mothur

Troubleshooting - MiSeq SOP help required for get.groups

Hello,
First time using Mothur, followed the tutorial successfully up until the get.groups command.
Then instead of the 4048 sequences from the count file I only get 64:

summary.seqs(fasta=current, count=current)
Using /Users/mothur/MiSeq_SOP/stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.count_table as input file for the count parameter.
Using /Users/mothur/MiSeq_SOP/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta as input file for the fasta parameter.

Using 8 processors.

	Start	End	NBases	Ambigs	Polymer	NumSeqs

Minimum: 1 376 249 0 3 1
2.5%-tile: 1 376 252 0 3 2951
25%-tile: 1 376 252 0 4 29503
Median: 1 376 252 0 4 59005
75%-tile: 1 376 253 0 5 88507
97.5%-tile: 1 376 253 0 6 115059
Maximum: 1 376 256 0 6 118009
Mean: 1 376 252 0 4

of unique seqs: 2466

total # of seqs: 118009

It took 0 secs to summarize 118009 sequences.

Output File Names:
/Users/mothur/MiSeq_SOP/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.summary

mothur > summary.tax(taxonomy=current, count=current)
Using /Users/mothur/MiSeq_SOP/stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.count_table as input file for the count parameter.
Using /Users/mothur/MiSeq_SOP/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pds.wang.pick.taxonomy as input file for the taxonomy parameter.

It took 0 secs to create the summary file for 118009 sequences.

Output File Names:
/Users/mothur/MiSeq_SOP/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pds.wang.pick.tax.summary

mothur > get.groups(count=stability.trim.contigs.good.unique.good.filter.uniqu.precluster.denovo.vsearch.pick.pick.count_table, fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta, groups=Mock)

[NOTE]: The count file should contain only unique names, so mothur assumes your fasta, list and taxonomy files also contain only uniques.

Selected 64 sequences from your fasta file.
Selected 64 sequences from your count file.

Could anyone tell me what’s going wrong please?

Thanks in advance!

Hi there,

We had a small bug. Can you upgrade to 1.42.3 and try again?

pat

Hi, Thank you for your reply, I cant seem to get 1.42.3. I deleted the older version and I have downloaded ‘Mothur.mac_64.OSX-10.13.zip’, but when I open the mother terminal it still says 1.42.2, could you help? Thanks Natalie

Sorry - can you try again - we just reposted the correct executable this morning.

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