When I tried to run SAIGE step2 on chrX(chr23).
The error occurs when running step2 .Well begun at first,but when get into numPassMarker: 2000 will get error and stop.
But using the same code to run chr1-chr22 were successfully.
The error I receive is:
Minimum MAF of markers to be tested is 0.000361559
It is a binary trait
Analyzing 12344 cases and 21914 controls
isCondition is FALSE
Analysis started at 1686531956 Seconds
user system elapsed
140.705 17.299 139.631
[1] 1000
numPassMarker: 999
user system elapsed
264.712 17.772 264.130
[1] 2000
numPassMarker: 1999
*** Error in `/home/Tools/miniconda3/envs/saige/lib/R/bin/exec/R': corrupted size vs. prev_size: 0x00005612753cf690 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x7f5d4)[0x7fa96aca75d4]
/lib64/libc.so.6(+0x82eae)[0x7fa96acaaeae]
/lib64/libc.so.6(__libc_malloc+0x4c)[0x7fa96acad1ac]
/home/Tools/miniconda3/envs/saige/lib/R/bin/exec/../../lib/libR.so(Rf_allocVector3+0x80e)[0x7fa96b192fee]
/home/Tools/miniconda3/envs/saige/lib/R/bin/exec/../../lib/libR.so(R_alloc+0x4c)[0x7fa96b193d2c]
/home/Tools/miniconda3/envs/saige/lib/R/bin/exec/../../lib/libR.so(+0x230528)[0x7fa96b225528]
/home/Tools/miniconda3/envs/saige/lib/R/bin/exec/../../lib/libR.so(+0x141121)[0x7fa96b136121]
/home/Tools/miniconda3/envs/saige/lib/R/bin/exec/../../lib/libR.so(Rf_eval+0x80)[0x7fa96b150860]
/home/Tools/miniconda3/envs/saige/lib/R/bin/exec/../../lib/libR.so(+0x15d5af)[0x7fa96b1525af]
/home/Tools/miniconda3/envs/saige/lib/R/bin/exec/../../lib/libR.so(R_execMethod+0x243)[0x7fa96b1536d3]
/home/Tools/miniconda3/envs/saige/lib/R/library/methods/libs/methods.so(+0x5282)[0x7fa96b6f0282]
/home/Tools/miniconda3/envs/saige/lib/R/bin/exec/../../lib/libR.so(+0x1a64bb)[0x7fa96b19b4bb]
/home/Tools/miniconda3/envs/saige/lib/R/bin/exec/../../lib/libR.so(Rf_eval+0x74b)[0x7fa96b150f2b]
/home/Tools/miniconda3/envs/saige/lib/R/bin/exec/../../lib/libR.so(+0x15d5af)[0x7fa96b1525af]
/home/Tools/miniconda3/envs/saige/lib/R/bin/exec/../../lib/libR.so(Rf_applyClosure+0x19e)[0x7fa96b15337e]
/home/Tools/miniconda3/envs/saige/lib/R/bin/exec/../../lib/libR.so(+0x14adc6)[0x7fa96b13fdc6]
/home/Tools/miniconda3/envs/saige/lib/R/bin/exec/../../lib/libR.so(Rf_eval+0x80)[0x7fa96b150860]
/home/Tools/miniconda3/envs/saige/lib/R/bin/exec/../../lib/libR.so(+0x15d5af)[0x7fa96b1525af]
/home/Tools/miniconda3/envs/saige/lib/R/bin/exec/../../lib/libR.so(Rf_applyClosure+0x19e)[0x7fa96b15337e]
/home/Tools/miniconda3/envs/saige/lib/R/bin/exec/../../lib/libR.so(+0x14adc6)[0x7fa96b13fdc6]
/home/Tools/miniconda3/envs/saige/lib/R/bin/exec/../../lib/libR.so(Rf_eval+0x80)[0x7fa96b150860]
/home/Tools/miniconda3/envs/saige/lib/R/bin/exec/../../lib/libR.so(+0x15d5af)[0x7fa96b1525af]
/home/Tools/miniconda3/envs/saige/lib/R/bin/exec/../../lib/libR.so(Rf_applyClosure+0x19e)[0x7fa96b15337e]
/home/Tools/miniconda3/envs/saige/lib/R/bin/exec/../../lib/libR.so(Rf_eval+0x2b1)[0x7fa96b150a91]
/home/Tools/miniconda3/envs/saige/lib/R/bin/exec/../../lib/libR.so(Rf_ReplIteration+0x256)[0x7fa96b186216]
/home/Tools/miniconda3/envs/saige/lib/R/bin/exec/../../lib/libR.so(+0x1915d9)[0x7fa96b1865d9]
/home/Tools/miniconda3/envs/saige/lib/R/bin/exec/../../lib/libR.so(run_Rmainloop+0x49)[0x7fa96b186689]
/home/Tools/miniconda3/envs/saige/lib/R/bin/exec/R(main+0x1d)[0x5612623f605d]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x7fa96ac4a3d5]
/home/Tools/miniconda3/envs/saige/lib/R/bin/exec/R(+0x108d)[0x5612623f608d]
Hi, Thank you for providing this awesome tool.
When I tried to run SAIGE step2 on chrX(chr23). The error occurs when running step2 .Well begun at first,but when get into numPassMarker: 2000 will get error and stop. But using the same code to run chr1-chr22 were successfully.