lets start from the beginning so that you get an Idea of what I'am doing. My fist files are Paired-End-Reads which I put into Module that clips and merges (it's an ancient DNA sample). After that I filtered it with deconseq and got 1 fastq File of "clean" reads which is about 3gb big and contains 14.639.466 reads.
Now I want do do a metagenomic assembly from the clean fastq File. The length of the reads is ranging form 25 to 192. So I compiled velvet with the following parameters:
make 'CATEGORIES=1' 'MAXKMERLENGTH=17' 'OPENMP=1'
I used this Kmerlength because I wanted to include all the reads in my file and the Openmp for using the multithreading option. I am not entirely sure what the Categories Option does but what I get from the manual it seem ok to set this to one.
Then I executed Velveth with this command line:
./velveth out-dir 17 -fastq /path/to/the/file......
And it is creating the initial files. After that I borrowed a lot of memory (100gb) and tired to execute Velvet g with the the following parameters:
./velvetg out-dir -exp_cov auto
Then the program starts and until now I've seen two possible outcomes. One is this strange Error I'am not understanding:
Scanning pre-graph file out-dir/PreGraph for k-mers velvetg: Key length 24 greater than max allowed value (17) Recompile Velvet to deal with this word length.: No such file or directory
Why is there suddenly a greater key length? I thought the only thing that velveth is doing is constructing a Hashtable. So recompiled it with 'MAXKMERLENGTH=27' and ran it again.
Then I encountered the second output: PBS Killed Job Memory Limit exceeded.
Any thoughts on this? Anybody with experience in metagenomic assembly? How much Memory you think I need for the task or am I doing something fundamentally wrong? If I could I would ask somebody at our group but I am the only one here working with Velvet so I have no one to ask.
As always with kind regards and thanks in advance,