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mozack / abra

Assembly Based ReAligner
MIT License
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Excessive run time #23

Open dh10 opened 8 years ago

dh10 commented 8 years ago

150x whole exome (64 Mb) not completed after 24 hours w 18 cores while building all_contigs.fasta (which continues to increase in size). This is a reproducible sample specific issue as other samples at similar depth take 1.5 - 3 hours. Occurs with default settings.

mozack commented 8 years ago

We run into this sometimes with noisy FFPE samples. The workaround is to prune the assembly graphs more aggressively. You might try re-running this sample using the following params:

--mnf 5 --mbq 150

dh10 commented 8 years ago

Unfortunately, with new parameters, it still runs at least 12 hours with 18 cores before we stop it. It is fresh frozen material and not FFPE. I will look closer at the QC parameters of the samples that are associated with this issue. Thanks!