Closed alhafidzhamdan closed 4 years ago
Looks like an error I fixed today.
Please try again with the latest release.
You probably have colons or asterisks in some of your contig names. I thought no one else was using a weird reference genome! 43N is not related to your sample IDs but you probably have a contig named like HLA-A*02:43N in your reference FASTA file.
Ah yes I have identified them in my fasta file. Thanks @DarioS. Moving forward, what do you suggest that we should do? Any way that @jonbaber could cater for this issue? or do i need to remove the contigs somehow, or use another ref genome (hg38)- the latter would be least favourable.
Have you tried using the latest release as I suggested above?
Yes @jonbaber - still the same issue. Also, I actually now realised that i have issues with viral and repeatmasker annotation stage of GRIDSS. Perhaps that is causing the issue. Waiting for them to help me troubleshoot that stage.
Ok. Once you have sorted out the GRIDSS annotations let me know if it still doesn't work on the latest version of GRIPSS and I can take a look. The easiest way for me to fix the issue is if you can provide a minimal VCF that reproduces the error. Looking at the log above it will involve an entry with "...43N..." in the BEALN info field.
I had the same problem and it was fixed in GRIDSS version 2.9.4. Have you use the latest version? No need to wait for that advice.
I suspect for me it did not work as I used the optional --repeatmasker function as part of GRIDSS initial call. I will try without that option and run annotations for both repeatmasker and viral separately.
Hi GRIPSS has now worked- although seems to be OK without viral annotation. I used GRIDSS 2.10
Hi there,
I tried running GRIPSS with this:
But i got this error:
I'm not sure why it says -> For input string: "43N" as there is no such sample in our cohort. This error only occurs in some samples but not in others. Any ideas?