Error in execute

[carlosleher]

Dear Jesper

I am interested in using your tool in my research project however I'm having trouble running the examples data.

(image) razor@razor-IS2323:/media/razor/labdata/Kadu/IMAGE$ perl IMAGE.pl -region examples/Enhancers.txt -expression examples/GeneExpression.txt -fasta mm10.fa -RNADesign 1 1 2 2 3 3 4 5 -EnhancerDesign 1 1 2 2 3 3 4 5 -p 12 -n Test1

#### Welcome to IMAGE ####

Your region file contains 10000 regions and 5 conditions across 8 files
Your exon file contains 5000 genes and 5 conditions across 8 files
Your fasta file is mm10.fa
You are using 12 processors.

Starting the analysis
        Setting up for parallizing motif search
        Preparing input file for motif searching
        Scanning for motifs
        Running analysis in R
                1. Reading data into R
                2. Analyzing gene expression
                3. Converting motif hits to matrix - Takes a while
                4. Calculating motif activity - Full model stage
                5. Performing ridge regression
                        Sample 1 completed
                        Sample 2 completed
                        Sample 3 completed
                        Sample 4 completed
                        Sample 5 completed
                        Sample 6 completed
                        Sample 7 completed
                        Sample 8 completed
                6. Calculating motif activity - Reduced model stage
                7. Creating weight matrices
                8. Calculating factor activity - Full model stage
                        Sample 1 completed
                        Sample 2 completed
                        Sample 3 completed
                        Sample 4 completed
                        Sample 5 completed
                        Sample 6 completed
                        Sample 7 completed
Error in t.test.default(as.numeric(Significant[i, SampleOutline[SampleOutline[,  : 
  número de observações 'y' insuficiente
Calls: t.test -> t.test.default
Execução interrompida
                        Sample 8 completedError in readChar(con, 5L, useBytes = TRUE) : 
  não é possível abrir a conexão
Calls: load -> readChar
Execução interrompida
IMAGE completed in 206 seconds

When I try to use my data it appears as if it is in the wrong format. I downloaded the ATAC-seq files into bed from galaxy and used the iRNA software for the RNA-seq data.

If you can help me i would appreciate it

Best, Carlos

[JesperGrud]

Hi Carlos,

Did you resolve this issue? It seems to me that IMAGE is failing on the example files for you? If that is the case, please try running IMAGE within the conda environment specified in the environment.txt file in this repository in the 'code' branch.

[carlosleher]

Hello, Jesper

Yes, I already have all the packages installed and I also managed to run IMAGE to analyze my samples in general, with 6 conditions and 3 samples in each condition, however, when I try to do the same data, but with less conditions for to have a more accurate comparison between them, I'm having this error:

(image2) razor@razor-IS2323:/media/razor/labdata/Kadu/IMAGE$ perl IMAGE.pl  -region Enhancer21_WxB.txt -expression Expression21_WxB.txt -fasta mm10.fa -RNADesign 1 1 1 2 2 2 -EnhancerDesign 1 1 1 2 2 2 -n IMAGE21_WxB -p 20

#### Welcome to IMAGE ####

Your region file contains 158132 regions and 2 conditions across 6 files
Your exon file contains 19764 genes and 2 conditions across 6 files
Your fasta file is mm10.fa
You are using 20 processors.

Starting the analysis
    Setting up for parallizing motif search
    Preparing input file for motif searching
    Scanning for motifs
    Running analysis in R
        1. Reading data into R
Error in estimateCommonDisp.default(y[tagsinbin, ], group = group, lib.size = lib.size,  : 
  No genes satisfy rowsum filter
Calls: estimateTrendedDisp ... estimateTrendedDisp.default -> estimateCommonDisp -> estimateCommonDisp.default
Execução interrompida
        2. Analyzing gene expressionError in readChar(con, 5L, useBytes = TRUE) : 
  não é possível abrir a conexão
Calls: load -> readChar
Execução interrompida
Error in readChar(con, 5L, useBytes = TRUE) : 
  não é possível abrir a conexão
Calls: load -> readChar
Execução interrompida
IMAGE completed in 531 seconds

I've also tried using different datasets, but whenever I try to use it with just two conditions I get this error, I would really appreciate it if you could help me.