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vcf2gwas failing again and again #2

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vinod1981 opened this issue Jun 24, 2021 · 9 comments
Closed

vcf2gwas failing again and again #2

vinod1981 opened this issue Jun 24, 2021 · 9 comments

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@vinod1981
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vinod1981 commented Jun 24, 2021 •
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Hi,
I recently started exploring vcf2gwas but it is giving an error for which I couldn't find a solution.
Command:
vcf2gwas -v js.vcf.gz -pf Pheno_GWAS_Cd_test1.csv -ap -cf pca_gwas1.csv -ac -lmm -M 8000 -T 6

Error log: just from the end
Filtering and converting files

Converting to PLINK BED..
Error: File read failure.
Successfully converted to PLINK BED (Duration: 2 minutes, 16.8 seconds)

Adding phenotypes/covariates to .fam file

Editing .fam file..
All phenotypes chosen
Phenotype(s) added to .fam file
Traceback (most recent call last):
File "/vol/cluster-data/vkumar/miniconda3/envs/myenv/lib/python3.9/site-packages/vcf2gwas/analysis.py", line 238, in
covar_file_name = Processing.make_covarfile(fam, pheno_subset2, subset2, Y)
File "/vol/cluster-data/vkumar/miniconda3/envs/myenv/lib/python3.9/site-packages/vcf2gwas/utils.py", line 599, in make_covarfile
for i in Y:
TypeError: 'NoneType' object is not iterable
Successfully converted to PLINK BED (Duration: 2 minutes, 23.5 seconds)

Adding phenotypes/covariates to .fam file

Editing .fam file..
All phenotypes chosen
Phenotype(s) added to .fam file
Traceback (most recent call last):
File "/vol/cluster-data/vkumar/miniconda3/envs/myenv/lib/python3.9/site-packages/vcf2gwas/analysis.py", line 238, in
covar_file_name = Processing.make_covarfile(fam, pheno_subset2, subset2, Y)
File "/vol/cluster-data/vkumar/miniconda3/envs/myenv/lib/python3.9/site-packages/vcf2gwas/utils.py", line 599, in make_covarfile
for i in Y:
TypeError: 'NoneType' object is not iterable
Analysis successfully completed

Summarizing top SNPs..
Traceback (most recent call last):
File "/vol/cluster-data/vkumar/miniconda3/envs/myenv/lib/python3.9/site-packages/vcf2gwas/starter.py", line 428, in
filenames = Post_analysis.summarizer(path3, path2, pc_prefix3, snp_prefix, n_top, Log, prefix_list)
File "/vol/cluster-data/vkumar/miniconda3/envs/myenv/lib/python3.9/site-packages/vcf2gwas/utils.py", line 1002, in summarizer
for file in os.listdir(path):
FileNotFoundError: [Errno 2] No such file or directory: '/vol/cluster-data/vkumar/miniconda3/bin/output/lmm/summary/top_SNPs'

The problem is that there is a folder generated with name "lm" but I used "lmm" in the command and now it is searching for lmm folder in the path.

Then I changed the one sub-directory manually to lmm from lm and error shortened like this:

Preparing files

Checking and adjusting files..
Checking individuals in VCF file..
Checking individuals in phenotype file..
Not all individuals in phenotpye and genotype file match
Removed 0 out of 810 individuals, 810 remaining
Checking individuals in covariate file..
All covariate and genotype individuals match
Removed 0 out of 822 individuals, 822 remaining
In total, removed 12 out of 822 individuals, 810 remaining
Files successfully adjusted

Filtering and converting files

Converting to PLINK BED..
Successfully converted to PLINK BED (Duration: 35.6 seconds)

Adding phenotypes/covariates to .fam file

Editing .fam file..
Phenotype(s) added to .fam file
Traceback (most recent call last):
File "/vol/cluster-data/vkumar/miniconda3/envs/myenv/lib/python3.9/site-packages/vcf2gwas/analysis.py", line 238, in
covar_file_name = Processing.make_covarfile(fam, pheno_subset2, subset2, Y)
File "/vol/cluster-data/vkumar/miniconda3/envs/myenv/lib/python3.9/site-packages/vcf2gwas/utils.py", line 599, in make_covarfile
for i in Y:
TypeError: 'NoneType' object is not iterable
Analysis successfully completed

Summarizing top SNPs..
Couldn't find files to summarize!
Clean up successful

vcf2gwas has been successfully completed!
Runtime: 7 minutes, 43.9 seconds

This error is still there.
What to do?

Thanks,

Vinod
@frankvogt
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frankvogt commented Jun 25, 2021 via email

@vinod1981
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Hi Frank,
Thanks for reaching out.
But the vcf file is very big around 6G compressed. How to do that?
Thanks,

Vinod,

@frankvogt
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frankvogt commented Jun 25, 2021 via email

@vinod1981
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Hi Frank,
Should I share them here or on a specific email?
Thanks,
VInod,

@vinod1981
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vinod1981 commented Jun 25, 2021 via email

@frankvogt
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You can share the files with my email: frvogt@gmail.com

@frankvogt
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Bug was fixed where internally not all covariates were passed on when a certain combination of options was selected

@vinod1981
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Hi Frank,
Is it a reply for my other request or you are adding something to this issue?
Because in other issue, I am requesting if it is possible to just see the significant threshold line and not label the SNPs in Manhattan plot.
Thanks,
Vinod,

@frankvogt
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No this was just to clarify what the issue was and that it has been fixed

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@vinod1981 @frankvogt