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Error in the pipeline for test data #37
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Thanks for the tar ball. This is very helpful. You already posted the following error line but I need to look at the full log. Please post it here.
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Hi Jin, I am pasting the full log here. I have changed the directory $ATAC at the beginning which is the pipeline directory.
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Please run this command and post its output.
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Hi Jin, Here is the output for the command
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Can you remove
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Hi Jin, I have ran the commands and pasted the output here.
The singularity image was removed and was pulled again
After it Singularity container was built. I ran this command
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Can you run the followings too?
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Hi Jin, Here are the outputs for the commands
I have changed the folder name to $SOFTWARE
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I am very sorry bothering you but please run the following too:
Can you also remove your locally installed cutadapt ( |
Hi Jin, I am pasting the outputs for the commands here.
Also I have removed the cutadapt
It is working now after removing the cutadapt. Installing cutadapt locally seems to mess up the pipeline. |
Hi Jin, One more thing, I am facing is that ATAC-Seq pipeline does not finish properly. After QC step it gets stuck for a long time.
And it is still running. Is there a way to fix this. I can get it finished if I press |
Thanks for reporting this. I also figured it out and will make a hot fix. Please keep this issue open until then.
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Hi Jin, It was still running so I cancelled it but it took close to 7 hours 30 minutes before I cancelled it. |
Okay, please upload your log and tar ball. I guess that something is wrong with the |
Hi Jin, I am attaching the tar ball here for the atac pipeline I have run for the test data. |
Please run the following:
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Hi Jin, I am pasting the output for the commands here
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@shanmukhasampath : It's very hard to debug the second problem (hanging at Can you simply re-run the pipeline and see if it works for ataqc? BTW The |
Hi Jin, I am getting an error now for the test data
It was working few days and now I am getting this error. I am attaching the log file here |
Please git clone our dev branch including the above fix commit and try again. I hope this fixes the problem.
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Hi Jin, I have git cloned the directory and fixed the backend configuation file with
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Hi Jin, I have contacted the server administrator regarding this issue and admin mentioned that the command
is asking for
As per my understanding it is strange that the command is asking for that much memory as it only submits the commands using |
Please try to increase your Java heap size. Add the following to your
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Hi Jin, I have increased the Java heap size by adding the I got the memory allocation problem.
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https://plumbr.io/outofmemoryerror/unable-to-create-new-native-thread
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Hi Jin, I have checked the max user processes and here is the output of command
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Hi Jin, I have commented the shell command
I have ran the pipeline with backend singularity on a qlogin and it worked.
This time the pipeline did not get stuck at the qc report step. |
@shanmukhasampath : Thanks for this, but you should not comment it out. Please delete the line and try again. |
Hi Jin, I have tried by deleting the shell command in the qsub and still getting OutofMemory
Also, the singularity backend mode is only working on qlogin but not on the run mode
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Hi Jin,
I have pulled the ATAC-Seq pipeline and started experimenting with the test data. Initially it ran and executed. Today I am getting the following error. I am using sge_singularity backend to run the pipeline.
Pulled Singularity image for ATAC-Seq is as follows
And the commands to run the pipeline are
More info on
sge.json
The error I am getting is
Seems like unable to access the directory
Please help me fix this issue.
OS/Platform and dependencies
Attach logs
I have attached the logs.
debug_10.tar.gz
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