I am trying to run shhh.flows on a dataset which consists of 30 samples, with a total of 255623 reads. The sequences are encoding a protein coding gene. To do this analysis I run it on our local cluster where I have asked for 64 Gb of memory.
I had downloaded the latest version of mothur this week and installed it on my account on our cluster.
Running 64Bit Version
Last updated: 8/8/2012
So my command is this:
mothur > shhh.flows(file=OFS_ARHD.HTN0MRN04.flow.files, lookup=LookUp_Titanium.pat)
The output that I get is this:
Using 1 processors.
Processing OFS_ARHD.HTN0MRN04.PM10-A04.Ac114f.flow (file 1 of 30) <<<<<
[ERROR]: std::bad_alloc has occurred in the ShhherCommand class function getFlowData. Please contact Pat Schloss at firstname.lastname@example.org> , and be sure to include the mothur.logFile with your inquiry.
At this point I don’t know what is happening any why it is crashing. I do know that when I tried to run it with the previous version of Mothur v1.26.0, I got the same error. I have also tried to run this interactively or in batch mode. Any idea where I should look to see why mothur is giving this ERROR?