Variant Information

[iremdnzl]

Hi, here is my command line and error:

`nextflow run main.nf --profile conda --studyFile /home/idnzl/Desktop/QTL_analysis/run.tsv --vcf_has_R2_field FALSE --varid_rsid_map_file /home/idnzl/Desktop/QTL_analysis/varid_rsid_map.tsv.gz --max_cpus 8 --max_memory 30.GB

N E X T F L O W ~ version 24.10.2

Launching main.nf [suspicious_galileo] DSL2 - revision: 731a180922

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___ __ __ __ ___ /,-..--~'
|\ | |__ __ / / \ |__) |__ } { | \| | \__, \__/ | \ |___ \-.,--, .,.,'

eQTL-Catalogue/qtlmap v20.10.1"

Pipeline Name : eQTL-Catalogue/qtlmap
Pipeline Version : 20.10.1
Run Name : suspicious_galileo
Study file : /home/idnzl/Desktop/QTL_analysis/run.tsv
cis window : 1000000
Min # cis variants : 5
VCF has R2 field : false
Permutation run : false

of permutations : 1000

Nominal run : true

of batches : 400

of phenotype PCs : 6

of genotype PCs : 6

Additonal covariates : null
Run SuSiE : false
Write full SuSiE : true
VCF genotype field : GT
Max Memory : 30.GB
Max CPUs : 8
Max Time : 5d
Output dir : ./results
Working dir : /home/idnzl/Desktop/QTL_analysis/qtlmap/work
Container Engine : null
Current home : /home/idnzl
Current user : idnzl
Current path : /home/idnzl/Desktop/QTL_analysis/qtlmap
Script dir : /home/idnzl/Desktop/QTL_analysis/qtlmap
Config Profile : standard

executor > local (6)
[c5/324f8c] process > vcf_set_variant_ids (QTL_Dec2024) [100%] 1 of 1 ✔
[70/6277f7] process > extract_variant_info (QTL_Dec2024) [100%] 1 of 1 ✔
[6b/4a1de5] process > prepare_molecular_traits (QTL_Dec2024) [ 75%] 3 of 4, failed: 3, retries: 3
[- ] process > compress_bed -
[- ] process > extract_samples_from_vcf -
[- ] process > make_pca_covariates -
[- ] process > run_nominal -
[- ] process > merge_nominal_batches -
[- ] process > sort_qtltools_output -
[- ] process > extract_variant_info2 -
[- ] process > join_rsids_var_info -
[- ] process > reformat_sumstats -
[- ] process > tabix_index -
[18/017d2c] NOTE: Process prepare_molecular_traits (QTL_Dec2024) terminated with an error exit status (1) -- Execution is retried (1)
[18/7644f1] NOTE: Process prepare_molecular_traits (QTL_Dec2024) terminated with an error exit status (1) -- Execution is retried (2)
[72/f49eb6] NOTE: Process prepare_molecular_traits (QTL_Dec2024) terminated with an error exit status (1) -- Execution is retried (3)
ERROR ~ Error executing process > 'prepare_molecular_traits (QTL_Dec2024)'

Caused by:
Process prepare_molecular_traits (QTL_Dec2024) terminated with an error exit status (1)

executor > local (6)
[c5/324f8c] process > vcf_set_variant_ids (QTL_Dec2024) [100%] 1 of 1 ✔
[70/6277f7] process > extract_variant_info (QTL_Dec2024) [100%] 1 of 1 ✔
[6b/4a1de5] process > prepare_molecular_traits (QTL_Dec2024) [100%] 4 of 4, failed: 4, retries: 3 ✘
[- ] process > compress_bed -
[- ] process > extract_samples_from_vcf -
[- ] process > make_pca_covariates -
[- ] process > run_nominal -
[- ] process > merge_nominal_batches -
[- ] process > sort_qtltools_output -
[- ] process > extract_variant_info2 -
[- ] process > join_rsids_var_info -
[- ] process > reformat_sumstats -
[- ] process > tabix_index -
[18/017d2c] NOTE: Process prepare_molecular_traits (QTL_Dec2024) terminated with an error exit status (1) -- Execution is retried (1)
[18/7644f1] NOTE: Process prepare_molecular_traits (QTL_Dec2024) terminated with an error exit status (1) -- Execution is retried (2)
[72/f49eb6] NOTE: Process prepare_molecular_traits (QTL_Dec2024) terminated with an error exit status (1) -- Execution is retried (3)
ERROR ~ Error executing process > 'prepare_molecular_traits (QTL_Dec2024)'

Caused by:
Process prepare_molecular_traits (QTL_Dec2024) terminated with an error exit status (1)

Command executed:

Rscript /home/idnzl/Desktop/QTL_analysis/qtlmap/bin/prepare_molecular_traits.R
-p "phenotype_metadata.txt"
-s "sample_metadata.txt"
-e "QTL_Dec2024.tsv.gz"
-v "QTL_Dec2024.variant_information.txt.gz"
-o "."
-c 1000000
-m 5
-a null

#Merge phenotype covariates together
head -n 7 phenoPCA.tsv > QTL_Dec2024.pheno_cov.txt
tail -n+2 additional_covariates.tsv >> QTL_Dec2024.pheno_cov.txt

Command exit status:
1

Command output:
phenotype_id X55 X61 X64 X57 X67
1 0610009B22Rik 186.25385 382.04213 244.38957 236.31941 178.49496
2 0610010K14Rik 161.18121 188.21193 274.93827 184.19013 141.30851
3 1110004F10Rik 89.54512 64.61007 112.01189 38.22814 55.77968
4 1110051M20Rik 21.49083 53.37353 35.64015 41.70342 85.52884
5 1110065P20Rik 32.23624 101.12880 76.37174 83.40685 122.71529
6 1300017J02Rik 186.25385 230.34893 448.04755 399.65782 327.24076

Command error:
------ Options parsed ------
gene_meta_path: phenotype_metadata.txt
sample_meta_path: sample_metadata.txt
expression_matrix_path: QTL_Dec2024.tsv.gz
variant_info_path: QTL_Dec2024.variant_information.txt.gz
output_dir: .
cis_distance: 1000000
cis_min_var: 5
covariate_names: null

Reading gene metadata file

Reading sample metadata file

Reading expression matrix

 phenotype_id       X55       X61       X64       X57       X67

1 0610009B22Rik 186.25385 382.04213 244.38957 236.31941 178.49496
2 0610010K14Rik 161.18121 188.21193 274.93827 184.19013 141.30851
3 1110004F10Rik 89.54512 64.61007 112.01189 38.22814 55.77968
4 1110051M20Rik 21.49083 53.37353 35.64015 41.70342 85.52884
5 1110065P20Rik 32.23624 101.12880 76.37174 83.40685 122.71529
6 1300017J02Rik 186.25385 230.34893 448.04755 399.65782 327.24076

Importing variant info

Error: variant info is empty
Execution halted

Work dir:
/home/idnzl/Desktop/QTL_analysis/qtlmap/work/6b/4a1de58030934994428bbb50283f98

Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out

-- Check '.nextflow.log' file for details
`

I don't know where it is going wrong, could you help please?

[kauralasoo]

Hi! This suggests that there is some issue with the input VCF file. We have previously seen the same error when the VCF file does not contain INFO/R2 field and --vcf_has_R2_field FALSE is not specified. In your case --vcf_has_R2_field FALSE looks to be specified though, so I am not really sure what is happening. I would start by checking that the variant information file generated by the extract_variant_info (https://github.com/eQTL-Catalogue/qtlmap/blob/master/modules/extract_variant_info.nf) process is not empty.