Error with step 2

[brettChapman]

Hi

I'm using fastEPRR v2.0 and I'm getting a consistent error when reaching step 2 after I have ran step 1 on each chromosome.

I've been getting this error:

srun -n 1 singularity exec --bind /data/pangenome_20way/morex_v3_rerun/recombination_rates:/data/pangenome_20way/morex_v3_rerun/recombination_rates /data/fasteprr_builds/fasteprr.sif /usr/bin/Rscript workflow_54373.R
Total job: 1
Current job: 1
Loading required package: mboost
Loading required package: parallel
Loading required package: stabs
Total DXs in this job: 35402, current DX: 1
Curr dton: 61 xton: 171
0 0.5 1 2 5 10 20 40 70 110 170 
Error in if (currH <= zeroLow) { : missing value where TRUE/FALSE needed
Calls: FastEPRR_VCF_step2 -> lapply -> FUN -> sameConfig -> lapply -> FUN
Execution halted

The script which gets run is:

library(FastEPRR)
dir.create("/data/pangenome_20way/morex_v3_rerun/recombination_rates/fastEPRR_step2_output")
FastEPRR_VCF_step2(srcFolderPath="/data/pangenome_20way/morex_v3_rerun/recombination_rates/fastEPRR_output", jobNumber = 1, currJob = 1, DXOutputFolderPath="/data/pangenome_20way/morex_v3_rerun/recombination_rates/fastEPRR_step2_output")
dir.create("/data/pangenome_20way/morex_v3_rerun/recombination_rates/fastEPRR_results")
FastEPRR_VCF_step3(srcFolderPath="/data/pangenome_20way/morex_v3_rerun/recombination_rates/fastEPRR_output", DXFolderPath="/data/pangenome_20way/morex_v3_rerun/recombination_rates/fastEPRR_step2_output", finalOutputFolderPath="/data/pangenome_20way/morex_v3_rerun/recombination_rates/fastEPRR_results")

Thank you for any help you can provide.

[brettChapman]

I've ran fastEPRR version 2.0 on a VCF file which had previously been ran some time last year by a work colleague of mine, which worked for him. However with the version 2.0 I downloaded and installed I'm getting errors and neither of us are sure what's wrong.

I've just tried running with fastEPRR version 1.0 and the problem disappears and runs ok. Has the code for version 2.0 been changed recently?

[brettChapman]

Since I can run version 1.0 without issue, is there any advantage of using version 2.0 over version 1.0?

[yangwukaidi]

I also have the same problem. Have you solved this problem？