k-hench
commented
4 months ago Hi @jiangzy26 and @gaoisbest :wave: ,
I believe I run into the same issue, with FastEPRR failing in step 2 with the error:
Error in .local(A, ...) : leading principal minor of order X is zeroI am running the following command:
library(FastEPRR)
FastEPRR_VCF_step2(srcFolderPath = "results/recombination/fasteprr_1",
jobNumber = 31,
currJob=5,
DXOutputFolderPath = "results/recombination/fasteprr_2" )which leads to the this output in my log file:
Total job: 31
Current job: 5
Loading required package: mboost
Loading required package: parallel
Loading required package: stabs
Total DXs in this job: 1, current DX: 1
Curr dton: 1 xton: 2
0 0.5 1 2 5 10 20 40 70 110 170
Error in .local(A, ...) : leading principal minor of order 2 is zero
Calls: FastEPRR_VCF_step2 ... <Anonymous> -> Cholesky -> Cholesky -> .local -> .Call
In addition: Warning messages:
1: In .qr.rank.def.warn(r) :
matrix is structurally rank deficient; using augmented matrix with additional 12 row(s) of zeros
2: In .local(A, ...) :
CHOLMOD warning 'not positive definite' at file 'Cholesky/t_cholmod_rowfac_worker.c', line 449
Execution haltedThe same R script appears to work alright for most of the other currjob values (all but 1,4,5,6,7,13).
For those problematic values, the error message is similar, but X in the order [X] is zero value differs:
grep "Err" logs/fasteprr/step2_*logs/fasteprr/step2_1.log:Error in .local(A, ...) : leading principal minor of order 4 is zero
logs/fasteprr/step2_13.log:Error in .local(A, ...) : leading principal minor of order 3 is zero
logs/fasteprr/step2_4.log:Error in .local(A, ...) : leading principal minor of order 4 is zero
logs/fasteprr/step2_5.log:Error in .local(A, ...) : leading principal minor of order 2 is zero
logs/fasteprr/step2_6.log:Error in .local(A, ...) : leading principal minor of order 2 is zero
logs/fasteprr/step2_7.log:Error in .local(A, ...) : leading principal minor of order 2 is zero
Do you have any idea what is off here? :eyes:
The R environment I am using is bundled within a the docker container khench/r_recrate:v0.2:
library(FastEPRR)
sessionInfo()R version 4.4.0 (2024-04-24)
Platform: x86_64-pc-linux-gnu
Running under: Debian GNU/Linux 11 (bullseye)
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3.10.3
LAPACK: /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3.10.3; LAPACK version 3.9.0
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
time zone: UTC
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] FastEPRR_2.0
loaded via a namespace (and not attached):
[1] compiler_4.4.0
zhou-sumei
Hi, I got this problem, Could you share your help? Thank you very much.
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