Error while running TRASH

[mardal42]

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]

Fixed in latest version (don't use the tar.gz) #16 (comment)

[tytrhr]

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

[pgonzale60]

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

[tytrhr]

@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]

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]

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]

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

[aurelpetit]

Hello,

Just a quick ping on this issue. I am still encountering the same error, it appears to remain present.
I would very much appreciate any help,

Thanks a lot in advance.