Using V19 RDP Reference File with Galaxy Tutorial

[jmkagle]

I’m fairly new to this, so I’m sorry if this is a newbie question.

I tried to download and use the Version 19 16S rRNA Reference (PDS) instead of the older provided taxonomy files in the Galaxy 16S Microbial Analysis with mothur (extended) tutorial (Hands-on: 16S Microbial Analysis with mothur (extended) / 16S Microbial Analysis with mothur (extended) / Microbiome) and the Classify.seqs step failed. At first it wouldn’t run because the file type was wrong, but I fixed that (I think). Is there something else I need to do to get Classify.seqs to work with the new reference files in the tutorial?

I got the following error for the failed taxonomy file:
/corral4/main/jobs/058/867/58867357/tool_script.sh: line 23: 11594 Done echo ‘classify.seqs( fasta=fasta.dat, reference=alignment.template.dat, taxonomy=tax.taxonomy.dat, method=wang, ksize=8, iters=100, cutoff=80, probs=true, count=count.dat, relabund=false, output=simple, printlevel=-1, processors=’${GALAXY_SLOTS:-8}’ )’
11595 | sed ‘s/ //g’
11596 Segmentation fault (core dumped) | ./mothur
11597 | tee mothur.out.log

[pschloss]

Hi there,

It looks like the galaxy folks might be doing something to the files to generate that type of code. I’d suggest following up wiht them. I really don’t know much about how galaxy works.

Sorry!
Pat