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lifebit-ai / nf-rnaseq-salmon

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Memory error in the STAR alignment process. #4

Open manu-lifebit opened 2 years ago

manu-lifebit commented 2 years ago

The pipeline gets a 137 memory error when aligns the reads with STAR. Some memory options in the base.config file were adjusted but it's not enough to avoid the error. This should be investigated if we want to produce read counts with STAR aligned reads.

You can check the error in this run: https://cloudos.lifebit.ai/public/jobs/61dc96698c574a01e8d6806e

manu-lifebit commented 2 years ago

The error was finally addressed in https://github.com/lifebit-ai/nf-rnaseq-salmon/pull/7. Basically the base.config parameters were adjusted to fit a full human dataset (70GB allocated for the aligner step) thus avoiding the error. The issue can be closed.