Error when running kage index

Question

Error when running kage index

Opened this issue 14 days ago · 5 comments

Hi,

I'm trying to run the kage index step of kage but I get the following error:
TypeError: init() missing 1 required positional argument: 'dtype'

My input VCF is only including SV.
The command I used was:

kage index -r primary.fa -v primary_all_norm_sort_SV.vcf -o index -k 31

Best regards!

Answer 1 · 2024-09-02T17:08:15.000Z

Hi!

Thanks for reporting! That seems a bit strange. Do you get a longer stacktrace (output) that you could share?

Answer 2 · 2024-09-03T00:12:22.000Z

Thank you , here is my log file.
log.txt

Best regards!

Answer 3 · 2024-09-03T09:02:50.000Z

Thanks for sharing the log.

It seems that the problem actually is that you run out of memory because some large memory allocation in the indexing process. The error message you get is just another error when formatting the first error message. I'm not sure why KAGE is trying to allocate that much memory, but I'm looking into it.

Would you by any chance be able to share the VCF and reference you are using with me? That would make it a bit easier to find exactly what the problem is, but I understand if this is data that it is not possible to share :)

Answer 4 · 2024-09-04T13:41:37.000Z

Hi,

I change my VCF file and reference to run the kage index step of kage. But it report another error.
here is my log file.
log.txt

Best

Answer 5 · 2024-09-11T13:05:33.000Z

Hi!

Sorry for the late reply. This seems like a memory issue again, which happens when KAGE tries to fetch the reference genome sequence around your variants.

May I ask how many variants you have in your VCF? Are these SVs?

Again, if you would be able to share your vcf and reference that would be very useful, but understand if not possible :)