CNV calling error in Step 6

Hello,

Thank you for providing your tool for calling CNVs from Visium data!

I am currently attempting to rerun the analysis for the dataset used in your publication (Patient 4 Rep1). Based on the Leiden Clustering, I generated an annotate.csv file and a Graph_based.csv, and I created a FeatureCSV from the count matrix after converting HUGO Symbols to Ensembl IDs.

Based on cnr files in ~/analysis/spatial/grouped_spots/CNVs/cnr I can observer some changes in log2 coloumn which kind of make

However, I encountered the following error during Step 6:

Step 6, finalizing CNV calling...
During startup - Warning messages:
1: Setting LC_CTYPE failed, using "C"
2: Setting LC_COLLATE failed, using "C"
3: Setting LC_TIME failed, using "C"
4: Setting LC_MESSAGES failed, using "C"
5: Setting LC_MONETARY failed, using "C"
6: Setting LC_PAPER failed, using "C"
7: Setting LC_MEASUREMENT failed, using "C"

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: gplots

Attaching package: 'gplots'

The following object is masked from 'package:stats':

    lowess

Loading required package: gtools
[1] "No gains and losses provided."
[1] "Grouping by genes."
[1] "Everything is good!"
[1] "All arguments have names"
Error in seq.default(m, 0, length.out = 40) :
  'from' must be a finite number
Calls: cnvs -> cnvPlot2 -> seq -> seq.default
Execution halted

overview of input files: filteredFeatureCSV:

"ensembl_gene_id","AAACAAGTATCTCCCA-1","AAACATTTCCCGGATT-1","AAACCTAAGCAGCCGG-1"
"ENSG00000243485",0,0,0
"ENSG00000237613",0,0,0
"ENSG00000186092",0,0,0
"ENSG00000284733",0,0,0
"ENSG00000284662",0,0,0
"ENSG00000177757",0,0,0
"ENSG00000225880",0,0,0
"ENSG00000230368",0,0,0
"ENSG00000187634",0,0,0
"ENSG00000188976",2,1,1
"ENSG00000187961",0,2,0
"ENSG00000187583",0,0,1
"ENSG00000187642",0,0,0
"ENSG00000188290",0,1,0
"ENSG00000187608",55,40,2

clusterCSV:

Barcode,Graph.based
AAACAAGTATCTCCCA-1,Cluster0
AAACATTTCCCGGATT-1,Cluster2
AAACCTAAGCAGCCGG-1,Cluster2
AAACGAGACGGTTGAT-1,Cluster3
AAACGGGCGTACGGGT-1,Cluster2
AAAGGGATGTAGCAAG-1,Cluster1
AAAGTGTGATTTATCT-1,Cluster4
AAAGTTGACTCCCGTA-1,Cluster5
AAATAGGGTGCTATTG-1,Cluster5

annotate file:

cluster,annotate
Cluster0,Tumor
Cluster2,Tumor
Cluster3,Normal
Cluster1,Tumor
Cluster4,Tumor
Cluster5,Normal

tissue_position_list

ACGCCTGACACGCGCT-1,0,0,0
TACCGATCCAACACTT-1,0,1,1
ATTAAAGCGGACGAGC-1,0,0,2
GATAAGGGACGATTAG-1,0,1,3
GTGCAAATCACCAATA-1,0,0,4
TGTTGGCTGGCGGAAG-1,0,1,5
GCATCCTCTCCTATTA-1,0,0,6
GCGAGGGACTGCTAGA-1,0,1,7
TGGTACCGGCACAGCC-1,0,0,8
GCGCGTTTAAATCGTA-1,0,1,9

limin321 / stmut

CNV calling error in Step 6 #7