Cerulean error

[condomitti]

Hi guys,


I'm trying to run Cerulean to assemble PacBio reads.
I'm following their manual so nothing special in the commands. So far this is what I've completed successfully:

- sawriter .....
- blasr ......

and have the necessary files all in the same folder and with the same <dataname>. It's time now to run cerulean itself:

python src/Cerulean.py --dataname <dataname> --basedir <basedir> \
--nproc <numthreads>



When I run it I get an error after some minutes, on line 54 of the python file:

/usr/local/bin/cerulean: line 54: syntax error near unexpected token `('

That line is:

ArgumentParser(description="Cerulean hybrid assembler v0.1.1")


I'm using python 2.7.3 and ubuntu server, which should work fine.

Any clue on what could that error be related to?



Thanks in advance.


Cheers,
Condomitti.

[condomitti]

Ok mates, it's partly solved now...
The issue was somehow related to cerulean instalation. It had been installed from some repo that probably was not up to date. I downloaded the source from official repo and it worked.

The problem now is that Cerulean hangs for two days without producing any output or file. Looking at the python code of cerulean and debugging it, it's easy to see that it's the graph (the .dot file) load function which is hanging the software.
The sequence I'm working with is big, but it doesn't seem to be filling server memory or using CPU.

Has anyone got through this before?

Cheers,
Condomitti.

[akorobeynikov]

You may want to give SPAdes a try in its hybrid mode assembling Illumina + PacBio reads instead of Cerulean. You can also feed SPAdes your current contigs as 'trusted contigs'.

[condomitti]

Thanks, akorobeynikov! I'll give it a try very soon.

Cheers,
Condomitti.