Several researchers are encountering difficulties with SOAPdenovo2 and said that the old SOAPdenovo used to run lot faster.
Maybe we got lucky, but we never encountered the same problem. We are not sure whether Nick Loman’s problems were only with the latest update of SOAPdenovo2 made few weeks back, or whether they appeared also in the version released about a year ago (r223).
In our case, the program always ran to completion at blazing speed (check few test cases here) and gave us reasonably correct assemblies. In fact, the recently released SOAPdenovo-trans, which is a transcriptome assembler written following parts of SOAPdenovo2, helped us assemble a large library that we could not do with Trinity.
If you encounter problems with SOAPdenovo2, please use ‘1>/dev/stderr 2>log’ to run the program and send the log file to Ruibang (email: rbluo at hku dot hk). Alternatively, you can post it here so that others can compare with their error notes to see, whether a common pattern arises. In case you want to venture into the source code to track the error by yourself, we discussed the code of SOAPdenovo2 here and in the wiki. SOAPdenovo mailing list is also very active and responses come within a day or two.
Looks like Nick will be sending his read files to Ruibang. We will check with Ruibang about any update made in the code.
Update: Problem solved. Please see comment section.