Error in hclust(d = dist(x = fegenie.scaled))

[manik-123]

Error in hclust(d = dist(x = fegenie.scaled)) :
NA/NaN/Inf in foreign function call (arg 10)
Calls: as.dendrogram -> hclust
Execution halted

[seanmcallister]

This error is still occurring:

(fegenie) sean-mini-server:2022_PCC_ManuscriptWork sean_server$ FeGenie.py -bin_dir bins -bin_ext faa -out heme_FeGenie_ALLPROTEINS -t 4 --orfs --all_results --makeplots
checking arguments
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All required arguments provided!

starting main pipeline...

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Looking for following iron-related functional category: iron_aquisition-heme_oxygenase
analyzing All_proteins_fullannotation.faa: 100%   

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Looking for following iron-related functional category: iron_aquisition-heme_transport
analyzing All_proteins_fullannotation.faa: 100%   

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Looking for following iron-related functional category: iron_aquisition-iron_transport
analyzing All_proteins_fullannotation.faa: 100%   

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Looking for following iron-related functional category: iron_aquisition-siderophore_synthesis
analyzing All_proteins_fullannotation.faa: 100%   

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Looking for following iron-related functional category: iron_aquisition-siderophore_transport
analyzing All_proteins_fullannotation.faa: 100%   

.
Looking for following iron-related functional category: iron_aquisition-siderophore_transport_potential
analyzing All_proteins_fullannotation.faa: 100%   

.
Looking for following iron-related functional category: iron_gene_regulation
analyzing All_proteins_fullannotation.faa: 100%   

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Looking for following iron-related functional category: iron_oxidation
analyzing All_proteins_fullannotation.faa: 100%   

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Looking for following iron-related functional category: iron_reduction
analyzing All_proteins_fullannotation.faa: 100%   

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Looking for following iron-related functional category: iron_storage
analyzing All_proteins_fullannotation.faa: 100%   

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Looking for following iron-related functional category: magnetosome_formation
analyzing All_proteins_fullannotation.faa: 100%   


Consolidating summary files into one master summary file
Looking for Thermincola S-layer cytochromes and Geobacter-related porin-cytochrome operons
Pre-processing of final outout file
Counting c-type heme-binding motifs
Final processing of output

Writen summary to file: heme_FeGenie_ALLPROTEINS/FeGenie-geneSummary-clusters.csv for visual inspection
Writen summary to file: heme_FeGenie_ALLPROTEINS/FeGenie-geneSummary.csv for downstream parsing and analyses
Writing heatmap-formatted output file: heme_FeGenie_ALLPROTEINS/FeGenie-heatmap-data.csv

Running Rscript to generate plots. Do not be alarmed if you see Warning or Error messages from Rscript. This will not affect any of the output data that was already created. If you see plots generated, great! If not, you can plot the data as you wish on your own, or start an issue on FeGenie's GitHub repository
Loading required package: ggplot2
null device 
          1 
                                [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9]
All_proteins_fullannotation.faa 1421   22   18 1424 1164  971  281  220    0
X.1                               NA   NA   NA   NA   NA   NA   NA   NA   NA
                                [,10] [,11] [,12] [,13]
All_proteins_fullannotation.faa     0   531    15   174
X.1                                NA    NA    NA    NA
Error in hclust(d = dist(x = fegenie.scaled)) : 
  NA/NaN/Inf in foreign function call (arg 10)
Calls: as.dendrogram -> hclust
Execution halted




...

Pipeline finished without crashing!!! Thanks for using :)