Error when trying to make MetaXcan run through Snakemake

Question

[r.tor]

I have been getting the following error running MetaXcan.

INFO - Loading model
ERROR - Error:Could not read input tissue database. Please try updating the tissue model files.

I've been trying to run Predict.py in my data using LCL prediction model. Here is the rul in my Snakefile:

rule prediction_gene_expr:
input:
       db = "./JTI_Cells_EBV-transformed_lymphocytes.db",     
       vcf = "./chr22.vcf.gz",                               # Geuvadis_phased_vcf
       liftover = "./hg19ToHg38.over.chain.gz"               # Downloaded from UCSC
output:
       pred_out = "./Cells_EBV-transformed_lymphocytes_predict.txt",
       summary = "./Cells_EBV-transformed_lymphocytes_summary.txt"
conda:
       "./conda_env.yaml"
shell:
       " python3 ./Predict.py"
       " --model_db_path {input.db}"
       " --model_db_snp_key varID" 
       " --vcf_genotypes {input.vcf}"
       " --vcf_mode genotyped"
       " --liftover {input.liftover}"
       " --on_the_fly_mapping METADATA \"{{}}_{{}}_{{}}_{{}}_b37\"" 
       " --prediction_output {output.pred_out}"
       " --prediction_summary_output {output.summary}"

I am using the GEUVADIS genotypes model so I specify varIDs to predict expression. Sine the reference of the vcf file is GRCh37, I used liftover and on_the_fly_mapping METADATA arguments.

This is the message I get after running the Snakfile:

Activating conda environment .snakemake/conda/f89852c9.
INFO - Loading samples
[W::bcf_hdr_check_sanity] GL should be declared as Number=G
INFO - Loading model
ERROR - Error:Could not read input tissue database. Please try updating the tissue model files.

I would appreciate any advice in regards.

Answer 1

[Jeremy Leipzig]

it might not like the GEUVADIS VCF header: https://github.com/samtools/bcftools/issues/1003

[r.tor]

Thanks. the provided like addresses the solution to get rid of the W::bcf_hdr_check_sanity issue that it's been solved. But I was not the main problem. Instead, the Error:Could not read input tissue database. is what it needs to take care of.

[Jeremy Leipzig]

can you connect to JTI_Cells_EBV-transformed_lymphocytes.db? e.g. sqlite3 JTI_Cells_EBV-transformed_lymphocytes.db