duplicate 'row.names' are not allowed

[SoniramDK]

Hello Ampvis2 people.

Im trying to use Ampvis2 inside ONT AmpSeq package, and I use my reads as an input, along with my metadata file that looks like this

SampleID,Group,Condition
bc92,Group A,Test 1
bc93,Group B,Test 2
bc94,Group C,Test 3
bc95,Group D,Test 4
bc96,Group E,Test 5

While the package is running, I get the following error:
Error in rule ampvis2_std_plots_sintax:
jobid: 53
input: results/final/99/OTUtable_tax_99_sintax.tsv
output: results/final/figs/99/Heatmap_99_sintax.png, results/final/figs/99/Rarefaction_99_sintax.png, results/final/figs/99/Ordination_99_sintax.png, results/final/figs/99/Boxplot_99_sintax.png, results/final/R-environment/99/R-environment_99_sintax.RData

Inside the log file I can see that the error has to do with the row names:

Loading required package: ggplot2
Warning messages:
1: package ‘ampvis2’ was built under R version 4.3.2
2: package ‘ggplot2’ was built under R version 4.3.3
Error in .rowNamesDF<-(x, value = value) :
duplicate 'row.names' are not allowed
Calls: amp_load ... row.names<- -> row.names<-.data.frame -> .rowNamesDF<-
In addition: Warning messages:
1: Could not find a column named OTU/ASV in otutable, using rownames as OTU ID's
2: non-unique values when setting 'row.names':
Execution halted

As I understand, the error has to do with the fact that the OTU column is not named as OTU, but inside my tsv file I can see that the column has the OTU name:

OTU bc92 bc93 bc94 bc95 bc96 kingdom phylum class order family genus species
OTU_1 0 0 1 0 0 k__Bacteria
OTU_10 0 0 0 1 0 k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales >OTU_100 0 0 1 0 0 k__Bacteria
OTU_101 0 0 0 0 1 k__Bacteria p__Firmicutes c__Bacilli
OTU_102 0 0 1 0 0 k__Bacteria
OTU_103 0 0 0 0 1 k__Bacteria
OTU_104 0 0 0 0 1 k__Bacteria p__Firmicutes
OTU_105 1 0 0 0 0 k__Bacteria
OTU_106 1 0 0 0 0
OTU_107 0 1 0 0 0 k__Bacteria
OTU_108 0 1 0 0 0 k__Bacteria
OTU_109 0 0 1 0 0 k__Bacteria
OTU_11 0 0 0 0 1 k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales >OTU_110 0 0 1 0 0 k__Bacteria
OTU_111 0 0 0 1 0 k__Bacteria
OTU_112 0 0 0 0 1 k__Bacteria
OTU_113 1 0 0 0 0 k__Bacteria
OTU_114 1 0 0 0 0 k__Bacteria p__Firmicutes
OTU_115 0 1 0 0 0 k__Bacteria
OTU_116 0 0 1 0 0 k__Bacteria
OTU_117 0 0 1 0 0 k__Bacteria
OTU_118 0 0 1 0 0 k__Bacteria
OTU_119 0 0 0 0 1 k__Bacteria p__Firmicutes c__Erysipelotrichia o__Erysipelotri>OTU_12 0 0 1 0 0 k__Bacteria

Also, checked for duplicates in the OTU names and did not find any.

Is there anybody that knows what might be the issue?

Kind regards,
SoniramDK

[KasperSkytte]

Hi. Please provide a reproducible example so that I can debug. But the error most likely refers to the sample ID's in the metadata.