I completed an anlaysis, that used more or less the SOP from mothur wiki.(Didn’t have the remove contaminants step, few other mods)
Then as I saw that the taxonomy contained a lot of sequences that were unclassified to the highest levels of taxonomy - I
decided to run again an analysis, but with these sequences removed.
I started from the point of SOP .final. files. Just in case I ran the classify.seqs command again.
classify.seqs(fasta=CNP.final.fasta, template=trainset6_032010.rdp.fasta, taxonomy=trainset6_032010.rdp.tax, cutoff=80, processors=7)
worked fine. Output File Names: CNP.final.rdp.taxonomy CNP.final.rdp.tax.summary
remove.lineage(taxonomy=CNP.final.rdp.taxonomy, name=CNP.final.names, group=CNP.final.groups, fasta=CNP.final.fasta, taxon=unclassified;-Bacteria;unclassified;, dups=T)
Seemed to work fine also. Output file names CNP.final.rdp.pick.taxonomy CNP.final.pick.names CNP.final.pick.fasta CNP.proovikaupa.pick.groups,
I renamed these files to format CNPU.final*, and continued with SOP. It worked fine until I had to use…
classify.otu(list=CNPU.final.an.list, name=CNPU.final.names, taxonomy=CNPU.final.taxonomy, label=0.03, cutoff=80)
It finished but with a lot of error messages …
X is not in your taxonomy file. I will not include it in the consensus.
X is represented by Y and is not in your taxonomy file. I will not include it in the consensus.
And then next…
make.shared(list=CNPU.final.tx.list, group=CNPU.final.groups, label=1)
Caused error messages - “[ERROR]: X is in your groupfile and not your listfile.” and “Please correct.Your group file contains 720345 sequences and list file contains 718362 sequences. Please correct. For a list of names that are in your group file and not in your list file, please refer to CNPU.final.tx.missing.name.”
It also seemed to freeze mothur. I had to kill the process.
Shouldn’t the remove.lineage command when done with all the fasta,names,group,taxonomy files options given keep all those files in synch?
Where did this imbalance between them creep in and how can I fix it?
It also seems weird that the wiki SOP would actually continue just as I did this time (as I mentioned on my first run I did no remove.lineage commands), should I be expecting these kind of trouble when I run SOP as written? When not then what might be the difference there?
PS. If needed I will post the entire (luckily) short run of commands (like a batch) in a post or in a link (maybe also link log-files), but I hope that maybe someone can answer and help me without me posting something so gangly up here.