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immunogenomics / goshifter

GoShifter
http://www.broadinstitute.org/mpg/goshifter/
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Error with goshifter.strat.py #4

Open vicb-s opened 5 years ago

vicb-s commented 5 years ago

Hi. I have problems with the goshifter.strat.py function. See example below. Can' t get passed the "Seed for random set to" message. The input files, including the precalculated LD proxy file, have been used with goshifter.py without any problems. My experience with GoShifter and similar softwares is limited, so there might be something I am doing wrong here. Some help would be appreciated.

./goshifter.strat.py --snpmap snpmappings.hg19.txt --annotation-a neuron.bed.gz --annotation-b glia.bed.gz --permute 1000 --proxies proxy_hg19_GoShifter.txt --out neuron.strat.glia

Seed for random set to: NQUORl3L4NA=

Usage: ./goshifter.strat.py --snpmap FILE --annotation-a FILE --annotation-b FILE --permute INT --ld DIR --out FILE [--rsquared NUM --window NUM --min-shift NUM --max-shift NUM --ld-extend NUM --no-ld]

SCZXH commented 5 years ago

I have faced the same problem. Could you please kindly tell me how to fix it?