Hi,
I am not sure if the following are issues too specific to be discussed here. I am running the 454 SOP from the mothur website in Mothur v.1.35.0 installed in the High Performing Computer center of my university. Here are two issues I have been encountering:
(1) In my mothur log file everything looks okay, except that when commands were written to use more than one processor, for example, if I write “processors=8”, then the command appears eight times in the mothur log file; I usually run Mothur in one single computer node, so I am not sure if a command appearing eight times in the log file is normal or whether this is a sign that in instead of using 8 processors, the computer is running the command eight times, which defeats the purpose of using more than one processor;
(2) The HPC facility uses PBS to manage jobs and after a job is complete I get a log file with the output of my commands and and an error file that should be blank if everything worked well. However, when running mothur, I usually get the following in my error file:
00:00 19Mb 0.1% Reading MERGED.shhh.trim.unique.good.filter.unique.precluster.temp
00:00 19Mb 0.1% Reading MERGED.shhh.trim.unique.good.filter.unique.precluster.temp
WARNING: Ignoring gaps in FASTA file ‘MERGED.shhh.trim.unique.good.filter.unique.precluster.temp’
00:00 19Mb 100.0% Reading MERGED.shhh.trim.unique.good.filter.unique.precluster.temp
00:00 19Mb 125 sequences
00:00 2.5Mb 0.8% 0/0 chimeras found (0.0%)
00:00 2.9Mb 100.0% 0/124 chimeras found (0.0%)
00:00 19Mb 0.1% Reading MERGED.shhh.trim.unique.good.filter.unique.precluster.temp
00:00 19Mb 0.1% Reading MERGED.shhh.trim.unique.good.filter.unique.precluster.temp
WARNING: Ignoring gaps in FASTA file ‘MERGED.shhh.trim.unique.good.filter.unique.precluster.temp’
00:00 19Mb 100.0% Reading MERGED.shhh.trim.unique.good.filter.unique.precluster.temp
00:00 19Mb 37 sequences
00:00 2.5Mb 2.7% 0/0 chimeras found (0.0%)
00:00 2.9Mb 100.0% 0/36 chimeras found (0.0%)
Is this something I should be concerned? I am not sure how to interpret these lines, but I am concerned on how reliable my results have been. I heard that sometimes the supercomputer may not know where to send temporary files and your data might be lost in this process. But my computer knowledge is very limited and I am not sure if this is the case. If anybody has had this experience and could share your interpretation/solutions I would really appreciate! Thank you in advance!