How To Find A Problem In An Input File Used When Running The Aligator For Pathway Analysis

Question

[sherriying]

I am running the pathway analysis from the GWAS using ALIGATOR. But I got the error message like "Fortran runtime error: Bad integer for item 1 in list input" . I know the problem is from the input file of SNP name and p value. But I don't know what is the exact the problem in the input file. I try to use subset of the input file, it works, which means there are some problems with some of the snp names. So, I wonder if someone has used ALIGATOR and have some experience with it?

Many thanks,

sherriying

[Istvan Albert]

nobody can troubleshoot an input file error that they know nothing about. At the very least you will need to post a few lines of the input file and we can advise then on what to do next.

Answer 1

[zx8754]

Readme file says:

Line 1: Contains the name of the file containing SNP ID numbers and p-values for ALL SNPs in the study. P-values do not need to be sorted, but please remove the 'rs' from the SNP ID numbers (see example_GWA.dat for an example). Maximum of 50 characters.

Line 2: Contains the name of your output file (maximum 50 characters) ...

Example GWA result file for input into ALIGATOR - example_GWA.dat

   11805303   0.732644
   10489629   0.545336
   2201841   0.462848
   12119179    7.96910E-02
   11209033   0.367433
   41396545   0.443732
   17375018   0.802623

Answer 2

[sherriying]

Thanks for the answer. I have found the error. There are some SNP ID including some character (mitochondria related snp). But I met another problem. When the program is running in the processs of replicating the gene list ( resampling 5000 times), the program stop in the middle of the replication. Why that?

[zx8754]

This is not an answer, post it as comment. Also, please avoid asking new question within a question.