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montilab / nf-gwas-pipeline

A Nextflow Genome-Wide Association Study (GWAS) Pipeline
GNU General Public License v3.0
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cannot run test #5

Closed PavitaKae closed 8 months ago

PavitaKae commented 3 years ago

Dear all, I follow your installation, it's look good but I cannot run test. ./nextflow gwas.nf -c gwas.config -with-docker montilab/gwas

I run on Mac environment

G W A S ~ P I P E L I N E

================================ outdir : /Users/pavita/nf-gwas-pipeline/results

vcf : /Users/pavita/nf-gwas-pipeline/data/toy_vcf.csv pheno : /Users/pavita/nf-gwas-pipeline/data/pheno_file_logistic.csv snpset : /Users/pavita/nf-gwas-pipeline/data/snpset.txt

phenotype : outcome covars : age,sex,PC1,PC2,PC3,PC4 model : logistic test : Score ref : hg19

-

executor > local (78) [6c/577702] process > qc_miss (chr_22) [100%] 22 of 22 ✔ executor > local (78) [6c/577702] process > qc_miss (chr_22) [100%] 22 of 22 ✔ [93/c59706] process > qc_mono (chr_22) [100%] 22 of 22 ✔ [1c/6fd96e] process > vcf_to_gds (chr_22) [100%] 22 of 22 ✔ [16/1dd261] process > merge_gds [100%] 1 of 1 ✔ [c0/c76091] process > nullmod_skip_pca_grm [100%] 1 of 1 ✔ [f1/ecf210] process > gwas_skip_pca_grm (chr_4) [ 6%] 1 of 16, failed: 1 [- ] process > caf_by_group_skip_pca_grm [ 0%] 0 of 22 [- ] process > merge_by_chr - [- ] process > combine_results - [- ] process > plot - [- ] process > annovar_input - [73/7ec72c] process > annovar_ref [100%] 1 of 1 ✔ [- ] process > annovar - [- ] process > add_annovar - [- ] process > report - Error executing process > 'gwas_skip_pca_grm (chr_3)'

Caused by: Process gwas_skip_pca_grm (chr_3) terminated with an error exit status (137)

Command executed:

04_gwas.R chr_3.gds annot.rds nullmod.rds Score true chr_3.csv chr_3_gwas.log

Command exit status: 137

Command output: [1] "Tue Sep 21 11:58:54 2021"

Command error: .command.sh: line 2: 7 Killed 04_gwas.R chr_3.gds annot.rds nullmod.rds Score true chr_3.csv chr_3_gwas.log

ZeyuanSong commented 3 years ago

Hi, can you find the error message in the hidden dot file .nextflow.log? Is there any error message in the chr_3_gwas.log file?

PavitaKae commented 3 years ago

Hi, I try to run it again. it's happen with all Chr in process gwas_skip_pca_grm. So,I check work folder, I not found input chr_xx.gds annot.rds nullmod.rds chr_xx.csv chr_3_gwas.log in work of gwas_skip_pca_grm. But i found all input file in results/GDS.

I use N E X T F L O W ~ version 21.04.3 it's a problem or not? what's version that you preferred?

ZeyuanSong commented 3 years ago

Hi, I run the test with Nextflow version 19.04.1. Are those files in results/GDS as small as empty (all same small sizes)? You may also try the other test example with 1KG data to see what happens.