Thanks in advance for the help.
I’ve been working quite a long time with HumanN2 on a metagenomics dataset and never had this error before, no i see it for several gene familie abundances. I have merged the samples, normalized them to cpm, regrouped and renamed them according to Kegg Orthology, hence the filename example
humann2_barplot -i “/120422_datasetx_genefamilies_merged_norm_KO_REGROUP_KO_RENAME_meta.tsv” -s similarity metadata -f K01428 -m TIMEANDFEEDING -o GraphX -g -r -w 1
gives the following:
"Regrouping to genera (before selecting/sorting strata)
Traceback (most recent call last):
File “/tools/software/bioinfo-tools/miniconda/miniconda3/envs/Humann2/bin/humann2_barplot”, line 11, in
File “/tools/software/bioinfo-tools/miniconda/miniconda3/envs/Humann2/lib/python2.7/site-packages/humann2/tools/humann2_barplot.py”, line 349, in main
table.sort( method )
File “/tools/software/bioinfo-tools/miniconda/miniconda3/envs/Humann2/lib/python2.7/site-packages/humann2/tools/humann2_barplot.py”, line 256, in sort
order = sch.leaves_list( sch.linkage( norm.transpose(), metric=“braycurtis” ) )
File “/tools/software/bioinfo-tools/miniconda/miniconda3/envs/Humann2/lib/python2.7/site-packages/scipy/cluster/hierarchy.py”, line 1109, in linkage
raise ValueError(“The condensed distance matrix must contain only "
ValueError: The condensed distance matrix must contain only finite values.”
I have been plotting genes out of this dataset regularly, only today I noticed this one, and tried some more genes. occurs sometimes.
Any ideas what could be causing it, is the data formatting? Did an infinite value sneak in some where?