MAGMA Annotation error

Question

[naomibreslin95]

I am trying to run the annotation for MAGMA using the Gene locations, build 37 and european populations.

When I run the following code:

magma --annotate window=20,20 --snp-loc NCBI37.3.gene.loc --gene-loc g1000_eur.bim --out build

It skips every line and gives the error:

WARNING: on line 5522658, chromosome code 'rs188565905' not recognised; skipping gene (ID = 4)

at every position.

Also only a log file is produced. All of my files are in the same directory and they were taken from the magma site. Any information on where the issue lies?

[Ram]

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

Answer 1

[h.mon]

I have never run MAGMA, but just by reading you command-line, it appears to me you are swapping the arguments:

--snp-loc NCBI37.3.gene.loc

--gene-loc g1000_eur.bim

Shouldn't be the other way around?

--snp-loc g1000_eur.bim --gene-loc NCBI37.3.gene.loc

The error message indicates the same:

hromosome code 'rs188565905' not recognised