error report

[KailiBio]

Hi. I got a new error repot show as below.

Error in apply(statemean, 1, range) : dim(X) must have a positive length Calls: createHeatmap -> array -> stateColor -> apply Execution halted

I found 'apply(statemean, 1, range)' comes from createGenomeTracks.R. Do you have an idea how can I solve this? Thanks!

Kaili

[guanjue]

First, you need to run this command outside of your output folder: In your case, your output folder is: /data/zusers/fankaili/ideas/test/run_IDEAS_result_chr1/ You need to run it in this folder: cd /data/zusers/fankaili/ideas/test/ time Rscript bin/get_heatmap.R run_IDEAS_result_chr1/run_IDEAS.para0 FALSE bin/createGenomeTracks.R

If this is not the issue, I wonder if you can check what is in the 'run_IDEAS.para0' file? If it is empty?

[KailiBio]

This is another issue. For the previous one, I gave it the bed file with at least 2 chrs, and it runs well in the first '[IDEAS Analysis]' step. It exhaulted at the '[ Create Custom Tracks ]' step this time, and I still trying to find what's statemean in createGenomeTracks.R

[guanjue]

Does the .inv file recreated?

[KailiBio]

Yeah, I do have .inv file.

Below is all the file I got when they exhaulted.

And this is the log file:

[KailiBio]

The files listed are in the result folder. I have .inv file in the work directory.

[guanjue]

Can you check if the .inv file to see if the number of bins in the chromosome (third column) matches with the number of bins in each chromosome in your bed file?

[KailiBio]

The .inv file is correct.

[guanjue]

I wonder if you can send me the para0, so I can check the bug tonight? my email address: gzx103@psu.edu

[KailiBio]

Already send it. Many Thanks!