Error while running locuscomparer

[nbbarrientos]

Hello Boxiang,

I was trying to run your tool and encountered the following error:

Error in .local(conn, statement, ...) :
could not run statement: MySQL server has gone away

I'm not entirely sure what the problem is. I would appreciate your help. Thank you.

Nelson Barrientos

[nbbarrientos]

Hello Boxiang,

I think I figured out the error from my previous comment by reducing the length of my data frames. However, I am now encountering the following problem:

Error in locuscompare(in_fn1 = leafcutter_snps, in_fn2 = gtex_CAD_snps, :
There must be one and only one chromosome.

I'm pretty sure I'm using snps from only one chromosome since the data frames I provide are from one locus only. Do you you have any suggestions as to what might be going on? Thanks.

Nelson Barrientos

[repeatpipettor]

Hi @nbbarrientos or @boxiangliu, were you ever able to solve the "There must be one and only one chromosome." issue? I encountered it recently as well and my input files also use SNPs from only one chromosome. My understanding is locuscompare calls get_position which calls positions from the MySQL server. Thanks for any help in advance.

[xinranxu0930]

I encountered a similar issue, but I was able to resolve it. The software locates SNPs based on their rsID. However, some SNPs do not have an rsID, and these are typically represented by a dot (“.”) in the rsID field.

When running locuscompare, you can either remove these SNPs or replace the “.” with their unique ID. The format for the unique ID is: chrom:position:alleleA_alleleB