/lib/python2.7/subprocess.py", line 710, in __init__
    errread, errwrite)
  File "/usr/local/lib/python2.7/subprocess.py", line 1335, in _execute_child
    raise child_exception
OSError: [Errno 2] No such file or directory

So I did make check. It shows like:

[qiu@QIUSERV Kmergenie]$ make check
scripts/test_install
Testing presence of specialk....
OK
Testing presence of Rscript....
Traceback (most recent call last):
  File "scripts/test_install", line 55, in <module>
    check_r()
  File "scripts/test_install", line 20, in check_r
    ret = call(['Rscript','--version'])
  File "/usr/local/lib/python2.7/subprocess.py", line 522, in call
    return Popen(*popenargs, **kwargs).wait()
  File "/usr/local/lib/python2.7/subprocess.py", line 710, in __init__
    errread, errwrite)
  File "/usr/local/lib/python2.7/subprocess.py", line 1335, in _execute_child
    raise child_exception
OSError: [Errno 2] No such file or directory
make: *** [check] Error 1

I have both Python and R in my system:

[qiu@QIUSERV Kmergenie]$ python
Python 2.7.10 (default, Jun 26 2015, 17:05:34)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-11)] on linux2
Type "help", "copyright", "credits" or "license" for more information.


[qiu@QIUSERV bin]$ ./R

R version 3.1.3 (2015-03-09) -- "Smooth Sidewalk"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

Could you let now what is wrong with it and how can I fix it? Many thanks!

Cheers,
Yanan

[Rayan Chikhi]

Hi, can you make sure that "Rscript" is in your $PATH? This seems to be issue here.

(e.g. running "Rscript" in the console not give an error)