cluster.split fails to write list,rabund,sabund when used after the set.dir(output=) command.
From the logfile:
mothur v.1.18.1
Last updated: 4/15/2011
…
mothur > cluster.split(fasta=amazon.fasta, name=amazon1.names, taxonomy=amazon.silva.taxonomy, splitmethod=fasta)
Splitting the file…
0 0
97 0
Output File Name:
amazon.fasta.0.dist
It took 0 to calculate the distances for 98 sequences.
It took 1 seconds to split the distance file.
Reading amazon.fasta.0.dist
********************###########
Reading matrix: ||||||||||||||||||||||||||||||||||||||||||||||||||||
Clustering amazon.fasta.0.dist
It took 0 seconds to cluster
Merging the clustered files…
It took 0 seconds to merge.
Output File Names:
amazon.dist
amazon.an.sabund
amazon.an.rabund
amazon.an.list
mothur > system(ls -ltr | tail -5)
-rw-r–r-- 1 jj jj 99186 May 9 09:20 amazon.dist
-rw-r–r-- 1 jj jj 5007 May 9 09:20 amazon.an.sabund
-rw-r–r-- 1 jj jj 5544 May 9 09:20 amazon.an.rabund
-rw-r–r-- 1 jj jj 37525 May 9 09:20 amazon.an.list
-rw-r–r-- 1 jj jj 1414 May 9 09:21 mothur.1304950827.logfile
mothur > system(mkdir tmp)
mothur > set.dir(output=tmp)
Mothur’s directories:
outputDir=tmp/
mothur > cluster.split(fasta=amazon.fasta, name=amazon1.names, taxonomy=amazon.silva.taxonomy, splitmethod=fasta)
Splitting the file…
0 0
97 0
Output File Name:
amazon.fasta.0.dist
It took 0 to calculate the distances for 98 sequences.
It took 0 seconds to split the distance file.
It took 0 seconds to cluster
Merging the clustered files…
It took 0 seconds to merge.
Output File Names:
tmp/amazon.dist
tmp/amazon…sabund
tmp/amazon…rabund
tmp/amazon…list
mothur > system(ls -ltr tmp | tail -5)
total 0
-rw-r–r-- 1 jj jj 0 May 9 09:22 amazon…sabund
-rw-r–r-- 1 jj jj 0 May 9 09:22 amazon…rabund
-rw-r–r-- 1 jj jj 0 May 9 09:22 amazon…list
mothur > system(ls -ltr | tail -5)
-rw-r–r-- 1 jj jj 37525 May 9 09:20 amazon.an.list
drwxr-xr-x 5 jj jj 170 May 9 09:22 tmp
-rw-r–r-- 1 jj jj 1372 May 9 09:22 amazon1.names.0.temp
-rw-r–r-- 1 jj jj 99187 May 9 09:22 amazon.fasta.0.dist
-rw-r–r-- 1 jj jj 2054 May 9 09:22 mothur.1304950827.logfile