chr problem

[KailiBio]

I found a problem while I running IDEAS on only one chr.
If we run IDEAS on several chr(for expample, chr1 & chr2), they will get output like "run_IDEAS.chr1.para" & "run_IDEAS.chr2.para" and everything is OK. But when I run IDEAS on file contains only one chr1 (for expample, chr1 only), the output file is "run_IDEAS.para" and on the following step it try to find file named "run_IDEAS.chr1.para"...

Error report like this:
Calls: createHeatmap -> read.table -> file
In addition: Warning message:
In file(file, "rt") :
cannot open file '/data/zusers/fankaili/ideas/test/run_IDEAS_result_chr1/run_IDEAS_chr1.chr1.para': No such file or directory
Execution halted

I guess there is some file name issue there.

[yuzhang123]

I'm wondering is this because the ".inv" file is used and it is not updated accordingly? or it is a bug in the R script. Thanks, Yu

…

On 7/20/18 9:25 AM, Kaili wrote: I found a problem while I running IDEAS on only one chr. If we run IDEAS on several chr(for expample, chr1 & chr2), they will get output like "run_IDEAS.chr1.para" & "run_IDEAS.chr2.para" and everything is OK. But when I run IDEAS on file contains only one chr1 (for expample, chr1 only), the output file is "run_IDEAS.para" and on the following step it try to find file named "run_IDEAS.chr1.para"... Error report like this: Calls: createHeatmap -> read.table -> file In addition: Warning message: In file(file, "rt") : cannot open file '/data/zusers/fankaili/ideas/test/run_IDEAS_result_chr1/run_IDEAS_chr1.chr1.para': No such file or directory Execution halted I guess there is some file name issue there. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#3>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AO6dnKlT-lvjdO9H5xoS6fKFMXotcwjUks5uIdoxgaJpZM4VYB8I>.

[guanjue]

Did you change the IDEAS_job_name name in the 'run_IDEAS.sh' file?
IDEAS_job_name=run_IDEAS

Guanjue

[guanjue]

Besides, I wonder if there is a file named as /data/zusers/fankaili/ideas/test/run_IDEAS_result_chr1/run_IDEAS.para0 in your output folder

If there is you can generate the heatmap by the following command without rerun the whole thing.
time Rscript bin/get_heatmap.R run_IDEAS_result_chr1/run_IDEAS.para0 FALSE bin/createGenomeTracks.R

[KailiBio]

I did change the name in 'run_IDEAS.sh' file, but thatis perfectly match all of my file. The problem is it generate 'name.chr*.para' file normally. When you give it the bed file with only one chr, it just generate 'name.para' but also try to find 'name.chr*.para' in the following step. So what I think is the '.chr*' issue.

Yeah, they did generate 'para0' file. I will try to make figures by that, thanks!

Kaili