cmp_seq error during Contig stage

[scott monsma]

hi all, I'm trying Soap De Novo 2.04 for a plant genome. I succeeded with the first stage using sparse_pregraph, but now when I run the contig stage, I get the following error output and no contigs
Here's my first command:

/home/scott/software/SOAPdenovo2-bin-LINUX-generic-r240/SOAPdenovo-63mer sparse_pregraph -s /media/data/ParchmanPiper/SoapDN2trimmed.config -K 17 -z 3000000000 -o /media/data/ParchmanPiper/SoapDN2_assembly/Piper_SoapDN2_graphk_prefix 1 > /media/data/ParchmanPiper/SoapDN2_assembly/pregraph.log 2 > /media/data/ParchmanPiper/SoapDN2_assembly/pregraph.err  -p 62 -a 500 -R

second command:

/home/scott/software/SOAPdenovo2-bin-LINUX-generic-r240/SOAPdenovo-63mer contig -g /media/data/ParchmanPiper/SoapDN2_assembly/Piper_SoapDN2_graphk_prefix -R 1>contig.log 2>contig.err -p 62

and contig.err:

Version 2.04: released on July 13th, 2012
Compile Jul  9 2013    11:57:16
********************
Contig
********************
Parameters: contig -g /media/data/ParchmanPiper/SoapDN2_assembly/Piper_SoapDN2_graphk_prefix -R -p 62

There are 18082916 kmer(s) in vertex file.
There are 102650802 edge(s) in edge file.
Kmers sorted.

102650802 edge(s) input.
163141434 pre-arcs loaded.
2983166680 markers overall.
3237208010 markers loaded.
25661537 none-palindrome edge(s) swapped, 0 palindrome edge(s) processed.

CAAGCGATGCACCGTTG
CAAGCGATGCACCGTTG
TATATAATTTCTCCA
TATATAATTTCTCCA

cmp_seq:    err

Any ideas? I don't think its  a ram issue, I've got 512Gb
thanks! Scott

[phillip kyriakakis]

I have the same problem. Since this is a new post and I can't find the answer anywhere I suppose this is not a common issue, or the answer is trivial.