I'm trying to make strain inference from my metagenomic reads, so I was following DESMAN complete example that includes the samples preprocessing, however I'm facing a problem at the ConfPlot.R step. As far as I understood (and please correct me if I'm wrong) this step provides a graphical representation (heatmap in this case) of the clusters taxonomical assignments. Knowing which clusters pertain to which bacteria one could identify the core genes and make the strain inference.
Until this step all ran smoothly. Here is the error:
$ ~/programas/CONCOCT/CONCOCT-0.4.0/scripts/ConfPlot.R -c SRR2081071_Taxa_Conf.csv -o SRR2081071_Taxa_Conf.pdf
Attaching package: ‘gplots’
The following object is masked from ‘package:stats’:
lowess
Error in hclustfun(distc) :
NA/NaN/Inf en llamada a una función externa (arg 11)
Calls: heatmap.2 -> hclustfun
Ejecución interrumpida
I have the 'gplots' and 'getopt' packages installed, so this shouldn't be the problem. Below the output of previous step:
$ ~/programas/CONCOCT/CONCOCT-0.4.0/scripts/Validate.pl --cfile=3_Concoct/SRR2081071/clustering_gt1000.csv --sfile=6_ClassifyContigNR/SRR2081071_K55_c10k_gt1000_AA_nr_species.csv --ffile=0_Assemblies_c10k/SRR2081071_K55_c10k.fasta --ofile=SRR2081071_Taxa_Conf.csv
N M TL S K Rec. Prec. NMI Rand AdjRand
6340 1151 5.4228e+06 15 32 0.913775 0.966000 0.876351 0.952381 0.873916
Hi all,
I'm trying to make strain inference from my metagenomic reads, so I was following DESMAN complete example that includes the samples preprocessing, however I'm facing a problem at the ConfPlot.R step. As far as I understood (and please correct me if I'm wrong) this step provides a graphical representation (heatmap in this case) of the clusters taxonomical assignments. Knowing which clusters pertain to which bacteria one could identify the core genes and make the strain inference.
Until this step all ran smoothly. Here is the error:
I have the 'gplots' and 'getopt' packages installed, so this shouldn't be the problem. Below the output of previous step:
I would appreciate some help here. Many thanks!