Command cluster_issue

allan_santos · March 20, 2020, 10:33pm

Hey folks,
I was clustering my sequences by cluster(column=… .dist, count=… .count, cutoff=0.03) using as method the standard opti. Then, nothing happened and it take so long time to conclude (maybe due to the only one processor as default). After a long time the connection failed and I could not get it.

I’m not sure if there any previous problem regarding reference files, since I’ve align with silva and classify.seqs with rdp …

Anyone has a comment or have any idea how to conclude cluster command??

Thanks a lot,

westcott · March 23, 2020, 2:33pm

I’d be happy to help you. Could you provide me with some more information?

What version of mothur are you running? On which OS?
How much RAM do you have, and how large is the column distance matrix file?

Kindly,
Sarah

allan_santos · March 23, 2020, 8:21pm

thanks westcott

just to reply your questions

Mothur v1.43 - OS Fedora 30
Available RAM is like approximately 130 GB and I’m not sure how large is that (since I’m a beginner on Mothur) however I’ve set a distance matrix of 0.03. Sorry whether this is not the right information.

thanks once again

westcott · March 24, 2020, 2:42pm

Thanks that’s helpful. The most common cause of the cluster command failing is insufficient RAM to process the distance matrix.

How big is the distance file you are clustering, and how long did the command run before it timed out?

Did you create the distance matrix with a cutoff to reduce its size?

mothur > dist.seqs(fasta=yourFastaFile.fasta, cutoff=0.03)
mothur > cluster(column=current, count=yourCountFile.count_table, cutoff=0.03)

allan_santos · March 24, 2020, 5:40pm

thanks for reply.
Regarding insufficient RAM is a quite strange because I’ve already done it before from the same server and OS.

So, the resultant file from dist.seqs was .dist and it is ~11 GB. However I’ve applied the command default of cluster.split according MiSeq SOP with fasta, count and taxonomy files and the run was working normally but after ~20 min of operation, the network presented an error and it was aborted. Therefore when I’ve applied the same cluster.split with column=file.dist, no long happened and the connection after ~20 min failed as well

allan_santos · March 24, 2020, 5:42pm

Yeah, I’ve created them with 0.03 size

allan_santos · March 24, 2020, 7:49pm

following below the result from dist.seqs(fasta=file.fasta, cutoff=0.03),
‘‘it took 6025 secs to find distanes for 296117 sequences. 126041703 distances be low cutoff 0.03.’’
output: FILE.dist

Then, I’ve performed cluster(column=current, count=file.count, cutoff=0.03) and nothing happened over a hour

westcott · March 25, 2020, 2:39pm

“However I’ve applied the command default of cluster.split according MiSeq SOP with fasta, count and taxonomy files and the run was working normally but after ~20 min of operation, the network presented an error and it was aborted.”

Was the error from mothur or the system?
Have you tried running cluster.split in 2 parts?

The file option allows you to enter your file containing your list of column and names/count files as well as the singleton file. This file is mothur generated, when you run cluster.split() with the cluster=f parameter, see below. This can be helpful when you have a large dataset that you may be able to use all your processors for the splitting step, but have to reduce them for the cluster step due to RAM constraints. For example:

mothur > cluster.split(fasta=final.fasta, count=final.count_table, taxonomy=final.taxonomy, taxlevel=4, cluster=f) - split the dataset by taxonomy and create files needed to cluster

mothur > cluster.split(file=current, processors=4) - cluster split files

A few system questions:

The cluster commands can take quite a bit of time to run. Do you have a time limit for the network to complete the command? Do you have access to all 130G of RAM while running the command?

allan_santos · March 26, 2020, 9:09pm

Dear westcott, i still hadn’t tried that option of cluster.split in 2 different step, and it worked. thank you so much.

allan_santos · March 31, 2020, 3:58am

Dear,
I don’t know what is going on but I’ve tried apply those command you said on previous comment with the same files just changing classify.seqs and the second one didn’t work (previously I applied them from a taxonomy file originated by RDP sign and now I am trying from a GG-generating file). Have you got any idea why they don’t working? There was no a big difference neither in total/unique sequences from both database nor for distance matrix generated

thanks

allan_santos · April 1, 2020, 4:27am

Maybe I’m struggling with RAM capacity but I’m not sure about that.
I’ve got 20 samples to process. Could I split them from get.groups (using fasta, taxonomy and count) into 2 different files and then apply cluster.split for each one? After that I could merge both resultant list files into the same list file to apply another commands? because I’ve no idea how to fix it …

westcott · April 1, 2020, 5:33pm

I don’t recommend merging list files, here’s why:

Could you post the logfile of your cluster.split runs? Also, with cluster.split if it’s a RAM issue setting runsensspec=f may help.

allan_santos · April 1, 2020, 9:33pm

Right, I could imagine regarding this issue …
I just didn’t understand why I could run cluster split after classify seqs with RDP-taxonomy file but I couldn’t do that after using GG database

so, following below the logfile
mothur.1585590231.logfile
mothur.1585614711.logfile

allan_santos · April 1, 2020, 11:20pm

Linux version

Using ReadLine
mothur v.1.43.0
Last updated: 03/30/2020
by
Patrick D. Schloss

Department of Microbiology & Immunology

University of Michigan
http://www.mothur.org

When using, please cite:
Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.

Distributed under the GNU General Public License

Type 'help()' for information on the commands that are available

For questions and analysis support, please visit our forum at https://forum.mothur.org

Type 'quit()' to exit program

[NOTE]: Setting random seed to 19760620.

Interactive Mode



mothur > cluster.split(file=gaviao.precluster.pick.pick.file, processors=48)

Using 48 processors.
gaviao.precluster.pick.pick.fasta.14.dist
gaviao.precluster.pick.pick.fasta.62.dist
gaviao.precluster.pick.pick.fasta.89.dist
gaviao.precluster.pick.pick.fasta.200.dist

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

Clustering gaviao.precluster.pick.pick.fasta.176.dist

Clustering gaviao.precluster.pick.pick.fasta.200.dist

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

Clustering gaviao.precluster.pick.pick.fasta.163.dist

You did not set a cutoff, using 0.03.

Clustering gaviao.precluster.pick.pick.fasta.99.dist

You did not set a cutoff, using 0.03.

Clustering gaviao.precluster.pick.pick.fasta.47.dist

tp	tn	fp	fn	sensitivity	specificity	ppv	npv	fdr	accuracy	mcc	f1score

You did not set a cutoff, using 0.03.

tp	tn	fp	fn	sensitivity	specificity	ppv	npv	fdr	accuracy	mcc	f1score

tp	tn	fp	fn	sensitivity	specificity	ppv	npv	fdr	accuracy	mcc	f1score
0	11	0	10	0	1	0	0.52381	1	0.52381	0	0	
Clustering gaviao.precluster.pick.pick.fasta.202.dist



Clustering gaviao.precluster.pick.pick.fasta.171.dist

Clustering gaviao.precluster.pick.pick.fasta.172.dist

You did not set a cutoff, using 0.03.
6	1	0	3	0.666667	1	1	0.25	1	0.7	0.408248	
You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

Clustering gaviao.precluster.pick.pick.fasta.222.dist

Clustering gaviao.precluster.pick.pick.fasta.119.dist

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

tp	tn	fp	fn	sensitivity	specificity	ppv	npv	fdr	accuracy	mcc	f1score
0	0	0	10	
You did not set a cutoff, using 0.03.
0.8	


You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

tp	tn	fp	fn	sensitivity	specificity	ppv	npv	fdr	accuracy	mcc	f1score

You did not set a cutoff, using 0.03.

Clustering gaviao.precluster.pick.pick.fasta.145.dist

You did not set a cutoff, using 0.03.
3	22	0	3	
You did not set a cutoff, using 0.03.
5	40	0	0	
Clustering gaviao.precluster.pick.pick.fasta.185.dist

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.
0	0	
You did not set a cutoff, using 0.03.
0	
Clustering gaviao.precluster.pick.pick.fasta.97.dist

You did not set a cutoff, using 0.03.

Clustering gaviao.precluster.pick.pick.fasta.184.dist

Clustering gaviao.precluster.pick.pick.fasta.189.dist

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

Clustering gaviao.precluster.pick.pick.fasta.151.dist
0.5	1	1	0.88	1	0.892857	
Clustering gaviao.precluster.pick.pick.fasta.206.dist
0.663325	
Clustering gaviao.precluster.pick.pick.fasta.187.dist
1	1	1	1	
tp	tn	fp	fn	sensitivity	specificity	ppv	npv	fdr	accuracy	mcc	f1score
0	
You did not set a cutoff, using 0.03.

Clustering gaviao.precluster.pick.pick.fasta.213.dist

Clustering gaviao.precluster.pick.pick.fasta.188.dist

You did not set a cutoff, using 0.03.

Clustering gaviao.precluster.pick.pick.fasta.164.dist

tp	tn	fp	fn	sensitivity	specificity	ppv	npv	fdr	accuracy	mcc	f1score

You did not set a cutoff, using 0.03.

tp	tn	fp	fn	sensitivity	specificity	ppv	npv	fdr	accuracy	mcc	f1score

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

tp	tn	fp	fn	sensitivity	specificity	ppv	npv	fdr	accuracy	mcc	f1score

You did not set a cutoff, using 0.03.
0.666667	


tp	tn	fp	fn	sensitivity	specificity	ppv	npv	fdr	accuracy	mcc	f1score
1	8	0	1	
tp	tn	fp	fn	sensitivity	specificity	ppv	npv	fdr	accuracy	mcc	f1score

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.
1	1	1	1	


You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.
1	
tp	tn	fp	fn	sensitivity	specificity	ppv	npv	fdr	accuracy	mcc	f1score

tp	tn	fp	fn	sensitivity	specificity	ppv	npv	fdr	accuracy	mcc	f1score
3	1	0	2	
You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

Clustering gaviao.precluster.pick.pick.fasta.156.dist

You did not set a cutoff, using 0.03.
0.5	
You did not set a cutoff, using 0.03.
2	23	0	3	0	0.4	0	

1	
You did not set a cutoff, using 0.03.
172	176	6	52	0.6	0.767857	0.967033	1	0.966292	0.77193	1	0.966292	0.857143	0.736554	0.333333	0.855721	

1	
You did not set a cutoff, using 0.03.
1	1	
Clustering gaviao.precluster.pick.pick.fasta.130.dist

. . .

allan_santos · April 1, 2020, 11:31pm

Linux version

Using ReadLine
mothur v.1.43.0
Last updated: 03/30/2020
by
Patrick D. Schloss

Department of Microbiology & Immunology

University of Michigan
http://www.mothur.org

When using, please cite:
Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.

Distributed under the GNU General Public License

Type 'help()' for information on the commands that are available

For questions and analysis support, please visit our forum at https://forum.mothur.org

Type 'quit()' to exit program

[NOTE]: Setting random seed to 19760620.

Interactive Mode

mothur > cluster.split(fasta=current, count=current, taxonomy=current, taxlevel=4, cluster=f)
Using gaviao.precluster.denovo.vsearch.pick.pick.count_table as input file for the count parameter.
Using gaviao.precluster.pick.pick.fasta as input file for the fasta parameter.
Using gaviao.precluster.pick.gg.wang.pick.taxonomy as input file for the taxonomy parameter.

Using 48 processors.
Splitting the file...
/******************************************/
Running command: dist.seqs(fasta=gaviao.precluster.pick.pick.fasta.0.temp, processors=48, cutoff=0.03)

Using 48 processors.
/******************************************/

Sequence	Time	Num_Dists_Below_Cutoff

It took 28 secs to find distances for 11385 sequences. 1323120 distances below cutoff 0.03.


Output File Names: 
gaviao.precluster.pick.pick.fasta.0.dist

/******************************************/
Running command: dist.seqs(fasta=gaviao.precluster.pick.pick.fasta.1.temp, processors=48, cutoff=0.03)

Using 48 processors.
/******************************************/

Sequence	Time	Num_Dists_Below_Cutoff

It took 19 secs to find distances for 9145 sequences. 95337 distances below cutoff 0.03.

. . .

It took 1235 seconds to split the distance file.

Output File Names:

gaviao.precluster.pick.pick.file
gaviao.precluster.pick.pick.fasta.21.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.21.temp
gaviao.precluster.pick.pick.fasta.14.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.14.temp
gaviao.precluster.pick.pick.fasta.10.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.10.temp
gaviao.precluster.pick.pick.fasta.12.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.12.temp
gaviao.precluster.pick.pick.fasta.5.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.5.temp
gaviao.precluster.pick.pick.fasta.11.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.11.temp
gaviao.precluster.pick.pick.fasta.24.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.24.temp
gaviao.precluster.pick.pick.fasta.7.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.7.temp
gaviao.precluster.pick.pick.fasta.8.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.8.temp
gaviao.precluster.pick.pick.fasta.35.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.35.temp
gaviao.precluster.pick.pick.fasta.2.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.2.temp
gaviao.precluster.pick.pick.fasta.27.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.27.temp
gaviao.precluster.pick.pick.fasta.0.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.0.temp
gaviao.precluster.pick.pick.fasta.34.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.34.temp
gaviao.precluster.pick.pick.fasta.32.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.32.temp
gaviao.precluster.pick.pick.fasta.3.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.3.temp
gaviao.precluster.pick.pick.fasta.38.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.38.temp
gaviao.precluster.pick.pick.fasta.15.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.15.temp
gaviao.precluster.pick.pick.fasta.30.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.30.temp
gaviao.precluster.pick.pick.fasta.19.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.19.temp
gaviao.precluster.pick.pick.fasta.33.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.33.temp
gaviao.precluster.pick.pick.fasta.16.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.16.temp
gaviao.precluster.pick.pick.fasta.25.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.25.temp
gaviao.precluster.pick.pick.fasta.29.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.29.temp
gaviao.precluster.pick.pick.fasta.17.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.17.temp
gaviao.precluster.pick.pick.fasta.26.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.26.temp
gaviao.precluster.pick.pick.fasta.39.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.39.temp
gaviao.precluster.pick.pick.fasta.81.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.81.temp
gaviao.precluster.pick.pick.fasta.22.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.22.temp
gaviao.precluster.pick.pick.fasta.20.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.20.temp
gaviao.precluster.pick.pick.fasta.37.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.37.temp
gaviao.precluster.pick.pick.fasta.40.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.40.temp
gaviao.precluster.pick.pick.fasta.36.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.36.temp
gaviao.precluster.pick.pick.fasta.1.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.1.temp
gaviao.precluster.pick.pick.fasta.28.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.28.temp
gaviao.precluster.pick.pick.fasta.4.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.4.temp
gaviao.precluster.pick.pick.fasta.45.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.45.temp
gaviao.precluster.pick.pick.fasta.55.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.55.temp
gaviao.precluster.pick.pick.fasta.84.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.84.temp
gaviao.precluster.pick.pick.fasta.23.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.23.temp
gaviao.precluster.pick.pick.fasta.53.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.53.temp
gaviao.precluster.pick.pick.fasta.54.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.54.temp
gaviao.precluster.pick.pick.fasta.6.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.6.temp
gaviao.precluster.pick.pick.fasta.43.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.43.temp
gaviao.precluster.pick.pick.fasta.61.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.61.temp
gaviao.precluster.pick.pick.fasta.60.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.60.temp
gaviao.precluster.pick.pick.fasta.42.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.42.temp
gaviao.precluster.pick.pick.fasta.79.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.79.temp
gaviao.precluster.pick.pick.fasta.85.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.85.temp
gaviao.precluster.pick.pick.fasta.62.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.62.temp
gaviao.precluster.pick.pick.fasta.69.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.69.temp
gaviao.precluster.pick.pick.fasta.76.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.76.temp
gaviao.precluster.pick.pick.fasta.50.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.50.temp
gaviao.precluster.pick.pick.fasta.41.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.41.temp
gaviao.precluster.pick.pick.fasta.52.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.52.temp
gaviao.precluster.pick.pick.fasta.56.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.56.temp
gaviao.precluster.pick.pick.fasta.68.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.68.temp
gaviao.precluster.pick.pick.fasta.18.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.18.temp
gaviao.precluster.pick.pick.fasta.80.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.80.temp
gaviao.precluster.pick.pick.fasta.31.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.31.temp
gaviao.precluster.pick.pick.fasta.44.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.44.temp
gaviao.precluster.pick.pick.fasta.78.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.78.temp
gaviao.precluster.pick.pick.fasta.102.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.102.temp
gaviao.precluster.pick.pick.fasta.58.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.58.temp
gaviao.precluster.pick.pick.fasta.82.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.82.temp
gaviao.precluster.pick.pick.fasta.90.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.90.temp
gaviao.precluster.pick.pick.fasta.49.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.49.temp
gaviao.precluster.pick.pick.fasta.91.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.91.temp
gaviao.precluster.pick.pick.fasta.111.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.111.temp
gaviao.precluster.pick.pick.fasta.72.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.72.temp
gaviao.precluster.pick.pick.fasta.123.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.123.temp
gaviao.precluster.pick.pick.fasta.9.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.9.temp
gaviao.precluster.pick.pick.fasta.46.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.46.temp
gaviao.precluster.pick.pick.fasta.48.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.48.temp
gaviao.precluster.pick.pick.fasta.64.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.64.temp
gaviao.precluster.pick.pick.fasta.96.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.96.temp
gaviao.precluster.pick.pick.fasta.94.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.94.temp
gaviao.precluster.pick.pick.fasta.120.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.120.temp
gaviao.precluster.pick.pick.fasta.134.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.134.temp
gaviao.precluster.pick.pick.fasta.13.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.13.temp
gaviao.precluster.pick.pick.fasta.51.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.51.temp
gaviao.precluster.pick.pick.fasta.138.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.138.temp
gaviao.precluster.pick.pick.fasta.117.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.117.temp
gaviao.precluster.pick.pick.fasta.83.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.83.temp
gaviao.precluster.pick.pick.fasta.74.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.74.temp
gaviao.precluster.pick.pick.fasta.107.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.107.temp
gaviao.precluster.pick.pick.fasta.109.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.109.temp
gaviao.precluster.pick.pick.fasta.121.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.121.temp
gaviao.precluster.pick.pick.fasta.70.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.70.temp
gaviao.precluster.pick.pick.fasta.106.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.106.temp
gaviao.precluster.pick.pick.fasta.124.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.124.temp
gaviao.precluster.pick.pick.fasta.108.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.108.temp
gaviao.precluster.pick.pick.fasta.65.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.65.temp
gaviao.precluster.pick.pick.fasta.100.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.100.temp
gaviao.precluster.pick.pick.fasta.115.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.115.temp
gaviao.precluster.pick.pick.fasta.86.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.86.temp
gaviao.precluster.pick.pick.fasta.105.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.105.temp
gaviao.precluster.pick.pick.fasta.89.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.89.temp
gaviao.precluster.pick.pick.fasta.131.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.131.temp
gaviao.precluster.pick.pick.fasta.151.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.151.temp
gaviao.precluster.pick.pick.fasta.112.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.112.temp
gaviao.precluster.pick.pick.fasta.130.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.130.temp
gaviao.precluster.pick.pick.fasta.92.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.92.temp
gaviao.precluster.pick.pick.fasta.128.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.128.temp
gaviao.precluster.pick.pick.fasta.95.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.95.temp
gaviao.precluster.pick.pick.fasta.126.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.126.temp
gaviao.precluster.pick.pick.fasta.135.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.135.temp
gaviao.precluster.pick.pick.fasta.169.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.169.temp
gaviao.precluster.pick.pick.fasta.127.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.127.temp
gaviao.precluster.pick.pick.fasta.137.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.137.temp
gaviao.precluster.pick.pick.fasta.93.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.93.temp
gaviao.precluster.pick.pick.fasta.98.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.98.temp
gaviao.precluster.pick.pick.fasta.136.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.136.temp
gaviao.precluster.pick.pick.fasta.173.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.173.temp
gaviao.precluster.pick.pick.fasta.57.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.57.temp
gaviao.precluster.pick.pick.fasta.143.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.143.temp
gaviao.precluster.pick.pick.fasta.141.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.141.temp
gaviao.precluster.pick.pick.fasta.152.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.152.temp
gaviao.precluster.pick.pick.fasta.144.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.144.temp
gaviao.precluster.pick.pick.fasta.140.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.140.temp
gaviao.precluster.pick.pick.fasta.101.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.101.temp
gaviao.precluster.pick.pick.fasta.66.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.66.temp
gaviao.precluster.pick.pick.fasta.129.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.129.temp
gaviao.precluster.pick.pick.fasta.110.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.110.temp
gaviao.precluster.pick.pick.fasta.139.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.139.temp
gaviao.precluster.pick.pick.fasta.183.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.183.temp
gaviao.precluster.pick.pick.fasta.87.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.87.temp
gaviao.precluster.pick.pick.fasta.125.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.125.temp
gaviao.precluster.pick.pick.fasta.158.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.158.temp
gaviao.precluster.pick.pick.fasta.160.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.160.temp
gaviao.precluster.pick.pick.fasta.132.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.132.temp
gaviao.precluster.pick.pick.fasta.148.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.148.temp
gaviao.precluster.pick.pick.fasta.178.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.178.temp
gaviao.precluster.pick.pick.fasta.195.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.195.temp
gaviao.precluster.pick.pick.fasta.63.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.63.temp
gaviao.precluster.pick.pick.fasta.207.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.207.temp
gaviao.precluster.pick.pick.fasta.103.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.103.temp
gaviao.precluster.pick.pick.fasta.118.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.118.temp
gaviao.precluster.pick.pick.fasta.114.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.114.temp
gaviao.precluster.pick.pick.fasta.153.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.153.temp
gaviao.precluster.pick.pick.fasta.67.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.67.temp
gaviao.precluster.pick.pick.fasta.170.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.170.temp
gaviao.precluster.pick.pick.fasta.212.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.212.temp
gaviao.precluster.pick.pick.fasta.77.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.77.temp
gaviao.precluster.pick.pick.fasta.166.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.166.temp
gaviao.precluster.pick.pick.fasta.200.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.200.temp
gaviao.precluster.pick.pick.fasta.176.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.176.temp
gaviao.precluster.pick.pick.fasta.163.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.163.temp
gaviao.precluster.pick.pick.fasta.99.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.99.temp
gaviao.precluster.pick.pick.fasta.47.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.47.temp
gaviao.precluster.pick.pick.fasta.119.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.119.temp
gaviao.precluster.pick.pick.fasta.202.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.202.temp
gaviao.precluster.pick.pick.fasta.171.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.171.temp
gaviao.precluster.pick.pick.fasta.145.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.145.temp
gaviao.precluster.pick.pick.fasta.172.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.172.temp
gaviao.precluster.pick.pick.fasta.222.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.222.temp
gaviao.precluster.pick.pick.fasta.88.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.88.temp
gaviao.precluster.pick.pick.fasta.97.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.97.temp
gaviao.precluster.pick.pick.fasta.184.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.184.temp
gaviao.precluster.pick.pick.fasta.189.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.189.temp
gaviao.precluster.pick.pick.fasta.177.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.177.temp
gaviao.precluster.pick.pick.fasta.185.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.185.temp
gaviao.precluster.pick.pick.fasta.208.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.208.temp
gaviao.precluster.pick.pick.fasta.180.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.180.temp
gaviao.precluster.pick.pick.fasta.156.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.156.temp
gaviao.precluster.pick.pick.fasta.187.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.187.temp
gaviao.precluster.pick.pick.fasta.186.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.186.temp
gaviao.precluster.pick.pick.fasta.188.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.188.temp
gaviao.precluster.pick.pick.fasta.206.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.206.temp
gaviao.precluster.pick.pick.fasta.191.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.191.temp
gaviao.precluster.pick.pick.fasta.214.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.214.temp
gaviao.precluster.pick.pick.fasta.190.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.190.temp
gaviao.precluster.pick.pick.fasta.167.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.167.temp
gaviao.precluster.pick.pick.fasta.198.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.198.temp
gaviao.precluster.pick.pick.fasta.164.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.164.temp
gaviao.precluster.pick.pick.fasta.213.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.213.temp
gaviao.precluster.pick.pick.fasta.73.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.73.temp
gaviao.precluster.pick.pick.fasta.194.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.194.temp
gaviao.precluster.pick.pick.fasta.217.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.217.temp
gaviao.precluster.pick.pick.fasta.203.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.203.temp
gaviao.precluster.pick.pick.fasta.71.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.71.temp
gaviao.precluster.pick.pick.fasta.197.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.197.temp
gaviao.precluster.pick.pick.fasta.149.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.149.temp
gaviao.precluster.pick.pick.fasta.193.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.193.temp
gaviao.precluster.pick.pick.fasta.205.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.205.temp
gaviao.precluster.pick.pick.fasta.116.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.116.temp
gaviao.precluster.pick.pick.fasta.162.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.162.temp
gaviao.precluster.pick.pick.fasta.175.dist
gaviao.precluster.denovo.vsearch.pick.pick.count_table.175.temp


mothur > cluster.split(file=current, processors=48)
Using gaviao.precluster.pick.pick.file as input file for the file parameter.

Using 48 processors.
gaviao.precluster.pick.pick.fasta.14.dist
gaviao.precluster.pick.pick.fasta.62.dist
gaviao.precluster.pick.pick.fasta.89.dist
gaviao.precluster.pick.pick.fasta.200.dist

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

You did not set a cutoff, using 0.03.

Clustering gaviao.precluster.pick.pick.fasta.97.dist

Clustering gaviao.precluster.pick.pick.fasta.200.dist

Clustering gaviao.precluster.pick.pick.fasta.177.dist

Clustering gaviao.precluster.pick.pick.fasta.172.dist

Clustering gaviao.precluster.pick.pick.fasta.176.dist

Clustering gaviao.precluster.pick.pick.fasta.202.dist

Clustering gaviao.precluster.pick.pick.fasta.99.dist

Clustering gaviao.precluster.pick.pick.fasta.156.dist

Clustering gaviao.precluster.pick.pick.fasta.167.dist

Clustering gaviao.precluster.pick.pick.fasta.47.dist

Clustering gaviao.precluster.pick.pick.fasta.191.dist

Clustering gaviao.precluster.pick.pick.fasta.222.dist

Clustering gaviao.precluster.pick.pick.fasta.187.dist

Clustering gaviao.precluster.pick.pick.fasta.208.dist

Clustering gaviao.precluster.pick.pick.fasta.185.dist

Clustering gaviao.precluster.pick.pick.fasta.188.dist

Clustering gaviao.precluster.pick.pick.fasta.164.dist

Clustering gaviao.precluster.pick.pick.fasta.73.dist

Clustering gaviao.precluster.pick.pick.fasta.171.dist

Clustering gaviao.precluster.pick.pick.fasta.71.dist

Clustering gaviao.precluster.pick.pick.fasta.119.dist

Clustering gaviao.precluster.pick.pick.fasta.162.dist

Clustering gaviao.precluster.pick.pick.fasta.214.dist

Clustering gaviao.precluster.pick.pick.fasta.116.dist

Clustering gaviao.precluster.pick.pick.fasta.213.dist

Clustering gaviao.precluster.pick.pick.fasta.149.dist

Clustering gaviao.precluster.pick.pick.fasta.205.dist

Clustering gaviao.precluster.pick.pick.fasta.145.dist

Clustering gaviao.precluster.pick.pick.fasta.166.dist

Clustering gaviao.precluster.pick.pick.fasta.175.dist

Clustering gaviao.precluster.pick.pick.fasta.163.dist

Clustering gaviao.precluster.pick.pick.fasta.190.dist

Clustering gaviao.precluster.pick.pick.fasta.217.dist

Clustering gaviao.precluster.pick.pick.fasta.189.dist

Clustering gaviao.precluster.pick.pick.fasta.203.dist

Clustering gaviao.precluster.pick.pick.fasta.184.dist

Clustering gaviao.precluster.pick.pick.fasta.193.dist

Clustering gaviao.precluster.pick.pick.fasta.206.dist

Clustering gaviao.precluster.pick.pick.fasta.198.dist

Clustering gaviao.precluster.pick.pick.fasta.180.dist

Clustering gaviao.precluster.pick.pick.fasta.88.dist

Clustering gaviao.precluster.pick.pick.fasta.170.dist

Clustering gaviao.precluster.pick.pick.fasta.194.dist

Clustering gaviao.precluster.pick.pick.fasta.212.dist

Clustering gaviao.precluster.pick.pick.fasta.186.dist

Clustering gaviao.precluster.pick.pick.fasta.197.dist

Clustering gaviao.precluster.pick.pick.fasta.67.dist

tp	tn	fp	fn	sensitivity	specificity	ppv	npv	fdr	accuracy	mcc	f1score

tp	tn	fp	fn	sensitivity	specificity	ppv	npv	fdr	accuracy	mcc	f1score

tp	tn	fp	fn	sensitivity	specificity	ppv	npv	fdr	accuracy	mcc	f1score

allan_santos · April 2, 2020, 8:07pm

I got it using runsensspec=f … what does it mean?
thanks a lot

westcott · April 6, 2020, 7:33pm

The runsensspec variable is used to indicate you want mothur to run a sensitivity and specificity analysis on the complete list results. You can also run this analysis separately with the sens.spec command.

With larger datasets, you may not have enough memory (RAM) to fit the complete distance matrix into memory which is required for the sens.spec analysis. To resolve the memory issue, we made the sens.spec analysis optional. By setting runsensspec=false, mothur will skip the sens.spec analysis step.

LenaPa · November 28, 2021, 6:04pm

Hello,

I’m dealing with the same issue,

I’m trying to analyse 16S rRNA gene sequence data of 46 wine grapes and wine samples (92 sequences),

In the pipeline I use there is the following command:
cluster(column=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.dist, count=stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.count_table)

It has already worked in other samples (olives and soil) but in the dataset I’m running now It doesn’t !

Τhe problem is that it gets stuck on this command and even if I leave the program open for hours it doesn’t work,

Any ideas??

Thank you

Topic		Replies	Views
Issues with cluster command Commands in mothur	5	4390	December 19, 2012
Segmentation fault when clustering a 1.44 GB dist file mothur bugs	5	135441	November 14, 2009
memory differences between cluster.classic and cluster? mothur bugs	1	2731	October 17, 2012
what's the problem? mothur bugs	1	2609	September 24, 2012
Facing clustering issue Commands in mothur	10	291	September 19, 2022

Command cluster_issue

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