Make.contigs doesn't create stability.contigs.count_table

mothur bugs
1

Hi,

I couldn’t find stability.contigs.count_table to run commands like summary.seqs(fasta=stability.trim.contigs.fasta, count=stability.contigs.count_table). Please see attached the files make.contigs created. I didn’t have this problem earlier when I used Mothur. I tried various versions but none output count_table from make.contigs. Is it Ok to proceed?

image

2

Hi,

I suspect you have an older version of mothur. If you open that mothur logfile that’s at the top you’ll find the version number towards the top. This was a change that was made in recent versions of mothur.

Pat

3

Yeah, I thought so…but I used mothur/1.45.3 still the same result. I run Mothur from our supercomputer institute, and last year it worked fine.

4

Hi Pat,

Thank you for your response! We have updated the software to 1.48.0 and now I have the make.contigs function create all the output files as expected.

Output File Names:
stability.trim.contigs.fasta
stability.scrap.contigs.fasta
stability.contigs_report
stability.contigs.count_table

5

Hi Pat,

Hopefully one last question, I am running 12 samples to set up Mothur to run some clinical experiment samples. I followed the Miseq SOP. Could you tell me why the dist.seqs(fasta=final.fasta, cutoff=0.03) is taking ever to finish?Is it expected or am I doing something stupid? I am running it on a supercomputer using 900 GB of memory.

Thank you,
Sithara

6

I suspect you have a ton of sequences. Are you sequencing the V4 region or another region? Regardless, you should probably checkout using cluster.split instead. You can see how to use this in the mothur MiSeq SOP.

Pat

7

Ok Thank you! I think I have about 11 million seqs. I will try cluster.split and see how it works.

summary.seqs(fasta=current, count=current)
./stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.count_table ./stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.fasta

Using 32 processors.

	Start	End	NBases	Ambigs	Polymer	NumSeqs

Minimum: 1 340 173 0 3 1
2.5%-tile: 1 340 180 0 4 283720
25%-tile: 1 340 180 0 6 2837191
Median: 1 340 180 0 6 5674382
75%-tile: 1 340 180 0 6 8511572
97.5%-tile: 1 340 180 4 6 11065043
Maximum: 2 340 185 27 8 11348762
Mean: 1 340 179 0 5

of unique seqs: 412530

total # of seqs: 11348762

8

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