Problem occurred when scaffolding

[Prunoideae]

I'm using SOAPdenovo-fusion and SOAPdenovo-127mer to scaffold some mitochondrial contigs assembled by MEGAHIT, but a problem is that the scaffolding was frozen in mapping sequences for over 7 hours, while the data is only a 27 MB contigs file and two paired 5Gbps reads files.

A possible cause of this is because a thread number of 80 was specified in this run (well my server does have this much), which caused several frozen process, or severely truncated genome in my previous assemblies using SOAPdenovo2.

Is SOAPdenovo designed to be robust like MEGAHIT does? I've never meet such a phenomenon when using MEGAHIT with 80 threads. If not, what thread number should I limit to, to make the progress safe enough when scaffolding the sequences?

[voutcn]

@aquaskyline could you help to answer this question?

[Prunoideae]

Also, it's quite strange that the scaffold generated from SOAPdenovo-fusion has no depth information:

The loss of depth info makes it much more difficult to identify the target candidates in my pipeline, since the genome I'm assembling is a mitochondrial genome and thus possess a high depth.