GI-cluster R clustering taking a long time

[rorycave]

I am trying to use your software GI-cluster to help identify genomic Islands in my genomes. I notice when it runs the r program it get stuck on “cluster assignment” for a long time.

Can you help me?

[icelu]

Could you please send me the running information of the program?

On 19 Dec 2018, at 6:16 PM, rorycave notifications@github.com wrote:

I am trying to use your software GI-cluster to help identify genomic Islands in my genomes. I notice when it runs the r program it get stuck on “cluster assignment” for a long time.

Can you help me?

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[rorycave]

Rorys-MacBook-Pro:GI_Cluster rorycave$ sudo ./GI-Cluster.sh -s /Users/rorycave/GI_Cluster-master/GI_Cluster -o /Users/rorycave/GI_Cluster-master/GI_Cluster/sepi -n 716 -m window -p prodigal Password: ########################################## Running GI-Cluster for a complete genome Running GI-Cluster with gene predictions ########################################## Predicting genes with prodigal Computing known features related to genomic islands in the unit of genes ########################################## Analyzing GC Content for each gene/ORF ########################################## Analyzing codon usage for each gene/ORF ########################################## Analyzing k-mer frequency for each gene/ORF ########################################## Predicting ncRNA ########################################## Identifying mobility-related genes ########################################## Identifying phage-related genes ########################################## Identifying virulence factors ########################################## Identifying antibiotic resistance genes ########################################## Identifying novel genes ########################################## Merging features for each gene/ORF ########################################## Getting genome segements ########################################## Getting features of each genome segement ########################################## Running consensus clustering on the feature matrix Using features related to sequence compostion and gene functions Loading required package: R.utils Loading required package: R.oo Loading required package: R.methodsS3 R.methodsS3 v1.7.1 (2016-02-15) successfully loaded. See ?R.methodsS3 for help. R.oo v1.22.0 (2018-04-21) successfully loaded. See ?R.oo for help.

Attaching package: ‘R.oo’

The following objects are masked from ‘package:methods’:

getClasses, getMethods

The following objects are masked from ‘package:base’:

attach, detach, gc, load, save

R.utils v2.7.0 successfully loaded. See ?R.utils for help.

Attaching package: ‘R.utils’

The following object is masked from ‘package:utils’:

timestamp

The following objects are masked from ‘package:base’:

cat, commandArgs, getOption, inherits, isOpen, parse, warnings

Loading required package: optparse Loading required package: Ckmeans.1d.dp Loading required package: mclust Package 'mclust' version 5.4.2 Type 'citation("mclust")' for citing this R package in publications. Loading required package: fpc Loading required package: cluster Loading required package: apcluster

Attaching package: ‘apcluster’

The following object is masked from ‘package:stats’:

heatmap

Loading required package: kernlab Loading required package: clues cluster assignment: cluster assignment: cluster assignment: cluster assignment: cluster assignment: cluster assignment: cluster assignment: cluster assignment: cluster assignment: cluster assignment: cluster assignment: cluster assignment: cluster assignment: cluster assignment: cluster assignment: cluster assignment: cluster assignment: cluster assignment: cluster assignment: cluster assignment: cluster assignment: cluster assignment: cluster assignment: cluster assignment: cluster assignment: cluster assignment: cluster assignment: cluster assignment: cluster assignment: cluster assignment: cluster assignment: cluster assignment: cluster assignment: cluster assignment: cluster assignment:

On 19 Dec 2018, at 13:02, Bingxin Lu notifications@github.com wrote:

Could you please send me the running information of the program?

On 19 Dec 2018, at 6:16 PM, rorycave notifications@github.com wrote:

I am trying to use your software GI-cluster to help identify genomic Islands in my genomes. I notice when it runs the r program it get stuck on “cluster assignment” for a long time.

Can you help me?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/icelu/GI_Cluster/issues/1, or mute the thread https://github.com/notifications/unsubscribe-auth/ABCHIH_N66DDk8LGlRceLX7Rbkozltwqks5u6hIQgaJpZM4ZZ7jA.

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[icelu]

Could you please check the input and output files to see if there are any problems, particularly the file ended with feature.multi.percentage?

[rorycave]

I can’t see any problem with input files or feature.multi.percentage. I did find that the query2subject.csv, hits.csv, self.csv files were empty.

Would that cause any problems?

Thanks,

Rory

On 20 Dec 2018, at 01:50, Bingxin Lu notifications@github.com wrote:

feature.multi.percentage

[rorycave]

And the file .respeek was empty.

On 20 Dec 2018, at 01:50, Bingxin Lu notifications@github.com wrote:

feature.multi.percentage