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egaffo / circompara2

Improved bioinformatic pipeline to identify and quantify circRNA expression from RNA-seq data by combining multiple circRNA detection methods
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Error with setting HISAT2_EXTRA_PARAMS = "--rna-strandness RF" #7

Open mianlee opened 2 years ago

mianlee commented 2 years ago

Dear egaffo:

I am sorry to bother you again.

I was running circompara2 on CentOS 7 using docker.

Here is my command : "docker run -u id -u --rm -it -v $(pwd):/data egaffo/circompara2:v0.1.2.1 -j 2", it worked perfect. However, when I uncommented HISAT2_EXTRA_PARAMS = "--rna-strandness RF" , it gave me the following error:

51801657427757_ pic

scons:building terminated because of errors.

Our circRNA-seq library was build using stand-specific protocols.

Do you have any idea why this would occur? Thank you very much!

Best Mian

egaffo commented 2 years ago

You pasted output with no errors, it probably occurred above. Please, spot the error in the log or if you did not save the log output, run CirComPara2 with -j 1 so it will stop as soon as the error occurs.

mianlee commented 2 years ago

Because it gave the "scons: buidling terminated because of errors" and CirComPara2 just stopped running.

I will check the log file again.

Thanks !

egaffo commented 2 years ago

You do not see the actual error right before the final "scons: buidling terminated because of errors" because you run multiple tasks in parallel (two in your case, with the -j 2 option); therefore, the error occurred in one of the two tasks, and (hopefully) it printed an error message, but the second task continued running and printing its output. However, I see BWA logs followed by Segemehl logs in your screenshot, which puzzles me ... For a full debug I would need the whole log, vars.py and meta.csv file and to know if you are running in a cluster/distributed environment.