GUIDELINES ON TROUBLESHOOTING FUMA ERRORS

[Tanya Phung]

When you encounter a FUMA error, please follow the following steps:

1. Follow all of the steps in this guide

2. Check FAQ:

3. Search google user group for similar error to see if this issue has been answered before:

4. Read and re-read FUMA tutorial:

5. Post questions/issues on google user group

ERROR 0:

File upload failed.

This error is because your file upload failed. Please try again. Do not leave the page while uploading the file (after clicking the submit button).

1. Only click the "Submit Job" once.

2. Try using a different browser and/or hard refresh the page. (Ctrl + shift + r)

3. Try using VPN.

4. Try a personal computer from a home network. (Sometimes networks in working environments are very strict)

Make sure that your data is correctly formatted for FUMA

1. Make sure that there is a header (column name) in your input file.

   1. The header should not start with a comment character (#). Any lines that starts with # will be ignored.

   2. The number of column names should be equal to the number of columns in your input file.

      1. sometimes the input file has a row index which means that there is one fewer column name in the header as compared to when the actual data starts.

2. rsID if exists has to be in rsID format. See tutorial.

3. Use gzip software to compress with .gz extension or ZIP software with .zip extension. Make sure you haven't renamed the file manually. Use the proper compression software instead.

4. The chromosome has to be numbers between 1 and 23 or X.

5. Position values have to be integer (not in scientific notation) (see previous thread: )

6. If your file contains chromosome and position, these have to be in hg19 coordinates.

7. Make sure that there is no missing data for the columns that are mandatory such as p-values (see previous thread: or or )

8. If you specify the name of chromosome, position, etc… during submission, make sure that these names exist in your input file (see previous thread: )

9. Make sure that the delimiter is consistent. In addition, Delimiter can be any of white space including single space, multiple space and tab. Because of this, each element including column names must not include any space (see previous thread: )

10. Check your file to make sure that there is no quotation around each value. It should be for example 1 instead of "1". This is usually caused when you save a file in R. To avoid this, one needs to set quote=F when saving a file in R (see previous thread: )

Below, we give a bit more details on what the error might mean:

ERROR 001:

This error means that the input file format was not correct.

ERROR magma:

This error can occur if the rsID and/or p-value columns are mistakenly labelled wrong. In addition to the steps above in ERROR 001:

1. If magma was not able to perform, make sure that you selected this option during submission

2. Search for magma to see if your issues have been asked and answered before

ERROR 003 - 004:

Error during SNPs filtering for Manhattan plot. This error can occur if the p-value column is mistakenly labelled wrong.

ERROR 005:

Error from lead SNPs and candidate SNPs identification / No significant SNPs were identified.

This error can occur when no candidate SNPs are identified. Note that indels are included in the FUMA from v1.3.0 but both alleles need to match exactly with the selected reference panel.

MHC region is also excluded by default.

• If there is no significant hit at your defined P-value cutoff for lead SNPs and GWAS-tagged SNPs, you can try to use a less stringent P-value threshold or provide predefined lead SNPs.

• If there are significant SNPs with very low minor allele frequency, try decreasing MAF threshold (default 0.01).

Manhattan plots and significant-top 10 SNPs in your input file are available from SNP2GENE.

You will also get this error if the chr:pos:rsID combination does not match with the reference panel (which is in hg19 format) (see previous thread:

ERROR 006:

Error from lead SNPs and candidate SNPs identification. This error can occur because:

1. invalid input parameters or

2. columns are mistakenly labelled wrong.

Please make sure your input file has the correct column names.

Please refer Tutorial for details.

ERROR 007:

Error during SNP annotation extraction. This error can occur because:

1. invalid input parameters or

2. columns are mistakenly labelled wrong.

Please make sure your input file has the correct column names.

Please refer Tutorial for details.

ERROR 008 - 009:

Error during extracting external data sources. This error can occur because

1. invalid input parameters or

2. columns are mistakenly labelled wrong.

Please make sure your input file has the correct column names.

Please refer Tutorial for details.

ERROR 010:

Error from chromatin interaction mapping. This error might be because one of the uploaded chromatin interaction files did not follow the correct format.

Please refer Tutorial for details.

ERROR 011:

Error during gene mapping. This error can occur because:

1. Invalid input parameters or

2. columns are mistakenly labelled wrong.

Please make sure your input file has the correct column names.

Please refer Tutorial for details.

ERROR 012:

Error from circos. This error is most likely due to server-side error. Please contact the developer for details.

ERROR celltype:

An error occurred during the process of your cell type specificity analyses. Please make sure that your provided inputs meet all the requirements and check the following:

1. Does your selected SNP2GENE job have MAGMA output? If you can see manhattan plot for gene-based test, this should not be the problem.

2. Is your uploaded file an output of MAGMA gene analysis with an extension "genes.raw"?

3. Does your file contain Ensembl gene ID? Otherwise, don't forget to UNCHECK the option to indicate that you are using Ensembl gene ID.

If any of those don't solve the problem, please contact to the developer.

ERROR timeout:

This error occurs when the system's processing time limit (8 hours) for a specific task or operation is exceeded. It often indicates that the system was unable to complete the task within the expected timeframe, possibly due to heavy load. Users encountering this error may need to retry the operation later or contact support if the issue persists.

ERROR Undefined:

This may be a result of job submission failure, job abort or perhaps a server-side error. If this persists please contact the developer for details.