Error With Velvet: Could Not Write Into File

Question

[Pasta]

Hello again,

I am trying Velvet to assemble RNA-seq data (44 million reads, Illumina, 50-nt PE) but I have another error :(

Here are the commands I ran:

 ./velveth MyAssembly/ 25 -shortPaired -fastq ~/Documents/BWA/BothReads_GFZ6.fq

then,

 ./velvetg MyAssembly/ -read_trkg yes

The error comes with velvetg:

.../...
[4133.126878] 1250000 / 753666 nodes visited
[4133.135819] 1260000 / 753666 nodes visited
[4133.140911] Concatenation...
[4133.209688] Renumbering nodes
[4133.214894] Initial node count 753666
[4133.237263] Removed 158102 null nodes
[4133.237281] Concatenation over!
[4133.237283] Clipping short tips off graph, drastic
[4148.762396] Concatenation...
[4517.223943] Renumbering nodes
[4517.223962] Initial node count 595564
[4517.237647] Removed 359948 null nodes
[4517.237664] Concatenation over!
[4517.237666] 235616 nodes left
[4517.314742] Writing into graph file MyAssembly//Graph2...
velvetg: Could not write into file

Velvetg did create a Graph2 file of 8.1 G but I guess did not finish writing in it. My 24G RAM was full but there was still 15G swap available. Do you have any idea ?

Thanks for your help

Answer 1

[Marina Manrique]

Hi Pasta,

in this answer of the Velvet user group you can see some tips to calculate the memory requirements for your assembly

http://listserver.ebi.ac.uk/pipermail/velvet-users/2009-July/000474.html

HTH,

Marina

[Torst]

Hi Marina, I taught him everything he knows ;-P

[Pasta]

Thank you Marina for this precious link

[Marina Manrique]

You're welcome :)

I was lucky to have met Simon at a conference, this guy is a Velvet expert :)

Answer 2

[Pasta]

I finally found the answer myself. The / partition was just full, and I put my programs in /usr/local/bin ...

I feel stupid on this one LOL

[Torst]

I was just about to say it looks like your disk has filled up, but you beat me to it!