Division by Zero in plinkSTR

[bibb]

Hello,

I'm using plinkSTR with a VCF coming from the STR imputation pipeline, and I got this error:

Traceback (most recent call last):
File "/projects/b1049/genetics_programs/gangSTR/bin/plinkSTR", line 11, in
load_entry_point('strtools==1.0.0', 'console_scripts', 'plinkSTR')()
File "/projects/b1049/genetics_programs/gangSTR/lib/python3.7/site-packages/strtools-1.0.0-py3.7.egg/plinkSTR/plinkSTR.py", line 354, in main
File "/projects/b1049/genetics_programs/gangSTR/lib/python3.7/site-packages/strtools-1.0.0-py3.7.egg/plinkSTR/plinkSTR.py", line 112, in PerformAssociation
ZeroDivisionError: float division by zero

I thought maybe it was a problem with my VCF and I tried different chromosomes, different imputed VCFs coming from other cohorts, running the program with different MAF thresholds since line 112 is about that, also with and without covariates, but I got the same error each time. I will appreciate your help in this

Best,

Bernabe

[nmmsv]

can you please check if the latest version of plinkSTR resolves this problem?

[bibb]

Hi, thanks for the fix, now I get the following error:

plinkSTR --vcf snp.str.chr22.v2.vcf.gz --covar PC1_5.ForVCF.covar --covar-name PC1,PC2,PC3,PC4,PC5 --out test.chr22 --fam VCF_file.fam --sex --logistic --infer-snpstr --allele-tests --allele-tests-length --remove-rare-str-alleles 0.01

Traceback (most recent call last):
  File "/home/bib0660/.local/bin/plinkSTR", line 11, in <module>
    load_entry_point('strtools==1.0.0', 'console_scripts', 'plinkSTR')()
  File "/projects/b1049/genetics_programs/gangSTR/lib/python3.7/site-packages/strtools-1.0.0-py3.7.egg/plinkSTR/plinkSTR.py", line 382, in main
    OutputAssoc(record.CHROM, record.POS, assoc, outf, assoc_type=GetAssocType(is_str, alt=alleles[i], name=record.ID))
  File "/projects/b1049/genetics_programs/gangSTR/lib/python3.7/site-packages/strtools-1.0.0-py3.7.egg/plinkSTR/plinkSTR.py", line 60, in GetAssocType
    if alt >= 0: return "%s-alt-%s"%(name,alt)
TypeError: '>=' not supported between instances of 'str' and 'int'

Is this a problem of the imputed VCF having both SNPs and STRs? should I separate them in different files?

Thanks!

Bernabe

[shubhamsaini]

@bibb This is because of incompatibility with Python 3. You can either use Python 2 to solve this, or get the development version of plinkSTR from the following link that supports both Python 2 and 3:
https://github.com/shubhamsaini/STRTools/blob/master/plinkSTR/plinkSTR.py

[LiterallyUniqueLogin]

Closing due to inactivity.