mothur

Blank File Returned for Cluster.split

Based on Sarah Westcott’s suggestion to my question on October 4th, I ran cluster.split command in two parts following https://mothur.org/wiki/Cluster.split#file.

cluster.split(fasta=AmphStability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.fasta,count=AmphStability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.pick.count_table,taxonomy=AmphStability.trim.contigs.good.unique.good.filter.unique.precluster.pick.nr_v128.wang.pick.pick.taxonomy, splitmethod=classify, taxlevel=4, cutoff=0.03,processors=8, cluster=f)

cluster.split(file=current, processors=8)

It ran and generated a number of .dist files (i.e. AmphStability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.fasta.3.dist) and temp count files (i.e. AmphStability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.pick.count_table.3.temp) and a AmphStability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.file; however when it got to the second cluster.split file it returned this error:

mothur > cluster.split(file=current, processors=8)
Using AmphStability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.file as input file for the file parameter.

Using 8 processors.
[ERROR]: AmphStability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.file is blank. Please correct.
[ERROR]: unknown file type. Are the files in column 2 of the file name files or count files? Please change unknown to name or count.




Detected 2 [ERROR] messages, please review.




srun: error: UV00000395-P002: task 0: Exited with exit code 1
Mothur Run Failed with exit code 1 !!!
Cleaning up directory

Any thoughts or suggestions???

Could you try setting the inputdir parameter to the location of the dist and count files?

mothur > cluster.split(file=current, processors=8, inputdir=locationOfDistFilesCreatedBySplit)

This topic was automatically closed 10 days after the last reply. New replies are no longer allowed.