run_FastQTL_threaded.py script doen't work

[Veliborka]

run_FastQTL_threaded.py script doen't work

[francois-a]

The error states that a specific chunk failed. Can you please try to run that separately and post the output?

/opt/fastqtl/bin/fastQTL --vcf /sbgenomics/Projects/cb8a783b-a338-4a0b-a63b-8d154c5f7ebd/all_test_vcf_tabix.vcf.gz --bed /sbgenomics/Projects/cb8a783b-a338-4a0b-a63b-8d154c5f7ebd/all_genes_expression_tabix.bed.gz --window 1e6 --maf-threshold 0.0 --ma-sample-threshold 0 --chunk 5 100 --out all_genes_expression_tabix_chunk005.txt.gz --log all_genes_expression_tabix_chunk005.log

[Veliborka]

Yes, and this is not the only chunk that failed. Many of them failed. I tried to run the command for some of the failed chunks (5, 9, 16 etc) and each time the error is the same. Follow the command and the logs for the chunk 9:

/opt/fastqtl/bin/fastQTL --vcf /data/all_mutations_vcf.tab.vcf.gz --bed /data/all_genes_new.tab.bed.gz --window 1e6 --maf-threshold 0.0 --ma-sample-threshold 0 --chunk 9 100 --out all_genes_expression_tabix_chunk009.txt.gz --log all_genes_expression_tabix_chunk009.log

Fast QTL

• Authors : Olivier DELANEAU, Halit ONGEN, Alfonso BUIL & Manolis DERMITZAKIS
• Contact : [email protected]
• Webpage : http://fastqtl.sourceforge.net/
• Version : v2.184_gtex

Perform nominal analysis (used to get raw p-values of association)

• Using p-value threshold = 1.0000000000
• Random number generator is seeded with 1531241022
• Considering variants within 1e+06 bp of the MPs
• Using minor allele frequency threshold = 0.0000
• Using minor allele sample threshold = 0
• Using INFO field AF threshold = 0.0000
• Chunk processed 9 / 100

Scanning phenotype data in [/data/all_genes_new.tab.bed.gz]

• 14200 phenotypes

Reading phenotype data in [/data/all_genes_new.tab.bed.gz]

• region = 1:183387737-214454445
• 445 samples included
• 150 phenotypes included

Reading genotype data in [/data/all_mutations_vcf.tab.vcf.gz] in VCF format

• region = 1:182387737-215454445
• 100000 lines parsed
• 200000 lines parsed
• 300000 lines parsed
• 400000 lines parsed
• 500000 lines parsed
• 600000 lines parsed
• 700000 lines parsed
  Killed

[francois-a]

It's not easy to guess the error from this output. Could this be a memory issue?