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hall-lab / svtyper

Bayesian genotyper for structural variants
MIT License
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problem in running svtyper #81

Closed ytguojian closed 6 years ago

ytguojian commented 6 years ago

Hi, Recently, I have used lumpy to call the SVs from citrus genome successfully. Then, I wanted to do the genotyping by svtyper. Here, it came some problems.
The svtyper can genotype successfully before it came to chromosome 7 at position around 4378666. The output file stopped at this position. There were no error messages and the procedure was still running. Do you know what is the problem?

Cheers,

ernfrid commented 6 years ago

Very exciting genome!

From your description, my best guess would be that you've hit a region of high depth and the program is stalled reading a large number of reads. I've also seen similar behavior when svtyper doesn't have enough memory allocated to it.

What version are you using and how much memory is available to the process? If you examine svtyper using top, is the CPU utilization high? How much memory usage is reported for the program while it is stalled?

ytguojian commented 6 years ago

The version is svtyper-0.0.4. Is that too old ? I will try a newer version to do this again and will talk to you later. Cheers,

ernfrid commented 6 years ago

I would definitely try the latest version. There have been many improvements since then that may help.

ytguojian commented 6 years ago

Hi， Yes, It is the version problem. The latest version is good. Thanks!