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It takes several days to preprocess BAM files for testing #51

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jingmeng-bioinformatics opened this issue Nov 4, 2019 · 2 comments
Open

It takes several days to preprocess BAM files for testing #51

jingmeng-bioinformatics opened this issue Nov 4, 2019 · 2 comments

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@jingmeng-bioinformatics
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Hi Sayed, I started preprocessing the whole genome bam files (tumor and matched normal) for testing on my local computer (--number_threads 1) four days ago, and it has not finished now. Why it takes such long time to preprocess the whole genome bam files?
@msahraeian
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@jingmeng-bioinformatics It depends on your sample coverages. For me, I usually run on a 28-threads cluster and it will take a couple of hours. So, If you run on 1 thread it may take a few days.

@jingmeng-bioinformatics
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jingmeng-bioinformatics commented Nov 5, 2019 •
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Ok, thank you for your reply.

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@msahraeian @jingmeng-bioinformatics