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gymreklab / GangSTR

A tool for profiling long STRs from short reads
GNU General Public License v2.0
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Warning in Gangstr run #110

Closed hchetia closed 3 years ago

hchetia commented 3 years ago

I am getting the foll. warnings during my Gangstr runs- [GangSTR-2.5.0] WARNING: Region exceeds maximum total processed reads per sample. What does this mean ?

best, hasna

zhangjinpengGithub commented 3 years ago

I have the same problem, could you tell me if this warning is serious?

nmmsv commented 3 years ago

We have set a maximum number of processed reads per locus since we noticed regions that were "sinks" for reads that had excessive running time (way too many reads mapped to those regions due to something like segmental duplications). However, this threshold is set somewhat arbitrarily for the 30X WGS samples that we were working with at the time. You can increase this threshold if you need to, using this input: --max-proc-read <int>

zhangjinpengGithub commented 3 years ago

I have the following error, is it serious? [GangSTR-2.5.0] SpanClassProb::Divide by Zero prevented!

We have set a maximum number of processed reads per locus since we noticed regions that were "sinks" for reads that had excessive running time (way too many reads mapped to those regions due to something like segmental duplications). However, this threshold is set somewhat arbitrarily for the 30X WGS samples that we were working with at the time. You can increase this threshold if you need to, using this input: --max-proc-read <int>