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zhqingit / giremi

GIREMI is a method that can identify RNA editing sites using one RNA-seq data set without requiring genome sequence data.
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GIREMI troubleshooting #18

Open ghost opened 8 years ago

ghost commented 8 years ago

I tried to use GIREMI for RNA-editing detection. Unfortunately, the ifRNAE column is not printed to the output file. The reason is probably that the main executable can't locate and open the giremi.r script as indicated in the output.Rout file:

Fatal error: cannot open file 'giremi.r': No such file or directory

The R script is found, of course, within the same directory as the giremi executable. I'll appreciate your help in understanding what can cause this sort of problem and how to fix it.

Additionally, while running a massage reads "error: repeat snv" is printed numerous times to the screen. What is the cause to this error?

Best, Adar

zhqingit commented 8 years ago

Hi Adar,

For the "error: repeat snv", I think your SNV list file includes the repeat SNV, which some times cause the results wired. So please remove them. For the issue "can't open giremi.r", I wonder if you can re-download the giremi.r and re-run it.

Best, Qing

2016-05-31 22:21 GMT-07:00 adarmaxomov notifications@github.com:

I tried to use GIREMI for RNA-editing detection. Unfortunately, the ifRNAE column is not printed to the output file. The reason is probably that the main executable can't locate and open the giremi.r script as indicated in the output.Rout file:

Fatal error: cannot open file 'giremi.r': No such file or directory

The R script is found, of course, within the same directory as the giremi executable. I'll appreciate your help in understanding what can cause this sort of problem and how to fix it.

Additionally, while running a massage reads "error: repeat snv" is printed numerous times to the screen. What is the cause to this error?

Best, Adar

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mt831 commented 6 years ago

Hi, I also get the output Rout file: Fatal error: cannot open file 'giremi.r': No such file or directory

And I try to re-download the giremi.r and re-run it. But it doesn't help. Are there any other solutions?

Thanks, Ting