Question for make.contigs

Commands in mothur
1

Hello,

I’m new to mothur.
I’m trying to follow MiSeq SOP tutorial but have a problem during this.

I made contig file using ‘make.contigs’, and I think that this should make ‘stability.trim.contigs.fasta’, ‘stability.contigs.count_table’, ‘stability.contigs.report’.

But my laptop made other files. see below.

image
image3840×1802 168 KB

I don’t have ‘stability.contigs.count_table’ file, so I can’t foward ‘unique.seqs’ step.

mothur > unique.seqs(fasta=stability.trim.contigs.fasta, count=stability.contigs.count_table)

Because I don’t have count_table, can’t give the count_table option.

How can I get through this?

Thanks,

Jun

2

OK. I found the reason.

I installed mothur using bioconda, and its version is 1.46.1.
I downloaded standalone version 1.47.0 and it works.

Since I’m familiar with using conda environment, is there any way to install version 1.47.0 on conda environment?

Jun

3

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