Unable to open...

[bgold04]

Hello, this is what I get!

(base) [bgold@centos8-local ExAc]$ ls -l
total 4749472
-rw-rw-r-- 1 bgold bgold       3503 Dec 10 20:04 custom.lua
-rw-rw-r-- 1 bgold bgold        189 Dec 10 20:01 ExAC1.toml
-rw-rw-r-- 1 bgold bgold 4862558270 Dec 10 20:38 ExAC.r1.sites.vep.vcf.gz
-rw-rw-r-- 1 bgold bgold     877783 Dec 11 08:08 ExAC.r1.sites.vep.vcf.gz.tbi
-rw-rw-r-- 1 bgold bgold          0 Dec 10 20:06 output.txt
-rw-rw-r-- 1 bgold bgold          0 Dec 10 20:17 output.vcf
-rw-rw-r-- 1 bgold bgold        375 Dec 10 19:19 plink.log
(base) [bgold@centos8-local ExAc]$ vcfanno -p 16 ExAC1.toml ExAC.r1.sites.vep.vcf.gz > output.vcf

=============================================
vcfanno version 0.3.3 [built with go1.16.5]

see: https://github.com/brentp/vcfanno
=============================================
vcfanno.go:113: [Flatten] unable to open file: /ExAC.r1.sites.vep.vcf
(base) [bgold@centos8-local ExAc]$ cat ExAC1.toml
[[annotation]]
file="ExAC.r1.sites.vep.vcf"
# the special name 'ID' pulls out the rs id from the VCF
fields = ["AC_AFR", "AC_AMR", "AC_EAS", "AF"]
ops=["first", "first", "first", "first"]

(base) [bgold@centos8-local ExAc]$ 

[bgold04]

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$ 

[brentp]

Your toml file contains:

file="ExAC.r1.sites.vep.vcf"

but that should be:

file="ExAC.r1.sites.vep.vcf.gz"