Closed bgold04 closed 1 year ago
still struggling with this... have tried another version (0.3.5) using the binary on OSX, still no joy. I will try in conjunction with a .bed file on CentOS8, then give up until I hear... I might also try building from source, but it appears to be something I don't know about....
(base) MacBook-Pro:ExAC bgold$ ls -l
total 9603800
-rwxrwxrwx 1 bgold staff 4900634602 Dec 11 08:55 ExAC.r1.sites.vep.vcf.gz
-rwxrwxrwx 1 bgold staff 888523 Dec 11 09:05 ExAC.r1.sites.vep.vcf.gz.tbi
-rwxrwxrwx 1 bgold staff 189 Dec 11 08:32 ExAC1.toml
-rw-r--r-- 1 bgold staff 3503 Dec 11 08:32 custom.lua
-rw-r--r-- 1 bgold staff 0 Dec 11 08:32 output.txt
-rw-r--r-- 1 bgold staff 0 Dec 11 09:32 output.vcf
-rw-r--r-- 1 bgold staff 375 Dec 11 08:32 plink.log
(base) MacBook-Pro:ExAC bgold$ /Users/bgold/vcfanno/vcfanno_osx -p 2 ExAC1.toml ExAC.r1.sites.vep.vcf.gz > output.vcf
=============================================
vcfanno version 0.3.5 [built with go1.19.3]
see: https://github.com/brentp/vcfanno
=============================================
vcfanno.go:113: [Flatten] unable to open file: /ExAC.r1.sites.vep.vcf
(base) MacBook-Pro:ExAC bgold$ /Users/bgold/vcfanno/vcfanno_osx -p 2 -lua custom.lua ExAC1.toml ExAC.r1.sites.vep.vcf.gz > output.vcf
=============================================
vcfanno version 0.3.5 [built with go1.19.3]
see: https://github.com/brentp/vcfanno
=============================================
vcfanno.go:113: [Flatten] unable to open file: /ExAC.r1.sites.vep.vcf
(base) MacBook-Pro:ExAC bgold$
Your toml file contains:
file="ExAC.r1.sites.vep.vcf"
but that should be:
file="ExAC.r1.sites.vep.vcf.gz"
Hello, this is what I get!