Hi,
I have a large dataset, so I used the cluster.split
command in two steps:
- First Step:
cluster.split(fasta=.fasta, count=.count_table, taxonomy=final.taxonomy, taxlevel=4, cluster=f)
Output File Names: Finding singletons (ignore ‘Removing group’ messages):
- mydata.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.file
- mydata.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.0.disttemp
- mydata.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.0.count.temp
Also, note that these temporary files are not in my working directory and not in my temporary files.
- Second Step:
cluster.split(file=mydata.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.file, count=.count_table)
It was using the temp dist files that created in the previous step and succesfully did the clustering and create the output.
Output file is opti_mcc.list
The problem is, I did not get the dist file from the first step. I only had temp dist files and did not merge those files to create the final dist file. I also noticed those files disappered.
This is a warning that I received in my cluster run (second step)
It took 550020 seconds to cluster. Merging the clustered files… It took 53 seconds to merge.
[WARNING]: Cannot run sens.spec analysis without a column file; skipping.
Output File Names:
mydata.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.opti_mcc.list
How can I get the distance file?
Thanks