landscapes new error

[AntonioBaeza]

Hi Clement, I am trying to render the TE landscape of the studied genome using dnaPT_landscapes.sh

This is an error that appears to be new

(base) ant@hillary:/dnaPipeTE/Project/dnaPipeTE_proj2$
(base) ant@hillary:/dnaPipeTE/Project/dnaPipeTE_proj2$ ./dnaPT_landscapes.sh -I /home/ant/dnaPipeTE/Project/dnaPipeTE_proj2
input dataset: /home/ant/dnaPipeTE/Project/dnaPipeTE_proj2
output folder: /home/ant/dnaPipeTE/Project/dnaPipeTE_proj2
output prefix: dnaPipeTE
super-family level: FALSE
custom ylim: FALSE
plotting Unknown: TRUE
[1] "load variables..."
Error in file(file, "rt") : cannot open the connection
Calls: read.table -> file
In addition: Warning message:
In file(file, "rt") :
cannot open file '/home/ant/dnaPipeTE/Project/dnaPipeTE_proj2/colors.land': No such file or directory
Execution halted
All done, results in /home/ant/dnaPipeTE/Project/dnaPipeTE_proj2/

Same script but error came with a little more of info this time:

(base) ant@hillary:/dnaPipeTE/Project/dnaPipeTE_proj2$ ./dnaPT_landscapes.sh -I /home/ant/dnaPipeTE/Project/dnaPipeTE_proj2
input dataset: /home/ant/dnaPipeTE/Project/dnaPipeTE_proj2
output folder: /home/ant/dnaPipeTE/Project/dnaPipeTE_proj2
output prefix: dnaPipeTE
super-family level: FALSE
custom ylim: FALSE
plotting Unknown: TRUE
[1] "load variables..."
[1] "Recognized classes:"
[1] "^DNA$"
[1] "^LINE$"
[1] "^LINE/CR1$"
[1] "^LINE/Dong-R4$"
Error in col.lands[i] <- cols$V2[grep(pattern = paste("^", levels(as.factor(land$TE_subclass))[i], :
replacement has length zero
Execution halted
All done, results in /home/ant/dnaPipeTE/Project/dnaPipeTE_proj2/
(base) ant@hillary:/dnaPipeTE/Project/dnaPipeTE_proj2$

[clemgoub]

Hello Antonio,

Both issues #5 and #6 have the same origin: somehow the script cannot locate the file color.land. I see from the post that you are launching the command from the output folder, so I assume that you have cloned dnaPT_utils directly in the output folder. There must be some sort of bug when the script is located in the output folder.

To make sure, I suggest that you get out of the output folder, maybe do cd /home/ant. There, clone dnaPT_utils again (git clone https://github.com/clemgoub/dnaPT_utils.git). Once installed, run:

./dnaPT_utils/dnaPT_landscapes.sh -I /home/ant/dnaPipeTE/Project/dnaPipeTE_proj2

The ouput will be in/home/ant/dnaPipeTE/Project/dnaPipeTE_proj2. If it works, this should also fix dnaPT_charts.sh

Cheers,

Clément

[AntonioBaeza]

thank you Clement! I works after following your recommendations!