After the conditional analysis, the colocalization results would be -nan for both samstats 1 and samsats2. What might be wrong? Below is the full log. Thank you very much!
[2024-05-19 08:27:45.392] [pwcoco_log] [info] Summary stats 1 is treated as a file.
[2024-05-19 08:27:45.393] [pwcoco_log] [info] Summary stats 2 is treated as a file.
[2024-05-19 08:27:45.393] [pwcoco_log] [info] OpenMP will attempt to use up to 8 threads.
[2024-05-19 08:27:45.397] [pwcoco_log] [info] Reading data from phenotype file: ../anti-b2scr1.sumstats.
[2024-05-19 08:27:45.400] [pwcoco_log] [warning] It is preferable to use the full summary statistics to estimate the phenotype variance; you can ignore this warning if the summary statistics file you have provided are the full summary statistics.
[2024-05-19 08:27:45.400] [pwcoco_log] [warning] You can calculate the full phenotype variance by using either the '--pve' flag or '--pve_file' flag.
[2024-05-19 08:27:45.407] [pwcoco_log] [info] Read a total of: 3711 lines in phenotype file ../anti-b2scr1.sumstats.
[2024-05-19 08:27:45.407] [pwcoco_log] [info] Phenotypic variance estimated from summary statistcs of all SNPs: 0.00
[2024-05-19 08:27:45.407] [pwcoco_log] [info] Reading data from phenotype file: ../b2scr1.sumstats.
[2024-05-19 08:27:45.408] [pwcoco_log] [warning] It is preferable to use the full summary statistics to estimate the phenotype variance; you can ignore this warning if the summary statistics file you have provided are the full summary statistics.
[2024-05-19 08:27:45.408] [pwcoco_log] [warning] You can calculate the full phenotype variance by using either the '--pve' flag or '--pve_file' flag.
[2024-05-19 08:27:45.416] [pwcoco_log] [info] Read a total of: 3711 lines in phenotype file ../b2scr1.sumstats.
[2024-05-19 08:27:45.416] [pwcoco_log] [info] Phenotypic variance estimated from summary statistcs of all SNPs: 0.00
[2024-05-19 08:27:45.477] [pwcoco_log] [info] Colocalisation analysis initialised with 3709 SNPs.
[2024-05-19 08:27:45.479] [pwcoco_log] [info] Unconditioned colocalisation results.
[2024-05-19 08:27:45.479] [pwcoco_log] [info] H0: 0.52; H1: 0.19; H2: 0.19; H3: 0.07; H4: 0.02; abf_all: 0.65.
[2024-05-19 08:27:45.485] [pwcoco_log] [info] Reading data from bim file: /mnt/c/Users/digim/OneDrive - cumc.columbia.edu/Genetic correlation and meta analysis/data_cleaning/g1000_eur.bim.
[2024-05-19 08:28:01.281] [pwcoco_log] [info] Number of SNPs read from .bim file: 22665064.
[2024-05-19 08:29:27.477] [pwcoco_log] [info] Number of SNPs matched from .bim file to the phenotype data: 3689.
[2024-05-19 08:29:27.642] [pwcoco_log] [info] Reading data from fam file: /mnt/c/Users/digim/OneDrive - cumc.columbia.edu/Genetic correlation and meta analysis/data_cleaning/g1000_eur.fam.
[2024-05-19 08:29:27.644] [pwcoco_log] [info] Successfully read 503 individuals from .fam file.
[2024-05-19 08:29:27.644] [pwcoco_log] [warning] Sample size for the reference panel is below the recommended size of 4000!
[2024-05-19 08:29:27.644] [pwcoco_log] [warning] Continuing analysis, but please consider using a larger reference panel.
[2024-05-19 08:29:27.955] [pwcoco_log] [info] Finished reading .bed file. Genotype data for 503 individuals and 3689 SNPs read.
[2024-05-19 08:29:27.956] [pwcoco_log] [info] Filtering SNPs with MAF <= 0.01.
[2024-05-19 08:29:27.957] [pwcoco_log] [info] After filtering based on MAF, there are 3511 SNPs remaining in the analysis (amount removed: 178).
[2024-05-19 08:29:27.962] [pwcoco_log] [info] [anti-b2scr1.sumstats] Total amount of SNPs matched from phenotype file with reference SNPs are: 3511.
[2024-05-19 08:29:28.230] [pwcoco_log] [info] [anti-b2scr1.sumstats] Performing stepwise model selection on 3511 SNPs; p cutoff = 5e-08, collinearity = 0.9 assuming complete LE between SNPs more than 10.0 Mb away).
[2024-05-19 08:29:28.231] [pwcoco_log] [info] [anti-b2scr1.sumstats] Selected SNP rs9902706 with chisq 40.28 and pval 2.20e-10.
[2024-05-19 08:29:28.302] [pwcoco_log] [info] [anti-b2scr1.sumstats] Selected entry SNP rs1003425 with cpval 2.00e+00.
[2024-05-19 08:29:28.302] [pwcoco_log] [info] [anti-b2scr1.sumstats] rs1003425 does not meet threshold
[2024-05-19 08:29:28.302] [pwcoco_log] [info] [anti-b2scr1.sumstats] Finally, 1 associated SNPs have been selected.
[2024-05-19 08:29:28.302] [pwcoco_log] [info] [anti-b2scr1.sumstats] (0 SNPs eliminated by backward selection.)
[2024-05-19 08:29:28.309] [pwcoco_log] [info] [b2scr1.sumstats] Total amount of SNPs matched from phenotype file with reference SNPs are: 3511.
[2024-05-19 08:29:28.632] [pwcoco_log] [info] [b2scr1.sumstats] Performing stepwise model selection on 3511 SNPs; p cutoff = 5e-08, collinearity = 0.9 assuming complete LE between SNPs more than 10.0 Mb away).
[2024-05-19 08:29:28.632] [pwcoco_log] [info] [b2scr1.sumstats] Selected SNP rs1801689 with chisq 4331.88 and pval 0.00e+00.
[2024-05-19 08:29:28.703] [pwcoco_log] [info] [b2scr1.sumstats] Selected entry SNP rs1003425 with cpval 2.00e+00.
[2024-05-19 08:29:28.703] [pwcoco_log] [info] [b2scr1.sumstats] rs1003425 does not meet threshold
[2024-05-19 08:29:28.703] [pwcoco_log] [info] [b2scr1.sumstats] Finally, 1 associated SNPs have been selected.
[2024-05-19 08:29:28.703] [pwcoco_log] [info] [b2scr1.sumstats] (0 SNPs eliminated by backward selection.)
[2024-05-19 08:29:28.704] [pwcoco_log] [info] There are 1 selected SNPs in the exposure dataset and 1 in the outcome dataset.
[2024-05-19 08:29:28.704] [pwcoco_log] [info] Performing 1 conditional and colocalisation analyses.
[2024-05-19 08:29:28.764] [pwcoco_log] [info] Colocalisation analysis initialised with 3478 SNPs.
[2024-05-19 08:29:28.765] [pwcoco_log] [info] Conditioned results for SNP1: rs9902706, SNP2: rs1801689
[2024-05-19 08:29:28.766] [pwcoco_log] [info] H0: -nan; H1: -nan; H2: -nan; H3: -nan; H4: -nan; abf_all: -nan.
[2024-05-19 08:29:28.823] [pwcoco_log] [info] Colocalisation analysis initialised with 3479 SNPs.
[2024-05-19 08:29:28.824] [pwcoco_log] [info] Conditioned results for SNP1: rs9902706, SNP2: unconditioned
[2024-05-19 08:29:28.824] [pwcoco_log] [info] H0: -nan; H1: -nan; H2: -nan; H3: -nan; H4: -nan; abf_all: -nan.
[2024-05-19 08:29:28.886] [pwcoco_log] [info] Colocalisation analysis initialised with 3506 SNPs.
[2024-05-19 08:29:28.887] [pwcoco_log] [info] Conditioned results for SNP1: unconditioned, SNP2: rs1801689
[2024-05-19 08:29:28.887] [pwcoco_log] [info] H0: -nan; H1: -nan; H2: -nan; H3: -nan; H4: -nan; abf_all: -nan.
[2024-05-19 08:29:28.892] [pwcoco_log] [info] Analysis finished. Computational time: 103.499974 secs
Hi,
After the conditional analysis, the colocalization results would be -nan for both samstats 1 and samsats2. What might be wrong? Below is the full log. Thank you very much!
[2024-05-19 08:27:45.392] [pwcoco_log] [info] Summary stats 1 is treated as a file. [2024-05-19 08:27:45.393] [pwcoco_log] [info] Summary stats 2 is treated as a file. [2024-05-19 08:27:45.393] [pwcoco_log] [info] OpenMP will attempt to use up to 8 threads. [2024-05-19 08:27:45.397] [pwcoco_log] [info] Reading data from phenotype file: ../anti-b2scr1.sumstats. [2024-05-19 08:27:45.400] [pwcoco_log] [warning] It is preferable to use the full summary statistics to estimate the phenotype variance; you can ignore this warning if the summary statistics file you have provided are the full summary statistics. [2024-05-19 08:27:45.400] [pwcoco_log] [warning] You can calculate the full phenotype variance by using either the '--pve' flag or '--pve_file' flag. [2024-05-19 08:27:45.407] [pwcoco_log] [info] Read a total of: 3711 lines in phenotype file ../anti-b2scr1.sumstats. [2024-05-19 08:27:45.407] [pwcoco_log] [info] Phenotypic variance estimated from summary statistcs of all SNPs: 0.00 [2024-05-19 08:27:45.407] [pwcoco_log] [info] Reading data from phenotype file: ../b2scr1.sumstats. [2024-05-19 08:27:45.408] [pwcoco_log] [warning] It is preferable to use the full summary statistics to estimate the phenotype variance; you can ignore this warning if the summary statistics file you have provided are the full summary statistics. [2024-05-19 08:27:45.408] [pwcoco_log] [warning] You can calculate the full phenotype variance by using either the '--pve' flag or '--pve_file' flag. [2024-05-19 08:27:45.416] [pwcoco_log] [info] Read a total of: 3711 lines in phenotype file ../b2scr1.sumstats. [2024-05-19 08:27:45.416] [pwcoco_log] [info] Phenotypic variance estimated from summary statistcs of all SNPs: 0.00 [2024-05-19 08:27:45.477] [pwcoco_log] [info] Colocalisation analysis initialised with 3709 SNPs. [2024-05-19 08:27:45.479] [pwcoco_log] [info] Unconditioned colocalisation results. [2024-05-19 08:27:45.479] [pwcoco_log] [info] H0: 0.52; H1: 0.19; H2: 0.19; H3: 0.07; H4: 0.02; abf_all: 0.65. [2024-05-19 08:27:45.485] [pwcoco_log] [info] Reading data from bim file: /mnt/c/Users/digim/OneDrive - cumc.columbia.edu/Genetic correlation and meta analysis/data_cleaning/g1000_eur.bim. [2024-05-19 08:28:01.281] [pwcoco_log] [info] Number of SNPs read from .bim file: 22665064. [2024-05-19 08:29:27.477] [pwcoco_log] [info] Number of SNPs matched from .bim file to the phenotype data: 3689. [2024-05-19 08:29:27.642] [pwcoco_log] [info] Reading data from fam file: /mnt/c/Users/digim/OneDrive - cumc.columbia.edu/Genetic correlation and meta analysis/data_cleaning/g1000_eur.fam. [2024-05-19 08:29:27.644] [pwcoco_log] [info] Successfully read 503 individuals from .fam file. [2024-05-19 08:29:27.644] [pwcoco_log] [warning] Sample size for the reference panel is below the recommended size of 4000! [2024-05-19 08:29:27.644] [pwcoco_log] [warning] Continuing analysis, but please consider using a larger reference panel. [2024-05-19 08:29:27.955] [pwcoco_log] [info] Finished reading .bed file. Genotype data for 503 individuals and 3689 SNPs read. [2024-05-19 08:29:27.956] [pwcoco_log] [info] Filtering SNPs with MAF <= 0.01. [2024-05-19 08:29:27.957] [pwcoco_log] [info] After filtering based on MAF, there are 3511 SNPs remaining in the analysis (amount removed: 178). [2024-05-19 08:29:27.962] [pwcoco_log] [info] [anti-b2scr1.sumstats] Total amount of SNPs matched from phenotype file with reference SNPs are: 3511. [2024-05-19 08:29:28.230] [pwcoco_log] [info] [anti-b2scr1.sumstats] Performing stepwise model selection on 3511 SNPs; p cutoff = 5e-08, collinearity = 0.9 assuming complete LE between SNPs more than 10.0 Mb away). [2024-05-19 08:29:28.231] [pwcoco_log] [info] [anti-b2scr1.sumstats] Selected SNP rs9902706 with chisq 40.28 and pval 2.20e-10. [2024-05-19 08:29:28.302] [pwcoco_log] [info] [anti-b2scr1.sumstats] Selected entry SNP rs1003425 with cpval 2.00e+00. [2024-05-19 08:29:28.302] [pwcoco_log] [info] [anti-b2scr1.sumstats] rs1003425 does not meet threshold [2024-05-19 08:29:28.302] [pwcoco_log] [info] [anti-b2scr1.sumstats] Finally, 1 associated SNPs have been selected. [2024-05-19 08:29:28.302] [pwcoco_log] [info] [anti-b2scr1.sumstats] (0 SNPs eliminated by backward selection.) [2024-05-19 08:29:28.309] [pwcoco_log] [info] [b2scr1.sumstats] Total amount of SNPs matched from phenotype file with reference SNPs are: 3511. [2024-05-19 08:29:28.632] [pwcoco_log] [info] [b2scr1.sumstats] Performing stepwise model selection on 3511 SNPs; p cutoff = 5e-08, collinearity = 0.9 assuming complete LE between SNPs more than 10.0 Mb away). [2024-05-19 08:29:28.632] [pwcoco_log] [info] [b2scr1.sumstats] Selected SNP rs1801689 with chisq 4331.88 and pval 0.00e+00. [2024-05-19 08:29:28.703] [pwcoco_log] [info] [b2scr1.sumstats] Selected entry SNP rs1003425 with cpval 2.00e+00. [2024-05-19 08:29:28.703] [pwcoco_log] [info] [b2scr1.sumstats] rs1003425 does not meet threshold [2024-05-19 08:29:28.703] [pwcoco_log] [info] [b2scr1.sumstats] Finally, 1 associated SNPs have been selected. [2024-05-19 08:29:28.703] [pwcoco_log] [info] [b2scr1.sumstats] (0 SNPs eliminated by backward selection.) [2024-05-19 08:29:28.704] [pwcoco_log] [info] There are 1 selected SNPs in the exposure dataset and 1 in the outcome dataset. [2024-05-19 08:29:28.704] [pwcoco_log] [info] Performing 1 conditional and colocalisation analyses. [2024-05-19 08:29:28.764] [pwcoco_log] [info] Colocalisation analysis initialised with 3478 SNPs. [2024-05-19 08:29:28.765] [pwcoco_log] [info] Conditioned results for SNP1: rs9902706, SNP2: rs1801689 [2024-05-19 08:29:28.766] [pwcoco_log] [info] H0: -nan; H1: -nan; H2: -nan; H3: -nan; H4: -nan; abf_all: -nan. [2024-05-19 08:29:28.823] [pwcoco_log] [info] Colocalisation analysis initialised with 3479 SNPs. [2024-05-19 08:29:28.824] [pwcoco_log] [info] Conditioned results for SNP1: rs9902706, SNP2: unconditioned [2024-05-19 08:29:28.824] [pwcoco_log] [info] H0: -nan; H1: -nan; H2: -nan; H3: -nan; H4: -nan; abf_all: -nan. [2024-05-19 08:29:28.886] [pwcoco_log] [info] Colocalisation analysis initialised with 3506 SNPs. [2024-05-19 08:29:28.887] [pwcoco_log] [info] Conditioned results for SNP1: unconditioned, SNP2: rs1801689 [2024-05-19 08:29:28.887] [pwcoco_log] [info] H0: -nan; H1: -nan; H2: -nan; H3: -nan; H4: -nan; abf_all: -nan. [2024-05-19 08:29:28.892] [pwcoco_log] [info] Analysis finished. Computational time: 103.499974 secs