runDYNAMITE.sh parallel processes

SchulzLab / TEPIC

Annotation of genomic regions using transcription factor binding sites and epigenetic data

MIT License

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runDYNAMITE.sh parallel processes #22

Closed ghost closed 7 years ago

ghost commented 7 years ago

Running the DYNAMITE pipeline in parallel (A vs B and A vs C) on several servers that share the same file system leads to interference on the file system level as several temporary files (stuff like _peaks_temp.bed or tempFasta.bed) are created in the same directory w/o using proper temporary file/folder names and thus may be deleted by another process, resulting in things like

rm: cannot remove `tempFasta.bed': No such file or directory

Florian411 commented 7 years ago

There was indeed one file without a unique identifier in the TEPIC pipeline. Please try again. However, there are no files called _peaks_temp.bedortempFasta.bed being generated anywhere, so if the problem still exists we might have to look at your particular use case.

ghost commented 7 years ago

I don't think so, if I search for tempFasta.bed, I find that file to be generated in TEPIC.sh - I thought running the full DYNAMITE pipeline implies a run of TEPIC as well?

Florian411 commented 7 years ago

Found and fixed! Thanks for pointing it out!.