Issue deploying Trinityrnaseq

[kamoors]

1 Trinityrnaseq in local command line exits from shell and stops function without any input

2 Terminal within DSRI disconnects and all running function is stopped

1

login to openshift as in documentation

oc get pods oc rsh trinityrnaseq5-2-qzcxm

cd /usr/local/src/work2/aerius-sample-sequencing/CD4K4ANXX

Trinity --seqType fq --max_memory 100G --CPU 64 --samples_file samples.txt --output /usr/local/src/work2/Trinity_output_zip_090221

Then the function starts like it should but at some points just exits without warnings or errors to my Windows folder

2

Same application / same Trinity function. I first tried to do my analysis through DSRI in the container's terminal. Everything was running fine but my analysis never finishes. At some point a red label ''disconnected'' appears and the terminal stops and the analysis never continues.

Is there any way to continue a function within a container ''in the background'' / without me being connected to DSRI? Because it appears that the cisco VPN disconnects/reconnects and this causes some problems with DSRI..

Thank you for the help!

[kamoors]

Also, I forgot to mention but I cannot access my persistent storage within the container.

It was supposed to be under usr/local/src/work

But that folder is empty. To access my files I added dynamic storage (that links with my persistent storage [which I access through File Browser])

[vemonet]

Hi @kamoors !

Those 2 issues are due to the process running attach to your terminal

You should be able to easily run it using the "Bash way": add nohup at the beginning and & at the end It will run in the back and all output that should have gone to your terminal will go to a file nohup.out in the repo

nohup Trinity --seqType fq --max_memory 100G --CPU 64 --samples_file samples.txt --output /usr/local/src/work2/Trinity_output_zip_090221 &

To check if it is still running:

ps aux | grep Trinity

Be careful make sure the terminal uses bash and not shell ("sh")

To use bash just type bash in the terminal:

bash

Then the function starts like it should but at some points just exits without warnings or errors to my Windows folder

Is it happening after a long time of connection? (e.g. after 1h of running the process?)

[kamoors]

@vemonet

Is it happening after a long time of connection? (e.g. after 1h of running the process?)

It happens very quickly after I start running the Trinity function. Otherwise it doesn't do that.

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I will try your solution! Thank you very much!

[kamoors]

Am I doing this right? I'm not really sure what should be happening... And if I type ps aux | grep Trinity

what indicates whether it's running or not?

Thank you!

P.S. The picture is obtained by using the terminal on DSRI not local. Should I do local instead?

[vemonet]

In the image you are still running with Shell, (you should see the current path at the start of the commandline if bash is properly enabled)

Note: it has been fixed