Hi,
I am trying to build a standard database using Kraken, but I am having trouble doing it.
The message I receive is
Found jellyfish v1.1.11
Skipping download of bacterial genomes, already downloaded here.
Skipping download of viral genomes, already downloaded here.
Kraken build set to minimize disk writes.
Creating k-mer set (step 1 of 6)...
Found jellyfish v1.1.11
Can't merge hash with different size
I posted this question on the google group for the software and I looked through the previous questions, but nobody answered there and I still can not figure out a way to do it.
I am not a Kraken user. But I have a little experience with being a biologist who uses bioinformatics software, databases, etc. I looked at the GOOGLE group for Kraken users, and it seems the group gets very little "traffic", with just a few dozen posts in the past year and most of them with less than 5 replies, most with not very good solutions to the problems.
My suggestion would be to look not only for people with the same problem you are having but also people who seem to be using Kraken for tasks similar to whatever you want to use Kraken for, and then try to contact them. Is there any chance you could travel to get some "hands on" help from someone who is using Kraken at a university near you?
Another approach (and you can try both at once) is to find other researchers at your school who are doing similar work and could team up with you to work on the Kraken problems. Does UVM have a "bioinformatics" shared facility yet? When I left there in 1995 we had been talking for a couple years about how to set up a facility that could be shared by many departments such as the medical school, biology, biochemistry, molecular genetics, etc...
https://groups.google.com/forum/#!topic/kraken-users/q3eci43aH_I
Hi Brian, Thanks for your answer. I am just starting looking into the microbiomes and kraken seemed very straight forward. Turns out it is not. Not even the author answers the emails I sent. Anyway, I am looking into other solutions and applying to hands on courses.
Thanks for your help!
It's never as simple as it seems... Don't give up on Kraken. The K-mer approach to classification has many advantages over BLAST and other tools for some types of jobs. I am sure you can get it running if you find someone to help you a bit.
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