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Murali-group / Beeline

BEELINE: evaluation of algorithms for gene regulatory network inference
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Not able to run GENIE3 and GRNBOOST2 #92

Open Aishwarya-Girish opened 1 year ago

Aishwarya-Girish commented 1 year ago

Hi,

I am not able to run GENIE3 and GRNBOOST2, perhaps due to some Arboreto error. The error message I get is :

OSError: Timed out trying to connect to 'inproc://172.17.0.5/9/1' after 10 s: Timed out trying to connect to 'inproc://172.17.0.5/9/1' after 10 s: connect() didn't finish in time

Attached below is an image of the same. Would be grateful if you could help me resolve the issue.

image image

ktakers commented 1 year ago

The tornado timeout appears to be the same issue reported in https://github.com/Murali-group/Beeline/issues/66, https://github.com/Murali-group/Beeline/issues/48, and https://github.com/Murali-group/Beeline/issues/42. According to the Arboreto issue https://github.com/aertslab/arboreto/issues/10 , GENIE3 can run successfully despite those timeout errors.

Can you please check under the directory outputs/example/GSD/GENIE3 to see if there's a rankedEdges.csv or an outFile.txt, which would indicate that GENIE3 did actually complete successfully?

Aishwarya-Girish commented 1 year ago

I checked under the outputs section. There is a GENIE3 folder alright, but not any ranked edges list. Maybe I'll run it again to check.

What about GRNBOOST2 ? The entire BEELINE algorithm just gets stuck at this and doesn't proceed further to allow any of the other algorithms to complete.

Awaiting your reply.

Thank you, Aishwarya Girish

On Fri, Apr 7, 2023, 2:35 AM ktakers @.***> wrote:

The tornado timeout appears to be the same issue reported in #66 https://github.com/Murali-group/Beeline/issues/66, #48 https://github.com/Murali-group/Beeline/issues/48, and #42 https://github.com/Murali-group/Beeline/issues/42. According to the Arboreto issue aertslab/arboreto#10 https://github.com/aertslab/arboreto/issues/10 , GENIE3 can run successfully despite those timeout errors.

Can you please check under the directory outputs/example/GSD/GENIE3 to see if there's a rankedEdges.csv or an outFile.txt, which would indicate that GENIE3 did actually complete successfully?

— Reply to this email directly, view it on GitHub https://github.com/Murali-group/Beeline/issues/92#issuecomment-1499631094, or unsubscribe https://github.com/notifications/unsubscribe-auth/A46K53ZVNS3PV62CZV7WYY3W74V3HANCNFSM6AAAAAAWVFRAEI . You are receiving this because you authored the thread.Message ID: @.***>

Aishwarya-Girish commented 1 year ago

I ran the pipeline again and I can see a "time.txt" folder in the outputs folder. However, I don't see any "rankedEdges.csv" file yet. I think it doesn't run despite the timeout error. Can you please check for the same?

Thank You, Aishwarya Girish

On Fri, Apr 7, 2023 at 8:41 AM Aishwarya G @.***> wrote:

I checked under the outputs section. There is a GENIE3 folder alright, but not any ranked edges list. Maybe I'll run it again to check.

What about GRNBOOST2 ? The entire BEELINE algorithm just gets stuck at this and doesn't proceed further to allow any of the other algorithms to complete.

Awaiting your reply.

Thank you, Aishwarya Girish

On Fri, Apr 7, 2023, 2:35 AM ktakers @.***> wrote:

The tornado timeout appears to be the same issue reported in #66 https://github.com/Murali-group/Beeline/issues/66, #48 https://github.com/Murali-group/Beeline/issues/48, and #42 https://github.com/Murali-group/Beeline/issues/42. According to the Arboreto issue aertslab/arboreto#10 https://github.com/aertslab/arboreto/issues/10 , GENIE3 can run successfully despite those timeout errors.

Can you please check under the directory outputs/example/GSD/GENIE3 to see if there's a rankedEdges.csv or an outFile.txt, which would indicate that GENIE3 did actually complete successfully?

— Reply to this email directly, view it on GitHub https://github.com/Murali-group/Beeline/issues/92#issuecomment-1499631094, or unsubscribe https://github.com/notifications/unsubscribe-auth/A46K53ZVNS3PV62CZV7WYY3W74V3HANCNFSM6AAAAAAWVFRAEI . You are receiving this because you authored the thread.Message ID: @.***>

elhaam commented 1 year ago

I faced the same issue. The way I solved this was by stopping and removing all docker images to solve this error: Please be cautious running the below command since it stops and removes all docker images, maybe you can select a specific docker image of your choice, instead.

docker stop $(docker ps -aq) && docker rm $(docker ps-aq)

tmmurali commented 1 year ago

@Aishwarya-Girish does the idea proposed by @elhaam work for you? If it does, we can close this issue.

Aishwarya-Girish commented 1 year ago

I am sorry sir, the idea doesn't work. GENIE3 and GRNBOOST2 still dont function due to the same issue

elhaam commented 8 months ago

@tmmurali @Aishwarya-Girish Another solution that has helped me in some cases is going to your Beeline/input/example/your_example/GENIE3 directory and removing subdirectories made for GENIE3. Also, remove subdirectories from Beeline/output/example/your_example/GENIE3 as well. Then run BoolODE.py again. This helped me run GENIE3 in some cases when I got the above error.

For a couple of experiments, I still couldn't run GENIE3 due to the above error, which was not resolved by the solutions I shared here.

kevchen03 commented 2 months ago

Hello @Aishwarya-Girish @tmmurali , Assuming that the run phase inside BLRunner is completed, a temporary solution that has worked for me is to comment out the for-loops for generateInputs and run. The rankedEdges.csv file is generated solely within the parseOutput function using the files generated by the run phase, so you should be able to comment out the generateInputs and run loops to skip straight to generating the rankedEdges.csv file.