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Taiji-pipeline / Taiji

All-in-one analysis pipeline
https://taiji-pipeline.github.io/
BSD 3-Clause "New" or "Revised" License
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Unable to use parallelism #1

Closed ravipatel4 closed 5 years ago

ravipatel4 commented 5 years ago

Hello, It looks like the pipeline is unable to use the workflow-level parallelism. I am using the following command to run the pipeline on ~50 ATAC- and RNA-Seq samples using a 32 cores / 128 GB RAM server. taiji-Linux-x86_64 run --config config.yml -N 16 However, the pipeline uses a single core. Is it possible to use multiple cores for the processor-intensive jobs, like TFBS finding in open chromatin using FIMO, so that the analysis can be performed in shorter amount of time? I am using the latest release (v 0.5.0) of the pipeline.

Thank you for your help.

kaizhang commented 5 years ago

Please wait 1~2 weeks for the v1.0 beta release. This issue will be fixed in the new release.

kaizhang commented 5 years ago

The beta version is released! https://github.com/Taiji-pipeline/Taiji/releases/tag/1.0.0.21 To use multiple cores (5 cores for example), add -n 5 +RTS -N5 to the end. Here is a tutorial in progress: https://taiji-pipeline.github.io/blog_ATAC-seq_walkthrough.html