installing dbNSFP takes forever about vep_plugins HOT 6 CLOSED

it worke, thanks a lot!

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Probably a problem with cat trying to find the file in the current directory. Did your second command work?

Thanks for the reply. Yes, I forgot to run head -n1 dbNSFP3.5a_variant.chr1 > h
command first.

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Hi, is the file size for dbNSFP_hg19.gz getting bigger? The final size is around 20G. I have to specify a separate directory for sorting because the tmp space is not big enough. I ran it like this: cat dbNSFP3.5a_variant.chr* | grep -v ^#chr | awk '$8 != "."' | sort -T /PATH_TO_SORT_DIR/ -k8,8 -k9,9n - | cat h - | bgzip -c > dbNSFP3.5a_grch37.txt.gz
It ran in 4 hours for me.

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Yes I saw that the tmp space grows trmendously, I'll try using a separate directory, thanks a lot for the trick , I'll get back to you after

from vep_plugins.

Hi, is the file size for dbNSFP_hg19.gz getting bigger? The final size is around 20G. I have to specify a separate directory for sorting because the tmp space is not big enough. I ran it like this: cat dbNSFP3.5a_variant.chr* | grep -v ^#chr | awk '$8 != "."' | sort -T /PATH_TO_SORT_DIR/ -k8,8 -k9,9n - | cat h - | bgzip -c > dbNSFP3.5a_grch37.txt.gz It ran in 4 hours for me.

Using your trick, for me gave this message cat: h: No such file or directory
and I used this command for that:
cd ./dbNSFP3.5a
cat dbNSFP3.5a_variant.chr* | grep -v ^#chr | awk '$8 != "."' | sort -T ./dbNSFP3.5a/tmp -k8,8 -k9,9n - | cat h - | bgzip -c > dbNSFP3.5a.txt.gz
Do you know why?

from vep_plugins.

Probably a problem with cat trying to find the file in the current directory.
Did your second command work?

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