GARM meta assembler python problem

[fireant]

Hi all,
I have been trying to use the new GARM metaasembler (http://garm-meta-assem.sourceforge.net/) to reconcile two contig sets from two different kmer assemblies. I have encountered a problem with the python code that I can't seem to figure out.
During the run I get an odd python module error
from optparse import OptionParser
ImportError: No module named optparse
mv: cannot stat `split.*': No such file or directory
ls: cannot access splits/split.*: No such file or directory
The split directory is empty... something wrong

I have checked the dependencies and they seem right and the optparse module is in my python library. Is this likely a version thing?
Python version 7.3.2

I have tried contacting the GARM contact person but received no reply, any help is greatly appreciated.

Nathan

[wolma]

GARM meta assembler python problem

hmm, there is certainly no such thing as Python version 7.3.2 .
What exact thing are you working with ? Which OS are you on and can you invoke python from a command line (in which case python --version may help) ?
Best,
Wolfgang

[fireant]

Oops sorry python 2.7.3 -- EPD 7.3-2(64-bit)
I am working on the texas advanced computer center stampede cluster.
linux
Nathan

[wolma]

I'm confused: the import error looks like python, but I just checked the sourceforge link you're giving and the GARM project does not mention Python anywhere. Seems to be written in Perl.
Is that the complete error message you've posted?

[fireant]

The pipeline uses python even though this is not listed as a dependency. I had trouble getting it to run until I added python to my module load list.
more detailed error message
'import site' failed; use -v for traceback
Traceback (most recent call last):
File "/work/phorid/GARM/bin/fastn_split.py", line 4, in <module>
from optparse import OptionParser
ImportError: No module named optparse
mv: cannot stat `split.*': No such file or directory
ls: cannot access splits/split.*: No such file or directory
The split directory is empty... something wrong
awk: cmd. line:1: fatal: cannot open file `filtered.coords' for reading (No such file or directory)
awk: cmd. line:1: fatal: cannot open file `filtered.coords' for reading (No such file or directory)
0 sequence found
0 sequence found
fasta files empty or wrong location...
readline() on closed filehandle COORDS at /work/02127/phorid/GARM/lib/GetData.pm line 24.
readline() on closed filehandle COORDS at /work/02127/phorid/GARM/lib/GetData.pm line 24.
readline() on closed filehandle COORDS at /work/phorid/GARM/bin/filter_GARM_coords_v0.3.pl line 27.
readline() on closed filehandle IN at /work/phorid/GARM/bin/filter_read.placed_GARM.pl line 15.
/usr/bin/perl: symbol lookup error: /home1/perl5/lib/perl5/x86_64-linux-thread-multi/auto/List/MoreUtils/MoreUt
ils.so: undefined symbol: Perl_xs_apiversion_bootcheck
Not found: /scratch/phorid/P_1_2_Garm/P_1_2_Garm/new_scaffolds.txt.fasta.agp.fixed.fasta.all_split.fasta or
/scratch/phorid/P_1_2_Garm/P_1_2_Garm/new_scaffolds.txt.fasta.all_split.fasta
cannot open at /work/phorid/GARM/bin/tag.pl line 13.
cannot open at /work/phorid/GARM/bin/tag.pl line 13.
cannot open at /work/phorid/GARM/bin/tag.pl line 13.

[wolma]

that's better, the

> 'import site' failed; use -v for traceback

part helps. This probably indicates some problem with choosing the right Python executable (site is loaded by Python at startup, not by any script).
I checked the source of the offending GARM/bin/fastn_split.py and it asks to be executed by

/usr/bin/python

which on local installations is a relatively safe bet, but since you said you're intending to work with the Enthought Python distribution that is definitely wrong.
Just try:
/usr/bin/python --version to convince yourself.

I guess the solution will be to change the shebang line (the one reading #!/usr/bin/python) according to your system setup, i.e. make it point to the EPD python.
If there areother python scripts in GARM, you will need to do this for all of them.

Hope that helps,
Wolfgang

[fireant]

Thanks for the help Wolfgang,
I get
login3$ /usr/bin/python --version
Python 2.6.6
Is this problem likely present in the perl scripts as well?