Open mpkol59 opened 3 days ago
Yes you are correct. Would you mind sending us the whole command line printout or the standard errors from inside the prs-single directories?
Thank you,
Tade
On Tue, Oct 22, 2024 at 12:46 PM mpkol59 @.***> wrote:
Hello there, Thank you for your great work on this software. I have encountered this error while trying to run BridgePRS using my East Asian and European ancestry data. My command line is as found below as well as the error message:
./bridgePRS tools check-pops -o mytestfulleas --pop EAS EUR --ld_path /path/AFR/CHRMS/1000G/ --sumstats_prefix /path/EAS/CHRMS/eas_chr /path/AFR/CHRMS/eur_chr --sumstats_size 1600 390278 --genotype_prefix /path/EAS/CHRMS/ceas_chr --phenotype_file /path/EAS/CHRMS/myeasphenos2.data
../../bridgePRS pipeline go -o out2 --config_files EAS.target.config EUR.base.config --phenotype y --debug_level 0
################################################################# Traceback (most recent call last): File "/path/BridgePRS/mytestfulleas/save/../../bridgePRS", line 372, in bridgePRS = BridgePRS(mps, sys.argv) ^^^^^^^^^^^^^^^^^^^^^^^^ File "/path/BridgePRS/src/Python/BridgePRS.py", line 27, in init elif self.args.module == 'pipeline': self.easyrun() ^^^^^^^^^^^^^^ File "/path/BridgePRS/src/Python/BridgePRS.py", line 46, in easyrun self.analyze(self.args.cmd, self.args.result_files, PATH = self.io.paths['home'])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/path/BridgePRS/src/Python/BridgePRS.py", line 69, in analyze self.run = BridgeRun(self).analyze(cmd, prs_results, PATH) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/path/BridgePRS/src/Python/Util/BridgeRun.py", line 65, in analyze self.results = [r1[0], r2[0]] + BridgeResult().read_combo(combine) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/path/BridgePRS/src/Python/Util/Bridge_Run/BridgeResult.py", line 40, in read_combo return [BridgeResult('prs-combine', combo.pop, True).add_triple([varexp[0], preds[0], snp_weights[0]]), BridgeResult('prs-weighted', combo.pop, True).add_triple([varexp[1], preds[1], snp_weights[1]])] ^^^^^^ UnboundLocalError: cannot access local variable 'varexp' where it is not associated with a value
##################################################################################
This is confusing since I ran the exact same command for my African and Eur populations and did not get this error. What I noticed is that the PRS-Single stage runs into some error at the beta estimation stage and just continues on to the final stage where the needed files for combining the models are then found missing, hence the error.
I would really appreciate your help with resolving this. Thanks as I look forward to hearing back from you.
Best wishes.
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Thank you very much for your swift response. Here it is:
BridgePRS Begins at Thu Oct 17 13:07:31 2024
Bridge Command-Line: ../../bridgePRS pipeline go -o out2 --config_files EAS.target.config EUR.base.config --phenotype y --debug_level 0
Checking Requirements:
System: platform=linux, cores(available)=128, cores(used)=127
Plink: found=false, path=NA (Using included version: /path/BridgePRS/src/Python/Xtra/plink)
R: found=true, path=/apps/spack/negishi/apps/r/4.2.2-gcc-12.2.0-524zdta/bin/R, version=4.2.2 (packages=up to date)
Python3: found=true, path=/apps/external/apps/conda/2024.09/bin/python3, matplotlib=false (NOTE: Please Install Matplotlib To Enable Plotting)
Complete
Complete
Reading Population Data: Target Data: Names: POP=EAS LDPOP=EAS LD_PATH=/path/AFR/CHRMS/1000G Sumstats: SOURCE_PREFIX=/path/BridgePRS/mytestfulleas/save/sumstats/ss.EAS. SOURCE_SUFFIX=.out.gz SUMSTATS_PREFIX=/path/BridgePRS/mytestfulleas/save/out2/save/sumstats/ss.EAS. SUMSTATS_SUFFIX=.out.gz SUMSTATS_FIELDS=ID,REF,A1,P,BETA SUMSTATS_SIZE=1600 QC-Snps: SNP_FILE=/path/BridgePRS/mytestfulleas/save/snps.eas_valid.txt Genotype/Phenotype: GENOTYPE_PREFIX=/path/EAS/CHRMS/ceas_chr PHENOTYPE_FILE=/path/BridgePRS/mytestfulleas/save/EAS.test_phenos.dat VALIDATION_FILE=/path/BridgePRS/mytestfulleas/save/EAS.valid_phenos.dat CHROMOSOMES=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22 PHENOTYPE_VARIABLES=y,PC1,PC2,PC3 DECLARED_PHENOTYPE=y **Target Config Made: /path/BridgePRS/mytestfulleas/save/out2/save/EAS.target.config
Base Data:
Names: POP=EUR
LDPOP=EUR
LD_PATH=/path/AFR/CHRMS/1000G
Sumstats: SOURCE_PREFIX=/path/BridgePRS/mytestfulleas/save/sumstats/ss.EUR.
SOURCE_SUFFIX=.out.gz
SUMSTATS_PREFIX=/path/BridgePRS/mytestfulleas/save/out2/save/sumstats/ss.EUR.
SUMSTATS_SUFFIX=.out.gz
SUMSTATS_FIELDS=ID,REF,A1,P,BETA
SUMSTATS_SIZE=390278
QC-Snps: SNP_FILE=/path/BridgePRS/mytestfulleas/save/snps.eas_valid.txt
Genotype/Phenotype: GENOTYPE_PREFIX=/path/EAS/CHRMS/ceas_chr
PHENOTYPE_FILE=/path/EAS/CHRMS/myeasphenos2.data
CHROMOSOMES=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22
PHENOTYPE_VARIABLES=y,PC1,PC2,PC3
DECLARED_PHENOTYPE=y
**Base Config Made: /path/BridgePRS/mytestfulleas/save/out2/save/EUR.base.config
Setting Program Parameters: Flags: OFF=VERBOSE,RESTART
Begin Module: Stage1: prs-single
JOB1: Clumping Pop Data (prs-single clump)..........(Parallelizing Across 127 Cores).........
BridgePipelineWarning: UNKNOWN R-OUTPUT IN STDERR (Program may have failed):
...................................................................................................Complete
[File(s) Generated: clump_prefix=out2/prs-single_EAS/clump/EAS_clump]
JOB2: Calculating SNP Weights (prs-single beta)...............................................Complete
[File(s) Generated: beta_prefix=out2/prs-single_EAS/beta/EAS_beta]
JOB3: Generating Polygenic Predictions (prs-single predict)....................
BridgePipelineWarning: UNKNOWN R-OUTPUT IN STDERR (Program may have failed):
...................................................................................................Complete
[File(s) Generated: predict_prefix=out2/prs-single_EAS/predict/EAS_predict]
JOB4: Quantifying PRS Result (prs-single quantify)..........................
BridgePipelineWarning: UNKNOWN R-OUTPUT IN STDERR (Program may have failed):
...................................................................................................Complete
[File(s) Generated: quantify_prefix=out2/prs-single_EAS/quantify/EAS_quantify]
Begin Module: build-model
JOB1: Clumping Pop Data (build-model clump).........(Parallelizing Across 127 Cores)..........Complete
[File(s) Generated: clump_prefix=out2/build-model_EUR/clump/EUR_clump]
JOB2: Calculating SNP Weights (build-model beta)..............................................Complete
[File(s) Generated: beta_prefix=out2/build-model_EUR/beta/EUR_beta]
JOB3: Generating Polygenic Predictions (build-model predict)....................
BridgePipelineWarning: UNKNOWN R-OUTPUT IN STDERR (Program may have failed):
...................................................................................................Complete
[File(s) Generated: predict_prefix=out2/build-model_EUR/predict/EUR_predict]
JOB4: Saving SNP Priors (build-model prior)...................................................Complete
[File(s) Generated: prior_prefix=out2/build-model_EUR/prior/EUR_prior]
Begin Module: Stage2: prs-prior
Previously Generated: model_file=out2/build-model_EUR/bridge.eur.build-model.result
JOB1: Calculating SNP Weights (prs-prior beta)..........................
BridgePipelineWarning: UNKNOWN R-OUTPUT IN STDERR (Program may have failed):
...................................................................................................Complete
[File(s) Generated: beta_prefix=out2/prs-prior_EAS-EUR/beta/EAS_beta]
JOB2: Generating Polygenic Predictions (prs-prior predict)....................
BridgePipelineWarning: UNKNOWN R-OUTPUT IN STDERR (Program may have failed):
...................................................................................................Complete
[File(s) Generated: predict_prefix=out2/prs-prior_EAS-EUR/predict/EAS_predict]
JOB3: Quantifying PRS Result (prs-prior quantify)..........................
BridgePipelineWarning: UNKNOWN R-OUTPUT IN STDERR (Program may have failed):
...................................................................................................Complete
[File(s) Generated: quantify_prefix=out2/prs-prior_EAS-EUR/quantify/EAS_quantify]
Begin Module: analyze
JOB1: Combining The Results (analyze combine).................................................Complete
Traceback (most recent call last):
File "/path/BridgePRS/mytestfulleas/save/../../bridgePRS", line 372, in
^^^^^^
UnboundLocalError: cannot access local variable 'varexp' where it is not associated with a value
Hello there, Thank you for your great work on this software. I have encountered this error while trying to run BridgePRS using my East Asian and European ancestry data. My command line is as found below as well as the error message:
./bridgePRS tools check-pops -o mytestfulleas --pop EAS EUR --ld_path /path/AFR/CHRMS/1000G/ --sumstats_prefix /path/EAS/CHRMS/eas_chr /path/AFR/CHRMS/eur_chr --sumstats_size 1600 390278 --genotype_prefix /path/EAS/CHRMS/ceas_chr --phenotype_file /path/EAS/CHRMS/myeasphenos2.data
../../bridgePRS pipeline go -o out2 --config_files EAS.target.config EUR.base.config --phenotype y --debug_level 0
################################################################# Traceback (most recent call last): File "/path/BridgePRS/mytestfulleas/save/../../bridgePRS", line 372, in
bridgePRS = BridgePRS(mps, sys.argv)
^^^^^^^^^^^^^^^^^^^^^^^^
File "/path/BridgePRS/src/Python/BridgePRS.py", line 27, in init
elif self.args.module == 'pipeline': self.easyrun()
^^^^^^^^^^^^^^
File "/path/BridgePRS/src/Python/BridgePRS.py", line 46, in easyrun
self.analyze(self.args.cmd, self.args.result_files, PATH = self.io.paths['home'])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/path/BridgePRS/src/Python/BridgePRS.py", line 69, in analyze
self.run = BridgeRun(self).analyze(cmd, prs_results, PATH)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/path/BridgePRS/src/Python/Util/BridgeRun.py", line 65, in analyze
self.results = [r1[0], r2[0]] + BridgeResult().read_combo(combine)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/path/BridgePRS/src/Python/Util/Bridge_Run/BridgeResult.py", line 40, in read_combo
return [BridgeResult('prs-combine', combo.pop, True).add_triple([varexp[0], preds[0], snp_weights[0]]), BridgeResult('prs-weighted', combo.pop, True).add_triple([varexp[1], preds[1], snp_weights[1]])]
^^^^^^ UnboundLocalError: cannot access local variable 'varexp' where it is not associated with a value ##################################################################################
This is confusing since I ran the exact same command for my African and Eur populations and did not get this error. What I noticed is that the PRS-Single stage runs into some error at the beta estimation stage and just continues on to the final stage where the needed files for combining the models are then found missing, hence the error.
I would really appreciate your help with resolving this. Thanks as I look forward to hearing back from you.
Best wishes.