When we run chimera.vsearch(), if it doesn’t find any chimeras it generates an empty accnos file. Downstream, when we run set.current(), Mothur aborts when it encounters this empty file. Is there a way to prevent this?
mothur > set.current(processors=48, fasta=/home/output9/hope.good.unique.pcr.unique.fasta, group=/home/output9/hope.good.pcr.groups_new, oligos=/home/amr.oligos, contigsreport=/home/output9/Undetermined.paired_old.contigs.report, summary=/home/output9/hope.good.unique.pcr.unique.summary, accnos=/home/output9/hope.good.unique.pcr.unique.denovo.vsearch.accnos, name=/home/output9/hope.good.unique.pcr.names, count=/home/output9/hope.good.unique.pcr.denovo.vsearch.pick.count_table)
[ERROR]: /home/output9/hope.good.unique.pcr.unique.denovo.vsearch.accnos is blank, aborting.
Point to the previous accnos file in the folder instead of to the last one?
That would be an option, except I am actually using a Python wrapper for Mothur (mothur-py) and it stubbornly calls set.current() every time a Mothur command is run. So even if I choose to point to a previous accnos file, it’s still going to run set.current() before I do that.
While working interactively with Mothur, I know I have seen a message that says something like,
“Accnos is file is empty. Deleting it.”
I can’t remember what method I was running, and I can’t find the word “empty” in any of my Mothur logfiles. Does anyone know what methods employ the action of deleting a file when it is empty? This would solve my problem, if all methods did this.
I cannot help with that then : )
What is the advantage of the package versus running mothur natively?
It’s easy to use it in a pipeline (QC workflow of amplicon data).
The set.current command does not allow you to set file types to blank files. This is by design since a blank file downstream will cause errors.
The chimera.vsearch command will create a blank accnos file if no reads are found to be chimeric. Previously we had removed all blank output files, but changed this for the chimera commands by user request.
Thanks, Sarah. We fixed the problem in our pipeline by manually deleting the accnos file if it is empty.
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