Mothur v1.47.0 trim.seqs no group or name file

1

Hello Mothur Community

I ran the following batch commands when using Mothur v 1.46

set.logfile(name=Testing123LogFile)
fastq.info(fastq=Testing123.fastq)
get.current()
trim.seqs(fasta=current, oligos=Oligos.txt, maxambig=0, maxhomop=6, bdiffs=0, pdiffs=0, minlength=265, keepfirst=285, flip=F, processors=32)
summary.seqs(fasta=current, processors=32)
unique.seqs(fasta=current)
get.current()
summary.seqs(fasta=current, processors=32)
count.seqs(name=current, group=current)
get.current()
align.seqs(fasta=current, reference=silva.v4.fasta, processors=25)
summary.seqs(fasta=current, count=current, processors=32)
get.current()
screen.seqs(fasta=current, count=current, summary=current, optimize=start-end-minlength-maxlength, criteria=95, processors=32)
summary.seqs(fasta=current, count=current, processors=32)
get.current()
filter.seqs(fasta=current, vertical=T, trump=.)
get.current()
summary.seqs(fasta=current, count=current, processors=32)
unique.seqs(fasta=current, count=current)
summary.seqs(fasta=current, count=current, processors=32)
get.current()
pre.cluster(fasta=current, count=current, diffs=2)
summary.seqs(fasta=current, count=current, processors=32)
get.current()
chimera.vsearch(fasta=current, count=current, dereplicate=t)
remove.seqs(accnos=current, fasta=current)
get.current()
summary.seqs(fasta=current, count=current, processors=32)
classify.seqs(fasta=current, count=current, template=silva.nr_v138_1.align, taxonomy=silva.nr_v138_1.tax, cutoff=80, processors=32)
get.current()
remove.lineage(fasta=current, count=current, taxonomy=current, taxon=Chloroplast-Mitochondria-unknown-Eukaryota)
summary.seqs(fasta=current, count=current, processors=32)
get.current()
summary.tax(taxonomy=current, count=current)
get.current()
rename.file(fasta=current, count=current, taxonomy=current, prefix=FinalCurationComplete)
split.abund(fasta=current, count=current, cutoff=1)
set.current(fasta=FinalCurationComplete.abund.fasta, count=FinalCurationComplete.abund.count_table)
get.current()
set.current(fasta=FinalCurationComplete.abund.fasta, count=FinalCurationComplete.abund.count_table)
get.current()
classify.seqs(fasta=current, count=current, reference=silva.nr_v138_1.align, taxonomy=silva.nr_v138_1.tax, cutoff=80 )

Now that I am using v 1.47 the count.seqs command is not recognizing my group and names files and is giving the following error message.

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image822×129 18.4 KB

When I looked at my log file a group and name file is not created after the trim.seqs command.

How can I change my commands to have a group and name file so subsequent command do not only use 1 processor since there is no group file?

Thank you for your help!

2

The 1.47.0 release does include several changes that will effect end user scripts and batch files. Some are forced and some are optional. The MiSeq_SOP MiSeq SOP reflects the changes. These are some of the highlights:

  1. Addition of mothurhome keyword. This can be used throughout mothur, but perhaps is most helpful for the make.file command.

mothur > make.file(inputdir=mothurhome, type=fastq, prefix=stability)

  1. Changes intended to move users to count tables over the name / group files. This starts with the make.contigs or trim.seqs commands. Both commands no longer output group files, instead they output count files. This will require updates to batches and scripts since there is no longer a group file outputted.

  2. Screening options are now added to make.contigs. You can still run them separately, but running them with make.contigs improves speed by avoiding reprocessing the files.

mothur > make.contigs(file=stability.files, maxambig=0, maxlength=275)

  1. Unique.seqs now outputs a count file by default.

  2. Chimeras are removed by default. You can still run the remove.seqs command without error, but it is not necessary.

  3. Blast options are removed, so any batches or scripts with Blast as an option will fail.

Try this instead:

set.logfile(name=Testing123LogFile)
fastq.info(fastq=Testing123.fastq)
get.current()
trim.seqs(fasta=current, oligos=Oligos.txt, maxambig=0, maxhomop=6, bdiffs=0, pdiffs=0, minlength=265, keepfirst=285, flip=F, processors=32)
summary.seqs(fasta=current, processors=32)
unique.seqs(fasta=current, count=current)
get.current()
summary.seqs(fasta=current, count=current, processors=32)
get.current()
…