Mothur Linux auto error code in syslog

mothur bugs
1

Hi,

I’ve recently switched to using a Linux OS on my desktop but I’m experiencing issues with error messages.
I’ve previously used Mothur to perform 16S analysis with a nice handy batch file based on the Mothur MiSeq SOP, which I tweek slightly for each processing run. This worked fine both on Mothur for Windows and Mac. Since the switch though, I’ve noticed the programme is printing loads of error messages in to the syslog directory (see below):

Oct 24 15:54:54 c18000517-lnx gnome-session[2394]: mothur >
Oct 24 15:54:54 c18000517-lnx gnome-session[2394]: [ERROR]: You are missing (
Oct 24 15:54:54 c18000517-lnx gnome-session[2394]: [ERROR]: Invalid.
Oct 24 15:54:54 c18000517-lnx gnome-session[2394]: mothur >
Oct 24 15:54:54 c18000517-lnx gnome-session[2394]: [ERROR]: You are missing (
Oct 24 15:54:54 c18000517-lnx gnome-session[2394]: [ERROR]: Invalid.
Oct 24 15:54:54 c18000517-lnx gnome-session[2394]: mothur >
Oct 24 15:54:54 c18000517-lnx gnome-session[2394]: [ERROR]: You are missing (
Oct 24 15:54:54 c18000517-lnx gnome-session[2394]: [ERROR]: Invalid.

What is so surprising is that the commands are running fine in the Mothur terminal and the outputs are all printing in to the working directory I am both running Mothur and retrieving .fastq files etc. from (an external HD)
I wonder if these issues I have been experiencing are because my home directory is based in the institutional network? Have any other Mothur Linux users experienced similar problems or is this just an issue with this specific instance of Mothur?

Any help will be massively appreciated.

Thanks!
Greg

2

Can you post what your batch file looks like and the exact command you are running from the command prompt in linux?

3

Pat,
Thanks for replying! Batch file included below:

_make.contigs(file=stability.file.txt, processors=4)_

_ summary.seqs(fasta=stability.file.trim.contigs.fasta)_
_ screen.seqs(fasta=stability.file.trim.contigs.fasta, group=stability.file.contigs.groups, maxambig=0, maxlength=275)_
_ summary.seqs()_
_ unique.seqs(fasta=stability.file.trim.contigs.good.fasta)_
_ count.seqs(name=stability.file.trim.contigs.good.names, group=stability.file.contigs.good.groups, processors=1)_
_ summary.seqs(count=stability.file.trim.contigs.good.count_table, processors=4)_
_ align.seqs(fasta=stability.file.trim.contigs.good.unique.fasta, reference=silva.v4.fasta)_
_ summary.seqs(fasta=stability.file.trim.contigs.good.unique.align, count=stability.file.trim.contigs.good.count_table, processors=8)_
_ screen.seqs(fasta=stability.file.trim.contigs.good.unique.align, count=stability.file.trim.contigs.good.count_table, summary=stability.file.trim.contigs.good.unique.summary, start=1968, end=11550, maxhomop=8)_
_ summary.seqs(fasta=current, count=current)_
_ filter.seqs(fasta=stability.file.trim.contigs.good.unique.good.align, vertical=T, trump=.)_
_ unique.seqs(fasta=stability.file.trim.contigs.good.unique.good.filter.fasta, count=stability.file.trim.contigs.good.good.count_table)_
_ pre.cluster(fasta=stability.file.trim.contigs.good.unique.good.filter.unique.fasta, count=stability.file.trim.contigs.good.unique.good.filter.count_table, diffs=2)_
_ chimera.uchime(fasta=stability.file.trim.contigs.good.unique.good.filter.unique.precluster.fasta, count=stability.file.trim.contigs.good.unique.good.filter.unique.precluster.count_table, dereplicate=t, processors=1)_
_ remove.seqs(fasta=stability.file.trim.contigs.good.unique.good.filter.unique.precluster.fasta, accnos=stability.file.trim.contigs.good.unique.good.filter.unique.precluster.denovo.uchime.accnos)_
_ summary.seqs(fasta=current, count=current, processors=4)_
_ classify.seqs(fasta=stability.file.trim.contigs.good.unique.good.filter.unique.precluster.pick.fasta, count=stability.file.trim.contigs.good.unique.good.filter.unique.precluster.denovo.uchime.pick.count_table, reference=silva.nr_v128.pcr.align, taxonomy=silva.nr_v128.tax, cutoff=70)_
_ remove.lineage(fasta=stability.file.trim.contigs.good.unique.good.filter.unique.precluster.pick.fasta, count=stability.file.trim.contigs.good.unique.good.filter.unique.precluster.denovo.uchime.pick.count_table, taxonomy=stability.file.trim.contigs.good.unique.good.filter.unique.precluster.pick.pds.wang.taxonomy, taxon=Chloroplast-Mitochondria-unknown-Archaea-Eukaryota)_
_ dist.seqs(fasta=stability.file.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta, output=lt, processors=8)_
_ summary.seqs(fasta=stability.file.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta, count=stability.file.trim.contigs.good.unique.good.filter.unique.precluster.denovo.uchime.pick.pick.count_table, processors=8)_
_ cluster.split(column=stability.file.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.dist, count=stability.file.trim.contigs.good.unique.good.filter.unique.precluster.denovo.uchime.pick.pick.count_table, cluster=f, method=opti, processors=8)_
_ cluster.split(file=stability.file.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.file, processors=4)_
_ make.shared(list=stability.file.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.opti_mcc.unique_list.list, count=stability.file.trim.contigs.good.unique.good.filter.unique.precluster.denovo.uchime.pick.pick.count_table, label=0.03)_
_ classify.otu(list=stability.file.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.opti_mcc.unique_list.list, count=stability.file.trim.contigs.good.unique.good.filter.unique.precluster.denovo.uchime.pick.pick.count_table, taxonomy=stability.file.trim.contigs.good.unique.good.filter.unique.precluster.pick.pds.wang.pick.taxonomy, label=0.03)_
_ count.groups(shared=stability.file.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.opti_mcc.unique_list.shared)_
_ make.biom(shared=stability.file.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.opti_mcc.unique_list.shared, constaxonomy=stability.file.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.opti_mcc.unique_list.0.03.cons.taxonomy)_

I copy and paste the commands from my plain text batchfile (opened in gedit) direct in to the mothur terminal. Judging from the logfiles printed to my working directory the errors appear to happen sporadically, in between commands (eg below with errors highlighted in bold):

mothur > align.seqs(fasta=stability.trim.contigs.good.unique.fasta, reference=silva.nr_v128.align)

Using 8 processors.

Reading in the silva.nr_v128.align template sequences… DONE.
It took 151 to read 190661 sequences.
Aligning sequences from stability.trim.contigs.good.unique.fasta …
It took 1051 secs to align 163289 sequences.

[WARNING]: 2 of your sequences generated alignments that eliminated too many bases, a list is provided in stability.trim.contigs.good.unique.flip.accnos.
[NOTE]: 2 of your sequences were reversed to produce a better alignment.

_Output File Names: _
stability.trim.contigs.good.unique.align
stability.trim.contigs.good.unique.align.report
stability.trim.contigs.good.unique.flip.accnos

_mothur > _

_mothur > _
[ERROR]: You are missing (
[ERROR]: Invalid.

_mothur > _

mothur > summary.seqs(fasta=stability.trim.contigs.good.unique.align, count=stability.trim.contigs.good.count_table, processors=8)

Using 8 processors.

_ Start End NBases Ambigs Polymer NumSeqs_
Minimum: 11897 22518 26 0 3 1
2.5%-tile: 13862 23444 252 0 3 53564
25%-tile: 13862 23444 253 0 4 535633
Median: 13862 23444 253 0 5 1071266
75%-tile: 13862 23444 253 0 5 1606899
97.5%-tile: 13862 23444 253 0 6 2088968
Maximum: 43020 43116 271 0 9 2142531
Mean: 13862 23444 252 0 4
# of unique seqs: 163289
total # of seqs: 2142531

It took 619 secs to summarize 2142531 sequences.

Output File Names:
_ stability.trim.contigs.good.unique.summary_

**mothur > **

**mothur > **
[ERROR]: You are missing (
[ERROR]: Invalid.

mothur >

What I really don’t understand though is why the errors are printed to this other directory (syslog)? Syslog is neither where the mothur terminal was launched from, nor has it been specifically set as a working directory.

Appreciate the help.
Greg

4

Just to clarify - the lines of my batchfile aren’t flanked by underscores. That is an artifact of me trying to insert the entire pasted file as preformatted text.

Apologies
Greg

5

If you hit enter at the mothur prompt, you will get the error messages you are seeing. This is more of a nuisance than a real problem.

You’re saying that you run mothur from your home directory and that mothur*logfile is outputted to syslog? Are you doing any set.dir commands in mothur? What is the path to the mothur executable?

6

I thought that might be the case. Weird that copying from gedit adds extra returns that aren’t incorporated when copying from text editor or notepad on windows or mac…

After the first instance of this happening I was using set.dir to direct outputs to my desired location (also the path to mothur.exe) with command:

set.dir(output=/media/jmhr5/GYD3data/MW_collab/seqs)

It’s confusing because all the files I would usually expect to see as outputs (.logfile, cons.taxonomy, biom, etc.) were all output exactly where I wanted but these error messages still seem to fill up the syslog file.