search

vlothec / TRASH

RepeatIdentifier
MIT License
50 stars 3 forks source link

Error while running TRASH #24

Open mardal42 opened 3 months ago

mardal42 commented 3 months ago

Hello, I tried to run TRASH several times, but it always ends about 1-2 hours in by the following error.

Error in { : task 1 failed - "cannot open the connection" Calls: %dopar% -> Execution halted

I would appreciate any help with identifying and fixing this issue. Thank you very much

pgonzale60 commented 2 months ago

Fixed in latest version (don't use the tar.gz) https://github.com/vlothec/TRASH/issues/16#issuecomment-1923237159

tytrhr commented 2 months ago

hello, I use the TRASH.v1.2.tar.gz and meet the same error. where is the latest version?

pgonzale60 commented 2 months ago

get the latest version by going to your terminal and pasting git clone https://github.com/vlothec/TRASH.git

tytrhr commented 2 months ago

@pgonzale60 Thank you so much! I have succefully run the TRASH. But the output plot has nothing in it and there is no circos plot. This is my command: bash TRASH/TRASH_run.sh extracted_sequences.fa --par 120 and the following is information: [1] "Available classes: NA" [1] "Available classes: NA" [1] "Available classes: NA" [1] "Available classes: NA" [1] "Available classes: NA" [1] "Available classes: NA" [1] "Available classes: NA" [1] "Available classes: NA" [1] "Available classes: NA" [1] "Available classes: NA" [1] "Available classes: NA" [1] "Available classes: NA" [1] "Available classes: NA" [1] "Available classes: NA" [1] "Available classes: NA" [1] "Available classes: NA" [1] "Available classes: NA" used (Mb) gc trigger (Mb) max used (Mb) Ncells 2866175 153.1 17662430 943.3 43121164 2303.0 Vcells 406873907 3104.3 733566861 5596.7 632535147 4825.9 [1] "plotting" [1] "circos" [1] "identify chromosomes" [1] "Identify main peaks" [1] "No tandem repeats in extracted_sequences.fa" [1] "finished plotting" [1] "TRASH finished, exiting" used (Mb) gc trigger (Mb) max used (Mb) Ncells 2886567 154.2 14129944 754.7 43121164 2303.0 Vcells 406923367 3104.6 733566861 5596.7 632535147 4825.9

I don't konw why.....Can you give me some advice? Thanks again! Looking forward to your reply.

pgonzale60 commented 2 months ago

Very glad to hear that it worked for you as well!

I had the same issue about the plot but I don't plan to use the plot so I moved on. If you are familiar with R, this seems a suitable next step: https://jokergoo.github.io/circlize_book/book/introduction.html

dprokopov commented 4 weeks ago

Hello, I still have a "cannot open the connection" error (TRASH was git cloned)

Error in { : task 1 failed - "cannot open the connection" Calls: %dopar% -> Execution halted

GooLey1025 commented 4 days ago

Hello, I still have a "cannot open the connection" error (TRASH was git cloned) me too

Error in { : task 1 failed - "cannot open the connection" Calls: %dopar% -> Execution halted