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precimed / mixer

Causal Mixture Model for GWAS summary statistics
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RuntimeError: exception: vector::_M_range_check: __n Error #95

Closed dxy257 closed 3 weeks ago

dxy257 commented 1 month ago

Could someone please help me with this? I am not sure what caused this error?

Singularity> python3 /home/dxy257/mixer/precimed/mixer.py fit1 --trait1-file /mnt/vstor/SOM_EPBI_XXZ10/dxy257/AD_kidney_function/mixer/sample_GWAS_data/SSGAC_EDU_2018_no23andMe_noMHC.csv.gz --out /mnt/vstor/SOM_EPBI_XXZ10/dxy257/AD_kidney_function/mixer/sample_GWAS_data/SSGAC_EDU_2018_no23andMe_noMHC.fit.rep1 --extract /mnt/vstor/SOM_EPBI_XXZ10/dxy257/AD_kidney_function/mixer/sample_GWAS_data/1000G_EUR_Phase3_plink/1000G.EUR.QC.prune_maf0p05_rand2M_r2p8.rep1.snps --bim-file /mnt/vstor/SOM_EPBI_XXZ10/dxy257/AD_kidney_function/mixer/sample_GWAS_data/1000G_EUR_Phase3_plink/1000G.EUR.QC.1.bim --ld-file /mnt/vstor/SOM_EPBI_XXZ10/dxy257/AD_kidney_function/mixer/sample_GWAS_data/1000G_EUR_Phase3_plink/1000G.EUR.QC.1.run4.ld --lib /home/dxy257/mixer/src/build/lib/libbgmg.so \

INFO:root:init(lib_name=/tools/mixer/src/build/lib/libbgmg.so, context_id=0) INFO:root:init_log(/mnt/vstor/SOM_EPBI_XXZ10/dxy257/AD_kidney_function/mixer/sample_GWAS_data/SSGAC_EDU_2018_no23andMe_noMHC.fit.rep1.log) INFO:root:log_message(***

  • mixer.py: Univariate and Bivariate Causal Mixture for GWAS
  • Version 1.2.0
  • (c) 2016-2020 Oleksandr Frei, Alexey A. Shadrin, Dominic Holland
  • Norwegian Centre for Mental Disorders Research / University of Oslo
  • Center for Multimodal Imaging and Genetics / UCSD
  • GNU General Public License v3

    Call: ./mixer.py fit1 \ --out /mnt/vstor/SOM_EPBI_XXZ10/dxy257/AD_kidney_function/mixer/sample_GWAS_data/SSGAC_EDU_2018_no23andMe_noMHC.fit.rep1 \ --lib /home/dxy257/mixer/src/build/lib/libbgmg.so \ --bim-file /mnt/vstor/SOM_EPBI_XXZ10/dxy257/AD_kidney_function/mixer/sample_GWAS_data/1000G_EUR_Phase3_plink/1000G.EUR.QC.1.bim \ --ld-file /mnt/vstor/SOM_EPBI_XXZ10/dxy257/AD_kidney_function/mixer/sample_GWAS_data/1000G_EUR_Phase3_plink/1000G.EUR.QC.1.run4.ld \ --trait1-file /mnt/vstor/SOM_EPBI_XXZ10/dxy257/AD_kidney_function/mixer/sample_GWAS_data/SSGAC_EDU_2018_no23andMe_noMHC.csv.gz \ --extract /mnt/vstor/SOM_EPBI_XXZ10/dxy257/AD_kidney_function/mixer/sample_GWAS_data/1000G_EUR_Phase3_plink/1000G.EUR.QC.prune_maf0p05_rand2M_r2p8.rep1.snps ) INFO:root:init(lib_name=/tools/mixer/src/build/lib/libbgmg.so, context_id=0) Traceback (most recent call last): File "/home/dxy257/mixer/precimed/mixer.py", line 23, in args.func(args) File "/home/dxy257/mixer/precimed/mixer/cli.py", line 646, in execute_fit1_or_test1_parser libbgmg = initialize_mixer_plugin(args) File "/home/dxy257/mixer/precimed/mixer/cli.py", line 562, in initialize_mixer_plugin libbgmg.set_ld_r2_coo_from_file(chr_label, args.ld_file.replace('@', str(chr_label))) File "/home/dxy257/mixer/precimed/mixer/libbgmg.py", line 126, in set_ld_r2_coo_from_file return self._check_error(self.cdll.bgmg_set_ld_r2_coo_from_file(self._context_id, chr_label, _p2n(filename))) File "/home/dxy257/mixer/precimed/mixer/libbgmg.py", line 418, in _check_error raise RuntimeError(self.get_last_error()) RuntimeError: exception: vector::_M_range_check: __n (which is 18446744072511363440) >= this->size() (which is 779354)

dxy257 commented 3 weeks ago

Hi there,

I have fixed the issue after modifying my GWAS summary stats file. I also had a file path error that I fixed on top of that. You may find this post helpful: https://github.com/precimed/mixer/issues/82

Best, Diya

On Sun, Jun 23, 2024 at 1:08 PM jiexiong22 @.***> wrote:

I had the same problem. Did you solve it？

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