I posted this in “commands in mothur” as well because it is part of a longer thread, but it may be more important for this category.

I’m still getting strange behavior from chimera.uchime.

I’m running it on a Windows machine. It’s on a hard drive with mother and my files and nothing else on it. This computer has 32 processors and 128GB of RAM. No other analyses are running on this machine in tandem. I started another run of chimera.uchime using 8 processors and when I returned to the computer ~2 hours later, there was a window up saying “mothur.exe. has stopped working. A problem has caused the program to stop working correctly. Please close the program.” However, I have not closed it because the terminal still shows activity - there is output coming across the screen. Also, the CPU usage still shows activity. Only 14.5 GB of the 128GB of RAM is being used. Why is there an error message saying mothur stopped working if there is still activity on the screen? The last logfile for mothur was generated 2 hours ago. It says “it took 7501 sec to check 24868 sequences from group Bathym34_1.” That’s it. What scrolls across the screen is really strange too. For example:

03:39:5023 : 3 99:55.17 % 49810.16/%3 62011561 /c3h4i5m0e1r acsh ifmoeurnads
03:39:54 0 39:53.97:%5 34 8 0 19/53.670%1 94 5c7h7i/m3e5r3a2s7 fcohuinmde r(a1

And yet again, temp files weren’t made for all my groups. This time, it looks like 7 (out of 10) were made. I will abort this run and restart with one processor. However, I have a colleague who ran a mothur analysis on this computer with no problem. His dataset was smaller than mine. This makes me think there is something wrong with my data. I redid the precluster step (the one immediately preceding the chimera step according to the Miseq SOP) when one of the earlier chimera attempts failed. I guess it didn’t help. The current run I am about to abort will be the 5th time I’ve tried this. Any guidance would be appreciated but also necessary for me to progress.