Cluster and the output files

Hi, everyone:

I am processing an archaeal community dataset generated by Miseq. Things went fairly well with the SOP to the end (I just skipped the error estimation, so the file name only contains two "pick"s.). However, when I was taking a look of the Chao index, it showed really really high values, which are not quite possible. I tried to find the reason and I figured out that after the cluster step, all the processing was only based on the unique sequences, not based on the 0.03 ones. I traced back to the cluster file and found maybe it’s the problem here since the steps afterwards told me that there is only the lable of unique (I opened the list files, and it is like that as well). I looked into the page of cluster, and found that this command should have generated three files, but I only got the list file. I wonder if the process didn’t finish or something wrong with my processing so I cannot get the label 0.03 counts.

Here I listed the relative command I did. If other commands are needed and asked for diagnosis, I will post them as well.

cluster(column=file.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.dist, count=file.trim.contigs.good.unique.good.filter.unique.precluster.uchime.pick.pick.count_table)

Reading matrix: |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||

unique 56016 108538 6947 1963 822 471 280 161 153 115 77 71 51 49 47 48 41 27 13 11 14 15 14 8 18 12 9 13 10 1
changed cutoff to 0.006993

Output File Names:

The following commands are here:

make.shared(, count=/Users/CYL/Documents/mothur/ARC_2014.trim.contigs.good.unique.good.filter.unique.precluster.uchime.pick.pick.count_table, label=0.03)

Output File Names:
and all the individual rabund files

classify.otu(, count=file.trim.contigs.good.unique.good.filter.unique.precluster.uchime.pick.pick.count_table,, label=0.03)

reftaxonomy is not required, but if given will keep the rankIDs in the summary file static. (From this step, it also showed that I don’t have the lable 0.03)
Your file does not include the label 0.03. I will use unique.
unique 120330

Output File Names:

Thank you very much!!!

Have a nice day!


Thank you!!!