cannot open file "PriorGWASs.tsv": Invalid argument

[Xuemin-Wang]

Dear Ninon,

Recently I always encounter an error above while running bGWAS v1.0.2. I have used this version previously but this error never occurred; however, when I re-run the same analysis without any modification, the same error still occurred. Have you recently updated the package?

I tried to investigate the issue but was unsuccessful. Will you be able to fix this issue?

Many thanks,
patrick

1. Here is the script for the analysis:
   B <- bGWAS(Z_matrices = file_directory,
   name = output_name,
   GWAS = MyGWAS,
   prior_studies = NULL,
   MR_threshold = 1e-6,
   MR_ninstruments = 3,
   MR_pruning_dist = 500,
   MR_pruning_LD = 0,
   MR_shrinkage = 1,
   stepwise_threshold = NULL,
   prior_shrinkage = NULL,
   sign_method = "p",
   sign_thresh = 1e-6,
   use_permutations= FALSE,
   res_pruning_dist = 500,
   res_pruning_LD = 0,
   save_files = TRUE,
   verbose = TRUE)

2. and here are the log output:

<<< Preparation of analysis >>>

Checking parameters
The name of your analysis is: "bGWAS_allEC_26traits_1e-6".
The Z-Matrix files are stored in "C:\Users\xueminW\Desktop\allEC_bGWAS_26traits_exclude_RAFFH".

Preparation of the data...

The conventional GWAS used as input is:ecac_mr_file_noUKBB_cleaned.txt.gz (ID = 1).
The analysis will be run in the folder: "C:/Users/xueminW/Desktop/allEC_bGWAS_26traits_exclude_RAFFH".
Files will be saved in: "C:/Users/xueminW/Desktop/allEC_bGWAS_26traits_exclude_RAFFH/bGWAS_allEC_26traits_1e-6".
The study ecac_mr_file_noUKBB_cleaned.txt.gz (ID=1) has been removed from the prior GWASs used to build the prior since it is used as conventionnal GWAS.
The p-value threshold used for selecting MR instruments is: 1e-06.
The minimum number instruments required for each trait is: 3.
The distance used for pruning MR instruments is: 500Kb.
Distance-based pruning will be used for MR instruments.
No shrinkage applied before performing MR.The p-value threshold used for stepwise selection will be derived according to the number of Prior GWASs used.
Using MR_shrinkage as default for prior_shrinkage:No shrinkage applied before performing calculating the prior.The p-value threshold used for stepwise selection will be derived according to the number of Prior GWASs used.
Significant SNPs will be identified according to p-value. The threshold used is :1e-06.
The distance used for pruning results is: 500Kb.
Distance-based pruning will be used for results.

Initializing the summary information file

List of files : C:/Users/xueminW/Desktop/allEC_bGWAS_26traits_exclude_RAFFH/bGWAS_allEC_26traits_1e-6/PriorGWASs.csv has been successfully created.
<><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>
<<< Identification of significant prior GWASs for MR >>>

Creating the Z-Matrix of strong instruments

Loading the ZMatrix...

Selecting studies :
25 studies
260,208 SNPs

Adding data from the conventional GWAS :

"ecac_mr_file_noUKBB_cleaned.txt.gz"
Done!
260,208 SNPs in common between prior studies and the conventional GWAS

Thresholding...

177,573 SNPs left after thresholding
25 studies left after thresholding
Pruning MR instruments...
distance : 500Kb
1,478 SNPs left after pruning
Oestradiol : removed (less than 3 strong instrument after pruning)
24 studies left after thresholding+pruning
1,477 SNPs left after removing studies with only one strong instrument
Error in file(file, ifelse(append, "a", "w")) :
cannot open the connection
In addition: Warning message:
In file(file, ifelse(append, "a", "w")) :
cannot open file 'PriorGWASs.tsv': Invalid argument