outFileNamePre x_STARtmp was not removed

[Leo Gu]

Hey guys, 

I am using STAR 2.4.0j and I found sometimes the output was fine, but the temporary folder was left there, even it was empty.

e.g., the following simple command:

STAR --genomeDir $genomeDir --readFilesIn $seqDir/R1.fq $seqDir/R2.fq --runThreadN $PN --outFilterType BySJout --outFileNamePrefix $PID.sm

According to the manual, if the job was finished successfully, this folder should be removed:

--outTmpDir

    string: path to a directory that will be used as temporary by STAR. All

    contents of this directory will be removed!

    - the temp directory will default to outFileNamePrex STARtmp

Do you have any idea about this? Thanks a lot!

[Alexander Dobin]

Hi Leo,

does it happen consistently - say, if you run exactly the same job twice? Is there anything strange with the directory permissions?

If Log.out contains ALL DONE in the last line, it means the run was completed successfully, and you do not need to worry if something is missing.

Cheers

Alex

[R. Parameswaran]

Hello All,

I am using STAR 2.5.2b (great program by the way), and am facing the same problem of not clearing the folders “_STARgenome”, “_STARpass1”, and “ _STARtmp” after a successful run.  Of course, we can manually delete them in the bash script, but I just want to make sure that there is nothing to be concerned about the results.  I checked the logs, and I do see "All Done" at the end.  So, can I ignore this issue, and assume I can rely on the results?

Many thanks,
Paramesh

===============

[Alexander Dobin]

Hi Paramesh,

_STARgenome and _STARpass1 are not removed automatically, they contain some useful information.

_STARtmp is supposed to be removed, but I have received reports that it does not happen on some systems - it must be some kind of system library incompatibility.

However, it does not affect any results and all these directories can be removed safely after the run is completed.

To verify that the run completed successfully, you can check one of the following:

1. Log.final.out file is generated and is not empty.

2. Last line of the Log.out file is "ALL DONE!"

3. Last line of the Log.final.out file is "ALL DONE!"

Cheers

Alex

[Parameswaran]

Thank you very much Alex!  That clarifies it for me.
Best,
Paramesh

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