Dear gao,
Thanks for your great software!

Here I got some issue about running FastEPRR 1.0 at step2 about installing mboost. I cannot installing the mboost package although I tried a lot still cannot solve that, so frustrate about this mboost package. Could you give some ways to solve that problem!

I've also tried installed mboost_2.9-7.zip locally, but the step2 of FastEPPR still performed the installing of mboost and failed for some dependencies which are so difficant to install! is there any parameter to close the installing?

Appreciate!
best regards,
yours,
Liu

Hi, I got this problem, Could you share your help? Thank you very much.

R version 4.3.2 (2023-10-31) -- "Eye Holes"
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用'help.start()'通过HTML浏览器来看帮助文件。
用'q()'退出R.

library(FastEPRR)

FastEPRR_VCF_step2(srcFolderPath="/data2/other_one_project/result/6-recombination_rate/FastEPRR_result/Chr01/step1", jobNumber = 1, currJob = 1, getCI = FALSE,

• trainingSet1 = "0;0.5;1;5;10;25;50;80;120;170;250", trainingSet2 = "260;300;350;450",DXOutputFolderPath = "/data2/other_one_project/result/6-recombination_rate/FastEPRR_result/Chr01/step2")
  Total job: 1
  Current job: 1
  载入需要的程辑包：mboost
  载入需要的程辑包：parallel
  载入需要的程辑包：stabs
  Total DXs in this job: 881, current DX: 1
  Curr dton: 0 xton: 9
  0 0.5 1 5 10 25 50 80 120 170 250
  260 300 350 450
  Total DXs in this job: 881, current DX: 2
  Curr dton: 1 xton: 6
  0 0.5 1 5 10 25 50 80 120 170 250
  260 300 350 450
  Total DXs in this job: 881, current DX: 3
  Curr dton: 1 xton: 10
  0 0.5 1 5 10 25 50 80 120 170 250
  260 300 350 450
  Total DXs in this job: 881, current DX: 4
  Curr dton: 1 xton: 5
  0 0.5 1 5 10 25 50 80 120 170 250
  Total DXs in this job: 881, current DX: 5
  Curr dton: 0 xton: 11
  0 0.5 1 5 10 25 50 80 120 170 250
  Total DXs in this job: 881, current DX: 6
  Curr dton: 6 xton: 22
  0 0.5 1 5 10 25 50 80 120 170 250
  Total DXs in this job: 881, current DX: 7
  Curr dton: 3 xton: 5
  0 0.5 1 5 10 25 50 80 120 170 250
  260 300 350 450
  Total DXs in this job: 881, current DX: 8
  Curr dton: 3 xton: 13
  0 0.5 1 5 10 25 50 80 120 170 250
  Total DXs in this job: 881, current DX: 9
  Curr dton: 1 xton: 2
  0 0.5 1 5 10 25 50 80 120 170 250
  Error in .local(A, ...) : leading principal minor of order 4 is zero
  Calls: FastEPRR_VCF_step2 ... -> Cholesky -> Cholesky -> .local -> .Call
  此外: There were 50 or more warnings (use warnings() to see the first 50)
  停止执行

Hi,

I'm having a problem when running the function FastEPRR_VCF_step2, the step1 function worked fine.

I used for the step2:

FastEPRR_VCF_step2(srcFolderPath = "/home/ckessler/scratch/recombination_rate/step1", 
                     replicateNum = 100, getCI = TRUE,
                     DXOutputFolderPath = "/home/ckessler/scratch/recombination_rate/step2")

Loading required package: mboost
Loading required package: parallel
Loading required package: stabs
Total DXs in this job: 1024, current DX: 1
Curr dton: 54 xton: 290
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

Any help would be greatly appreciated.

I can't seem to install the package in R. It says not available nor I can access the webpage of FastEPRR.

Princy

您好，我按照您文章中提供的地址以及您在别的回复中提供的地址依然无法下载FastEPRR，方便的话可以往我的邮箱发一份吗？[email protected]

Hi sumei,

I used R3.6.3 to run FastEPRR software on Linux platform and face with similar problem.

The commands were used as follows:

library(FastEPRR)
setwd("work_Path/step1_Path")

FastEPRR_VCF_step1(vcfFilePath = "chr1_phased_imputed.vcf.gz", winLength = 50000, winDXThreshold = 2, srcOutputFilePath = "work_Path/step1_Path/chr1")

There is no issue in step1, however, stop happened when running step2 using below code.

FastEPRR_VCF_step2(srcFolderPath = "work_Path/step1_Path", DXOutputFolderPath = "work_Path/step2_Path")

Total job: 1
Current job: 1
Loading required package: mboost
Loading required package: parallel
Loading required package: stabs
Total DXs in this job: 284, current DX: 1
Curr dton: 0 xton: 24
0 0.5 1 2 5 10 20 40 70 110 170
180 190 200 220 250 300 350
Total DXs in this job: 284, current DX: 2
Curr dton: 0 xton: 8
0 0.5 1 2 5 10 20 40 70 110 170
180 190 200 220 250 300 350
Total DXs in this job: 284, current DX: 3
Curr dton: 0 xton: 13
0 0.5 1 2 5 10 20 40 70 110 170
180 190 200 220 250 300 350
............................................................. #skip the middle log information
............................................................. #skip the middle log information
Total DXs in this job: 284, current DX: 211
Curr dton: 0 xton: 188
0 0.5 1 2 5 10 20 40 70 110 170
180 190 200 220 250 300 350
Total DXs in this job: 284, current DX: 212
Curr dton: 0 xton: 119
0 0.5 1 2 5 10 20 40 70 110 170
180 190 200 220 250 300 350
Total DXs in this job: 284, current DX: 213
Curr dton: 0 xton: 2
0 0.5 1 2 5 10 20 40 70 110 170
Error in Cholesky(forceSymmetric(XtX)) :
internal_chm_factor: Cholesky factorization failed
Calls: FastEPRR_VCF_step2 ... FUN -> dpp.blg -> -> Cholesky -> Cholesky
In addition: There were 50 or more warnings (use warnings() to see the first 50)
Execution halted

I found that FastEPRR may cannot deal with condition when xton equal to 2 ( xton: 2).
(1) Could you help to check it? You can do it by setting winDXThreshold = 2 in step1.

(2) Could you explain the meaning of collumn names in output file generated from step1? What's the meaning of "wdou","wxton","wH","wHetero","wavsk2","wavr2" ?

chr nsam wdou wxton wH wHetero wavsk2 wavr2 misInfo startPos endPos
1 626 0 15 27 0.864 0.299366933297507 0.129662675683414 NA 282128 332127
1 626 0 16 36 0.939649840255591 0.354471497170007 0.0993477367149401 NA 432128 482127

(3) Although FastEPRR_VCF_step1() function contain "qualThreshold" parameter, it doesn't work to filter SNPs. As VCF file usually is phased with Beagle software before using FastEPRR, the “QUAL” column information usually represent with "." in phased VCF file. Below is a part of information in Example VCF file:
So, "qualThreshold" parameter may need to remove from FastEPRR_VCF_step1() function. I'm sorry if I miss something or have a wrong understanding about this parameter.

##fileformat=VCFv4.1
##reference=/lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta
##source=omni.b37.chr1.haps.gz
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA18525 NA18526 NA18527
1 534247 . C T . . AC=33;AN=4246 GT 0|0 0|0 0|0
1 565286 . C T . . AC=4246;AN=4246 GT 1|1 1|1 1|1
1 569624 . T C . . AC=4229;AN=4246 GT 1|1 1|1 1|1

Thanks for your help and time!

Best,
Qi

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.

hello, could you send me a FastEPRR package（.tar.gz）, because the web URL is not valid（http://www.picb.ac.cn/evolgen）。my E-mail ：[email protected] 。thank you.

hello, I use your software to calculated the recombination rate, but it always occur error 'Please input valid character value 'srcFolderPath' (The parent directory of 'srcOutputFilePath' in step1 when i run FastEPRR_VCF_step2, could you help me how to solve it?

Dear gao,
Thanks for your great software!
Here I got some issue about running FastEPRR 2.0 at step2.
This is the error_log.

This is the output_file in /step1.

I get an error when I run the second step directly, but when I "grep NA" to process the result file from the first step, I can avoid this error, even if the result is not complete.

Could you please help me solve this problem?

Hi,
When I use the R software FastEPRR to detect the rho and find a question:

My R code:
library(FastEPRR)
FastEPRR_ALN(alnFilePath = "D_A/D_A.chr1A.haplo.fas",format = "fasta",
winLength = "10",stepLength = "2",outputFilePath = "D_A/D_A.chr1A.haplo.fas.rho")

the error:
Error in Cholesky(forceSymmetric(XtX)) :
internal_chm_factor: Cholesky factorization failed
此外: There were 50 or more warnings (use warnings() to see the first 50)

why?