I tried to run my Miseq data with the command cluster to cluster my sequences into OTUs but this step always failed with no reason. Thus I would like to ask for some help for it. Before that, I have done the dist.seqs command as the Miseq SOP described. I followed almost every steps that described in the Miseq SOP except the assessing error rate because I don’t have the database for assessing it. Thus I used my fasta file from the step before the error assessing step to run the dist.seqs. The command is as below (I do have 12 processors so I used them all):
dist.seqs(fasta=file.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta, cutoff=0.20, processors=12)
It took about 3.7 days to finish it and then generated a file:
Then I used the cluster command to run the following step:
However, it always gave me something like this:
Reading matrix: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||Killed
Also, it even quitted the mothur environment by itself with no other error message.
Since it got some problems like this, I also tried several times for the alternative ways, which is the cluster.split command. What I did was:
cluster.split(fasta=file.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta, count=file.trim.contigs.good.unique.good.filter.unique.precluster.uchime.pick.pick.count_table, taxonomy=file.trim.contigs.good.unique.good.filter.unique.precluster.pick.pds.wang.pick.taxonomy, splitmethod=classify, taxlevel=4, cutoff=0.15, processors=8)
That was like what the Miseq SOP described.
After several days of running, it gave me a lot of dist files and a lot of temp files. However, it didn’t seem to stop yet and gave me hundreds of error messages like:
[ERROR]: Could not open file.trim.contigs.good.unique.good.filter.unique.precluster.uchime.pick.pick.count_table.113.temp
Then it stopped here for many days already. If I take a look of the conditions of the server, only one CPU is running mothur still, but nothing really changed anymore. (when it started to run, the 8 CPU were all running) Also, I don’t think it’s right to see so many error messages there and it seemed to stop.
I have run these two steps (cluster and cluster.split) so many times but they just didn’t work. I have been stuck in this step for more than a half month. Could someone help me and guide me what I can do for it to generate a list file?
Thank you so much!