ReLERNN_SIMULATE not splitting vcf file properly

[menietoblazquez]

Dear users,

I have used ReLERNN with a previous individuals resequencing data with no problem at all.

However, I am running into problems with a new dataset. It seems ReLERNN fails in the step of splitting the vcf into the different chromosome vcfs. By looking at this directory for the analzsis that previously worked, I see there are files missing.

[s_menb@jupiter SS1]$ cd splitVCFs/ [s_menb@jupiter splitVCFs]$ ll total 4204 -rw-r--r--. 1 s_menb clusteruser 1285117 Mar 1 10:59 SS1.m2M2.recode.CLEAN_Chr1:0-61357614.hdf5 -rw-r--r--. 1 s_menb clusteruser 1284380 Mar 1 10:59 SS1.m2M2.recode.CLEAN_Chr2:0-58906861.hdf5 -rw-r--r--. 1 s_menb clusteruser 1162613 Mar 1 10:59 SS1.m2M2.recode.CLEAN_Chr3:0-53163979.hdf5 -rw-r--r--. 1 s_menb clusteruser 566572 Mar 1 10:59 SS1.m2M2.recode.CLEAN_Chr4:0-17018963.hdf5

My vcf file (for a single individual was created using Platypus and filtering for biallelic positions.

My bed file is tab separated as follows:

Chr1 0 61357614 Chr2 0 58906861 Chr3 0 53163979 Chr4 0 17018963

And below the error message:

Traceback (most recent call last): File "/cluster/software/relernn/ReLERNN-1.0.0_ve/bin/ReLERNN_SIMULATE", line 245, in main() File "/cluster/software/relernn/ReLERNN-1.0.0_ve/bin/ReLERNN_SIMULATE", line 160, in main thetaW=maxS/a ZeroDivisionError: division by zero

Any ideas or suggestions?

Best wishes

ME

[menietoblazquez]

This problem solved once I used a vcf file with more than one individual.

[andrewkern]

yes you need more than one sample to run this software