I can paste more data if desired, but in attempting to both automate and modularize the code, I have 3 batch files for analysis. Between the second, and third, I get all sorts of issues. for a workaround, I can put batch2 and batch3 in the same file, but it’s definately odd. The error seems to indicate that while running set.current, it can’t find a file, which is accurate, but is being declared in the previous batch program.
Am currently testing using the MiSeq SOP data, am happy to hand over the batch files if they will help.
=Matt
#end of 2nd logfile: mothur > get.current()
Current files saved by mothur:
accnos=stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.uchime.accnos
column=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.dist
fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta
group=stability.contigs.good.groups
list=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pds.wang.pick.tx.list
name=stability.trim.contigs.good.names
qfile=stability.trim.contigs.qual
rabund=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pds.wang.pick.tx.rabund
sabund=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pds.wang.pick.tx.sabund
shared=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pds.wang.pick.tx.shared
taxonomy=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pds.wang.pick.taxonomy
count=stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.uchime.pick.pick.count_table
processors=8
summary=stability.trim.contigs.good.unique.good.summary
file=stability.files
#beginning of 3rd batch run:
mothur > load.logfile(logfile=mothur.shared)
Extracting current files names…
/******************************************/ Running command: set.current(column=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.dist,list=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pds.wang.pick.tx.list,name=mothur.shared,rabund=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pds.wang.pick.tx.rabund,sabund=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pds.wang.pick.tx.sabund,shared=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pds.wang.pick.tx.shared) Unable to open stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pds.wang.pick.tx.shared. Trying default /usr/analysis/tools/mothur-1.36.1/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pds.wang.pick.tx.shared Unable to open /usr/analysis/tools/mothur-1.36.1/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pds.wang.pick.tx.shared Ignoring: /usr/analysis/tools/mothur-1.36.1/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pds.wang.pick.tx.shared
Using 1 processors.
Current files saved by mothur:
column=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.dist
list=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pds.wang.pick.tx.list
name=mothur.shared
rabund=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pds.wang.pick.tx.rabund
sabund=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pds.wang.pick.tx.sabund
/******************************************/