Running Velvet on DIAG - errors

[lavik17]

Hi everyone,
I have a large dataset of 125bp paired-end reads (after trimming). The size of the interleaved file is ~10Gb.
I've uploaded the file to DIAG and tried to run Velveth with the following command:

qsub -b y -P diag /diag/software/velvet/velveth auto 81,121,10 -shortPaired -fastq myfilename.fq

I've also tried the same thing with a k-mer of 21:

qsub -b y -P diag /diag/software/velvet/velveth k21 -shortPaired -fastq myfilename.fq

when I check the stats of the request with QSTAT, I can see that there is job request but it disappears after a few seconds.

The result is that velveth creates a folder in which there are three files (as should be): Log, Roadmaps, Sequences. But the sequences file is empty, the Log file only have 3 relevant lines in it:

Compilation settings:
CATEGORIES = 2
MAXKMERLENGTH = 101
LONGSEQUENCES

I've noticed that DIAG has an old version of velvet, 1.2.03, when the newest version is 1.2.10 but I think that it shouldn't cause the problem I am facing.
Does anyone know how should I proceed and make it work ? or can anyone recommend another grid where I can run my de-novo assembly ?

Thanks!

Adi

[lavik17]

update - I got some progress but still not working

I've managed to progress a bit, but its still not working

The new command I was playing with is:

qsub –b y –P diag /diag/software/velvet/velveth auto 81,101,10 –shortPaired –fastq /diag/home/Lavik/shuffled/filename.fq

This creates only one directory called auto_81

in it there are a Log file and sequence file. The Roadmaps file is missing.
The sequence file is of the expected size so I guess it holds the sequences.
The log file just reports the code I've entered.

The other velveth log file in my main directory is empty so there is no error report, velveth stops working without reporting anything and without creating Roadmap file needed for velvetg.

I would really appreciate any help on this one