Error001 for jobid 743563 forbidded access logs

[Isabel Fourie]

Good day

I uploaded summary stats in chr38, followed all instructions and tried to troubleshoot. However, the job keeps failing after running for more than an hour. The logs say forbidden access or something like that, so not much help. I'd appreciate your help.

Thank you

Kind regards

Isabel

[Tanya Phung]

Hi Isabel, 

There was a problem of not recognizing chrX, but I have just pushed a fix to automatically convert chrX to chr23. 

However, it seemed that some of your variants are in CRCh37, and some are not in GRCh38 or GRCh37 at all. 

For example, I checked a few of your variants: 

'11', '176614', 'c', 'g': this is in GRCh37

https://gnomad.broadinstitute.org/variant/11-176614-G-C?dataset=gnomad_r2_1

'4', '189999278', 'a', 'g': this does not exist in either

'13', '80902327', 'a', 'g': this does not exist in either

When you run your job on FUMA SNP2GENE selecting that your input is in GRCh38, before the job ran into the error with chrX, none of the variants are found in dbSNP version 157. Please make sure which genomic build your data is in before submitting. 

Best,
Tanya

[Tanya Phung]

Hi Isabel, 

Thanks for providing additional information. I had looked for your variants using the exact match of effect allele and other allele and that's why I could not find it on gnomad. 

The issue was because your alleles were not in capital letters. I have updated the code to also accept non capital letters for alleles and it was successful when I ran it with a small subset. As there are >20 million snps in your file, I suggest that you try again with a smaller subset. 

Best,
Tanya