error during creation of .txt file

[royshikha]

Mam kindly help me with these error..

i am getting this in error in .txt file
amar@amar-Virtual-Machine:~/JAFFA-version-1.09/NegSim-IDFixed$ cat NegSim-IDFixed.txt

R version 3.2.1 (2015-06-18) -- "World-Famous Astronaut"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
  

also attaching log_filter file..
Kindly help...

[royshikha]

dear mam,

  There is problem with construction of .txt file from .psl.I tried to run your trancriptome blat table file in R independently but the process stoped at finoverlap function of IRanges.Your script is using findoverlap function with drop.self and drop.redundant =TRUE .But R IRanges dunction does not has these argument drop self and drop redundant in latest release.Kindly provide me with the solution.

[Nadia Davidson]

Hi Royshikha,

This was a bug that was fixed in the last version of JAFFA. Can you try installing that and see if the error is resolved? You should not need to re-download or re-install any of the reference files.

Cheers,

Nadia.

[royshikha]

hell mam,


  You were right.I did my analysis with previous version of JAFFA and it ran.

Thanks and regards
Shikha Roy