##ERROR: FAILED: Parsing input file 'mikk_small_hapVariants_updated_noheaders.csv' failed in function ReadFile_geno in src/gemma_io.cpp at line 744, for GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021

[fetche-lab]

More description of the bug and steps to reproduce it I have been running the following code:

./gemma-0.98.5 -g mikk_small_hapVariants_updated_noheaders.csv -p ../medaka_data/mikk_GN1038_pheno.txt -gk -o mikk_GN1038.stats

And the running error is as follows:

GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021
Reading Files ... 
**** FAILED: Parsing input file 'mikk_small_hapVariants_updated_noheaders.csv' failed in function ReadFile_geno in src/gemma_io.cpp at line 744 

I need help with linking the line from the source code with the behavior of the file, as to why even after converting it to the required formatting, as in the example file, I keep getting the same error.

Expected behavior for the program to run In running the code with example working files, I expect to get the following output. Code:

./gemma-0.98.5 -g mouse_hs1940.geno.csv -p mouse_hs1940.pheno.txt -gk -o mouse.stats

Output

GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021
Reading Files ... 
## number of total individuals = 1940
## number of analyzed individuals = 1410
## number of covariates = 1
## number of phenotypes = 1
## number of total SNPs/var        =    12226
## number of analyzed SNPs         =    10768
Calculating Relatedness Matrix ... 
================================================== 100%
**** INFO: Done.

Links to the directories containing the example files and the problematic files

01 Working files There are two files, genotype and phenotype files

• mouse_hs1940.geno.csv (genotype file)
• mouse_hs1940.geno.txt (phenotype file) The GitHub link to the working files and the output :
• https://github.com/fetche-lab/GeneNetwork_24L/tree/main/Data_processing/working_files
• https://github.com/fetche-lab/GeneNetwork_24L/tree/main/Data_processing/working_files/output
  • contains a .cXX.txt file and .log.txt file

02 Error files Two files:

• mikk_small_hapVariants_updated_noheaders.csv (genotype file)
• mikk_GN1038_pheno.txt (phenotype file) The GitHub link to the files:
• https://github.com/fetche-lab/GeneNetwork_24L/tree/main/Data_processing/error_files

Check list:

1. [X] I have found an issue with GEMMA
2. [X] I have searched for it on the issue tracker (incl. closed issues)
3. [X] I have searched for it on the mailing list
4. [X] I have tried the latest release of GEMMA
5. [X] I have read and agreed to below code of conduct
6. [X] If it is a support/install question I have posted it to the mailing list
7. [X] If it is software development related I have posted a new issue on the issue tracker or added to an existing one
8. [X] In the message I have included the output of my GEMMA run
9. [X] In the message I have included the relevant .log.txt file in the output directory
10. [X] I have made available the data to reproduce the problem (optional)

To find bugs the GEMMA software developers may ask to install a development version of the software. They may also ask you for your data and will treat it confidentially. Please always remember that GEMMA is written and maintained by volunteers with good intentions. Our time is valuable too. By helping us as much as possible we can provide this tool for everyone to use.

[IsobelGuthrie]

Hi there, I'm also getting this error - did you manage to find a solution?

[caitlinh42]

I am also getting this error, is there a solution?